[1] "ofn"        "-oTBRCA-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BRCA-TP/19785967/transformed.cor.cli.txt"

nPatients in clinical file=1098, in cluster file=1080, common to both=1080
[1]   82 1080
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              206               874 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              206               874 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              706               374 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              706               374 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              123               957 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              123               957 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73              1007 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               73              1007 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              135               945 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              135               945 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              212               868 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              212               868 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               76              1004 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               76              1004 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               73              1007 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               73              1007 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              316               764 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              316               764 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              212               868 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              212               868 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              209               871 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              209               871 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              150               930 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              150               930 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              309               771 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              309               771 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              266               814 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              266               814 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              290               790 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              290               790 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              529               551 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              529               551 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              141               939 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              141               939 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              119               961 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              119               961 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               214                866 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               214                866 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               124                956 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               124                956 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               138                942 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               138                942 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                94                986 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                94                986 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               229                851 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               229                851 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               191                889 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               191                889 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                92                988 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                92                988 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               143                937 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               143                937 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                87                993 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                87                993 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               464                616 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               464                616 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               142                938 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               142                938 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               107                973 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               107                973 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               217                863 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               217                863 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               177                903 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               177                903 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               153                927 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               153                927 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               190                890 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               190                890 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               223                857 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               223                857 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               416                664 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               416                664 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               451                629 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               451                629 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               196                884 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               196                884 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                99                981 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                99                981 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              151               929 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              151               929 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              136               944 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              136               944 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              243               837 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              243               837 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               52              1028 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               52              1028 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              182               898 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              182               898 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              211               869 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              211               869 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              186               894 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              186               894 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              103               977 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              103               977 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              353               727 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              353               727 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              312               768 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              312               768 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              140               940 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              140               940 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              228               852 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              228               852 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              187               893 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              187               893 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              276               804 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              276               804 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              112               968 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              112               968 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              120               960 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              120               960 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              399               681 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              399               681 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               93               987 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               93               987 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              313               767 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              313               767 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              283               797 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              283               797 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               173                907 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               173                907 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               229                851 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               229                851 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               275                805 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               275                805 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               365                715 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               365                715 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               151                929 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               151                929 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               131                949 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               131                949 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               433                647 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               433                647 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               266                814 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               266                814 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               320                760 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               320                760 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               173                907 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               173                907 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               593                487 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               593                487 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               579                501 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               579                501 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               275                805 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               275                805 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               320                760 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               320                760 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               321                759 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               321                759 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               193                887 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               193                887 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               161                919 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               161                919 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                93                987 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                93                987 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                55               1025 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                55               1025 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               180                900 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               180                900 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               482                598 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               482                598 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              190               890 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              190               890 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              190               890 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              190               890 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 1080 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=143,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=755,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 1080 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "NUMBER_OF_LYMPH_NODES"
[10] "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=65, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
276 624 136  40 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
276 624 136  40 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
276 624 136  40 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
276 624 136  40 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
507 358 119  77 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
507 358 119  77 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
507 358 119  77 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
507 358 119  77 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=8, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=31, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED   178  26
  1P GAIN WILD-TYPE 739 121
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              204               860 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               26               121 
$`1P GAIN MUTATED`
TCGA-3C-AALJ TCGA-A1-A0SF TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U 
       42.81        48.10         7.96        19.20        73.84        87.25 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX 
      101.98        36.13        24.79        75.25         5.19        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0EO TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 
       67.33        33.76        80.28        44.88        17.13         8.38 
TCGA-A2-A0T7 TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YM TCGA-A2-A1G0 
       20.75        49.48        18.61        19.33        31.73        20.25 
TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0DA 
       42.44        33.93        50.37        50.83         7.30        35.67 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I 
       31.73        25.15        29.56        31.36        24.26        21.73 
TCGA-A7-A3IZ TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       10.59        14.50        21.17        11.05        10.29         9.37 
TCGA-A8-A06Z TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09M 
        1.02         9.99        24.99         0.99        43.00        33.07 
TCGA-A8-A09R TCGA-AC-A2BM TCGA-AC-A2FG TCGA-AC-A2QJ TCGA-AC-A3W6 TCGA-AC-A5EI 
        8.98        99.35        60.92        14.66        19.79        14.53 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A7VC 
       19.33        14.96        13.71        18.67        13.58         0.03 
TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM 
        1.12         1.78         1.71         9.96         7.36         0.16 
TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FY TCGA-AO-A03R TCGA-AO-A0J2 
        0.33         7.59         7.04         0.33        68.75        32.78 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A128 TCGA-AO-A129 
       50.70        72.00        65.10        26.24       106.78       108.03 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AQ-A04L TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TT 
       64.04        48.36       130.09        32.91        84.10       109.02 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A24K TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A2LQ 
      108.36       103.86        50.89        98.76        93.30        40.54 
TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0RU 
       57.27       143.38       281.29        65.72       112.37       282.90 
TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AW TCGA-BH-A0B3 
      245.10        43.59        68.12        18.84        20.45        39.55 
TCGA-BH-A0B7 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       84.13        43.53        74.89        49.05        89.06        90.97 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0DV TCGA-BH-A0E6 TCGA-BH-A0EE 
       13.91        78.28         2.56        67.86         9.63        31.00 
TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FN 
       41.00        20.38        25.81        31.53        97.48        72.07 
TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A5IZ TCGA-C8-A12M TCGA-C8-A12V TCGA-C8-A135 
       72.07        38.60        18.64        11.77        12.66        12.92 
TCGA-C8-A1HM TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A143 
       12.33         9.50        14.43        13.02        20.88        14.17 
TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JL TCGA-D8-A1JT 
       14.17        16.50        55.50        15.78        20.09        13.32 
TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XW 
       18.58        27.58        12.39        21.80        14.50        43.04 
TCGA-D8-A1XY TCGA-D8-A27R TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N 
       16.54        10.09        46.59        40.41        40.11        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 
       38.60        31.96        18.51        63.62        69.96        19.43 
TCGA-E2-A159 TCGA-E2-A15K TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 
       25.05         9.04        76.57        33.70        60.36        73.64 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NE TCGA-E9-A1NF 
      106.75       102.61        22.29        34.16        35.77        35.24 
TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-EW-A1J3 
       32.09        46.59        34.45        30.18        30.44        16.57 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A423 
       25.94        22.82        41.13         7.86        19.99        10.16 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DD TCGA-GM-A2DF 
       16.77        24.99       109.87        59.57        75.02        70.85 
TCGA-GM-A2DH TCGA-HN-A2OB TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YO 
       72.10        62.47        13.22         7.10        32.75        14.47 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 
       14.79        16.08        15.68        58.52        36.36        20.38 
TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-Z7-A8R6 
       28.21         8.91         9.93        18.48        21.07       107.05 

$`1P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68        31.79        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X 
      143.15        18.02        78.41       121.94        63.12        55.43 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       77.19        98.99       107.93        34.55        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        50.43        44.28        17.52 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YL TCGA-A2-A0YT 
       18.21        50.47        21.90        21.67        48.46        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        17.36        60.72        22.45        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        39.65        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       56.28        47.31        35.93        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       26.96        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E 
       35.47        30.61        37.45        33.11        29.79        20.19 
TCGA-A7-A13G TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.61        23.74        23.80        20.61        22.32        11.34 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VX 
       13.74        17.92        14.73        12.10        10.72        10.42 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       29.03        31.00        26.01        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
       32.05        10.98         8.98         7.99         9.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       31.00        33.01       112.08        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        1.02        50.04        49.05        45.07        29.98         1.02 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       25.02        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95        22.95        73.91         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FM 
       73.05        40.57        86.66        90.71        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       74.14        33.04        19.33        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       14.83        22.19        24.13        25.05        14.99        16.57 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62V 
       15.48        23.24        24.79        29.26        16.80        11.44 
TCGA-AC-A62Y TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR 
       17.42        12.26         1.68         8.22        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        2.96         7.46         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW 
        7.96         7.00         7.17         6.90         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T 
       80.28        61.35        66.77        81.63        95.70        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        21.40        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE 
       20.32        22.36        53.03        21.53        50.86        76.77 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
      108.72        90.58        98.27        57.30        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93         5.65        15.62        32.52         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW 
       19.20       140.55        98.33         5.26        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM 
      134.14       107.21       125.16       101.00        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       96.00        86.07        93.90        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27        77.69       105.30        32.58 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.66        89.00        99.62        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IG 
       77.62        12.13       275.87       129.57        50.70       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      233.62        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       113.79       206.86       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.88       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        85.35        70.16       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       59.84        25.55        63.09        81.44        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       70.22        81.63        51.68        37.22        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       61.51        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 
       76.60        53.95        45.57        49.94        77.95        41.75 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       44.02        45.83        77.98        23.44        38.01        29.98 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DX TCGA-BH-A0DZ 
       17.26        15.65         3.22        38.47        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
        4.41        15.68        14.30        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK 
       53.26        24.56        23.08        52.96        26.50         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       66.05         7.36        51.39        51.16        67.50        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       17.69        89.16        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
      144.59        28.14        26.14        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q 
        9.44        11.93        11.77        12.66        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       13.51         1.87        12.59         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       10.92        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M7 
        8.28         9.67         9.53         0.03        24.56        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       12.95        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       20.58        13.97        13.48        21.14        19.20        17.49 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.15        18.90        12.03        53.00        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.12        19.40        20.38        21.01        12.20 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       14.70        17.79        16.73        25.74        23.90        18.15 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        15.22        14.73        19.92        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         1.61        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       43.00        34.42        27.52        37.51        28.44        28.87 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       34.26        32.02        69.34        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M 
       18.21        12.92        55.63        53.92        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       50.79        19.56        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       77.65        37.41        70.36        33.73        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
        3.88        22.19        60.99        11.08        54.18        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A1LL 
       24.59        75.81        28.90        50.07         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       26.99        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1NH 
       36.20        36.56        39.55        41.62        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        24.82        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02        11.15        48.23        45.01        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 
       46.65         6.58        21.27        47.64        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       23.90        23.84        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       13.25        15.68        28.77        29.95        29.85        40.41 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       17.49        23.51        15.22        31.30        33.21         7.40 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        79.10        83.34        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.84        11.57        21.24        13.28        10.62        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP 
       29.23        25.05        17.06        15.32        14.70        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
        2.63         7.46        14.50        19.53        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       17.49        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD 
       17.36        14.07        19.73        40.11        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 
       86.96         0.16         0.26        18.81        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        18.87        17.39        17.26        13.94        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
        3.81        66.84        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 
       16.04       108.07 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.03              0.03 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           282.90            275.87 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            30.72             27.07 
[1] "0.0 - 282.9 (30.7)" "0.0 - 275.9 (27.1)"
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P GAIN MUTATED        16       15        1        2        68        56
  1P GAIN WILD-TYPE      73       70        5        4       285       196
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           0         24          6         12        2
  1P GAIN WILD-TYPE         2        130         23         53       18
                   vv
clus                STAGE TIS STAGE X
  1P GAIN MUTATED           1       0
  1P GAIN WILD-TYPE         0      13
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 16                73
  STAGE IA                15                70
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               68               285
  STAGE IIB               56               196
  STAGE III                0                 2
  STAGE IIIA              24               130
  STAGE IIIB               6                23
  STAGE IIIC              12                53
  STAGE IV                 2                18
  STAGE TIS                1                 0
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED    40 132  24   9
  1P GAIN WILD-TYPE 236 492 112  31
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1              40               236
  T2             132               492
  T3              24               112
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P GAIN MUTATED   107  66  19  13
  1P GAIN WILD-TYPE 400 292 100  64
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0             107               400
  N1              66               292
  N2              19               100
  N3              13                64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   167   3
  1P GAIN WILD-TYPE 722  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    167    3
  1P GAIN WILD-TYPE  722   19
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0             167               722
  1               3                19
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED   203   3
  1P GAIN WILD-TYPE 865   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED    203    3
  1P GAIN WILD-TYPE  865    9
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE             203               865
  MALE                 3                 9
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    81 103
  1P GAIN WILD-TYPE 348 415
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     81  103
  1P GAIN WILD-TYPE  348  415
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               81               348
  YES             103               415
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P GAIN MUTATED                            0                           161
  1P GAIN WILD-TYPE                          1                           609
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P GAIN MUTATED                               19                   3
  1P GAIN WILD-TYPE                            181                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1P GAIN MUTATED                       4                                6
  1P GAIN WILD-TYPE                     5                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1P GAIN MUTATED                    1             12
  1P GAIN WILD-TYPE                 16             35
D1V9, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                161               609
  INFILTRATING LOBULAR CARCINOMA                19               181
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                12                35
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  1     7
  1P GAIN WILD-TYPE                                0    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                          46   142
  1P GAIN WILD-TYPE                       135   603
D1V11, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          7                53
  BLACK OR AFRICAN AMERICAN                     46               135
  WHITE                                        142               603
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     5 173
  1P GAIN WILD-TYPE  34 702
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      5  173
  1P GAIN WILD-TYPE   34  702
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO             173               702
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED   607  91
  1Q GAIN WILD-TYPE 310  56
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              698               366 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               91                56 
$`1Q GAIN MUTATED`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        42.81        40.14        48.56        48.36         9.96 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN 
       43.43        48.10        47.24        20.88         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       19.20        18.21        78.41        73.84        87.25       101.98 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CQ TCGA-A2-A0CS 
       36.13       136.73        24.79       114.81        88.60        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
       75.25         5.19        98.99        56.81        67.33        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ 
       61.58        25.22       101.72        89.36        80.28        79.76 
TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        31.82        63.29        99.19        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A25A 
       31.73        23.77        23.47        22.45        20.25       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       42.44        17.19       105.34        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4S2 
       91.07        29.98        50.37        50.83         7.30        21.14 
TCGA-A7-A0CD TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       38.30        35.47        30.61        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       20.19        25.15        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       23.80        21.73        20.61        10.59        10.29        11.28 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X TCGA-A8-A06Y 
        9.37        10.42        13.02         1.02        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       18.97         9.99         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       45.07        15.06         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       19.96        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00         1.02        49.05        45.07        29.98        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       25.02         8.98        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23C 
       19.04        13.02        21.04        27.02        17.03         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       22.95        73.91         5.72         1.48        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI 
       40.57        86.66        60.92        26.04        74.14        19.33 
TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QQ TCGA-AC-A3TM 
       14.66         6.48        16.31        14.83        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        16.57        19.79        15.48        24.79        29.26 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       14.53        19.33        14.96        13.71        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X 
       13.58        12.26         1.68        20.19         1.12         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL 
        9.96         7.36         0.16         0.33         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         7.04         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XW TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0J5 
        0.33         5.59        81.63        68.75        32.78        26.04 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD 
       20.32        22.36        53.03        21.53        50.70        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       65.10        26.24        62.04        55.33        71.80        99.25 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F 
      106.78       108.03        90.58        98.27        64.04        48.36 
TCGA-AO-A12G TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L 
       41.62        61.87        70.39        17.79        24.79       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR 
        5.65        32.52        32.91        19.20       140.55         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       84.10       109.02       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV 
       97.68        98.33        96.00        93.90        37.81        61.28 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.53        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 
        2.76       104.28       112.77        32.58        98.76        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK 
       93.30        85.64        93.83       166.42        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       73.35        33.30        38.96        77.62       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       12.13       275.87       129.57        65.72       112.37       233.62 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH 
       84.59       165.76       129.07       140.88       255.68       212.25 
TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU 
      234.28       263.28       162.05       102.77       100.70       282.90 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        79.63        18.35        21.47       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
      245.10        58.88        43.59       101.52        73.51       170.17 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
        7.07        85.35        70.16        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        62.93        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC 
       40.83        39.55        70.22        84.13        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 
       72.23        74.14        53.95        45.57        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI 
       44.02        89.06        90.97        45.83        23.44        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        17.26        15.65         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
       67.86        70.88        15.68         9.63        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H7 TCGA-BH-A0H9 
       24.49        31.00        15.16        37.78        23.08        41.00 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18K 
       27.25         5.59        23.93        32.91         4.90        90.84 
TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       26.66        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV 
       51.39        51.16        67.50        91.99        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FJ 
       55.69        49.58        25.81        31.53        97.48        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        45.63        72.07        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A5IZ TCGA-BH-A5J0 
       38.60       130.16         6.44        20.12        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         5.26         9.70        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y 
       11.77        12.66        11.77        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HI 
       12.56         3.16        13.51        12.92        12.33        11.28 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Z 
       12.03        10.42        12.33        12.95        12.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         9.53         0.03         9.50        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       12.95        13.02        13.41        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        21.14        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       55.50        15.78        18.15        18.90        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS 
       20.09        20.12        20.09        19.40        20.38        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA 
       13.32        14.70        18.58        16.73        25.74        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM 
       18.15        12.39        15.22        14.73        21.80        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       55.30        15.85        16.31        16.64        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27I 
       16.54        15.52         9.93        14.14        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       48.03         4.80        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A109 
       33.37        16.18        12.66        25.22        34.42        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X 
       44.68        38.24        38.60        75.98        34.26        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       69.34        18.51        63.62        69.96        23.24        19.43 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H 
       25.05        23.34        17.29        20.71        18.21        12.92 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15T TCGA-E2-A1AZ 
       53.92         9.04        20.58        11.05        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       53.62        32.35        37.25        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1L6 TCGA-E2-A1L7 
       33.70        28.44         3.88        22.19        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       73.64        19.66        50.07       106.75       102.61         8.75 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A574 TCGA-E2-A9RU 
       26.99        34.55        43.56         8.28        38.76        17.69 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF 
       22.29        34.16        36.20        36.56        35.77        35.24 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       18.94         9.86        24.82        34.95         2.56         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        45.01        32.09         1.12         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22A TCGA-E9-A22E TCGA-E9-A22G 
       46.59        34.45        32.05        39.09        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       40.50        20.12         0.69         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
       29.72        38.07        30.18        30.44        23.84        26.70 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       26.40        27.85        12.20        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P3 
       25.94        22.82        29.95        29.85        41.13        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH 
       23.11         7.86        19.99         6.15        10.52        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA 
       55.00        52.73        25.91        10.16        23.51        16.77 
TCGA-EW-A6SB TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DD 
       24.99         7.40       109.87        59.57        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A4E0 
       70.85        72.10       101.62       110.50        38.20        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.22         7.10        13.28        32.75        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       15.32        14.70        14.47        14.79        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       16.08        15.68         7.46        19.53        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       22.39         2.10        58.52        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O 
       36.36        28.87        20.38        41.92        26.04        17.36 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LZ 
       28.21        19.73         8.91        64.21        86.96         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA17 
       18.81        18.48        21.07        20.68        13.84        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       17.03         3.81        11.41        52.96        29.03        15.35 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

$`1Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-4H-AAAK TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SJ 
      129.14        11.44         8.52        14.37        14.27        13.68 
TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04V 
       31.79        28.01       143.15        18.02       121.94        63.12 
TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 
       55.43        99.12        92.48       107.93       107.93        34.55 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX 
      118.45        74.40        72.00        34.29        61.94        24.72 
TCGA-A2-A0SU TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 
       54.64        18.21        50.47        17.36        60.72        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3XV 
       19.56        16.47        52.47        18.15        10.59        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       56.28        47.31        35.93        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0D9 TCGA-A7-A0DC 
       26.96        21.90        35.31        34.29        37.45        29.79 
TCGA-A7-A13G TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3RF TCGA-A7-A6VY TCGA-A8-A06P 
       23.61        22.32        11.34        13.41         8.75        13.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A07I TCGA-A8-A07J 
       17.98        53.06        29.03         9.01        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08I TCGA-A8-A08J 
       32.05        10.98        36.95        13.02        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A09D TCGA-A8-A09N 
        9.99        31.00        33.01        33.01        50.04         1.02 
TCGA-A8-A09T TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2QH 
       19.04         0.99        38.04        90.71        87.12        33.04 
TCGA-AC-A3BB TCGA-AC-A3QP TCGA-AC-A3YI TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A7VB 
       32.45        22.19        23.24        16.80        11.44         8.22 
TCGA-AC-A7VC TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR 
        0.03         1.32         2.30         2.96         7.46         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         6.44         5.65         7.96         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        0.33         5.33        80.28        61.35        66.77        95.70 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 
       47.87        58.95        29.13        21.40        52.18        37.48 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12E 
       50.86        76.77        50.24       115.27       108.72        57.30 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A1H2 
       40.57        14.73        82.62         0.53        26.93        15.62 
TCGA-AQ-A54N TCGA-AR-A0TQ TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        2.56        98.33        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       133.22        83.87       134.14       107.21 
TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A24H 
       86.07        99.32        17.23        94.29        86.43       160.90 
TCGA-AR-A24O TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z 
      118.59        97.84       105.27        77.69       105.30        98.66 
TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A2LH TCGA-AR-A5QQ TCGA-B6-A0IC TCGA-B6-A0IG 
       99.62        71.05        20.25        10.59        50.70       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RQ 
       18.77       127.33        68.45        81.17        78.02       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WY TCGA-B6-A0X4 TCGA-B6-A0X5 
       89.46       157.41        97.48       113.79        28.27        68.94 
TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 
      139.17        37.87        59.84        39.16        81.63        51.68 
TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0DE TCGA-BH-A0DH 
       75.48        76.60        49.94        77.95        77.98        38.01 
TCGA-BH-A0DQ TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EI 
        3.22        16.27         4.41        14.30        44.81        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HB 
       30.35        10.78        53.26        24.56        52.96        26.50 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       51.32        50.79        24.95        42.35        44.81        23.05 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A1ES TCGA-BH-A1ET 
       35.93        20.12        72.56        37.74       113.82        82.85 
TCGA-BH-A1EY TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       17.69        89.16        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FR TCGA-BH-A204 TCGA-BH-A208 
       74.73       122.89        36.92       144.59        83.31        57.83 
TCGA-BH-A28O TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FZ TCGA-C8-A12N 
       10.65        10.52       109.28        20.88        18.87        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.66        12.66        12.66         1.87        12.59         4.11 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HO TCGA-C8-A26V 
        4.08        10.92        11.34         0.16        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A27A TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.53        12.95        24.56        12.49        19.46        56.81 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1X6 
       13.48        19.20        53.00        14.01        21.01        17.79 
TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU 
       23.90        17.16        14.50        19.92        16.41        12.99 
TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27L 
       15.32        14.24        17.42        16.04        13.05        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-E2-A105 TCGA-E2-A108 
       13.48         1.61        18.51        21.67        43.00        27.52 
TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A155 TCGA-E2-A156 
       40.96        33.17        43.33        32.02        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15O TCGA-E2-A15P 
       14.79        22.82        21.63        55.63        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       56.94        14.07        87.22        33.01        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1LA TCGA-E2-A1LB 
       77.65        59.18        60.99        11.08        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LL TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N3 
       28.90        43.04        30.61        34.92        34.29        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1R0 
       32.88        36.82        39.55        41.62        25.84        28.27 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RI TCGA-E9-A228 
        6.12        11.15        40.24        46.65        47.64        42.25 
TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A2JT 
       37.74        38.37        41.03        38.99         1.94         9.47 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1IY 
       32.91        23.90         0.79        25.81        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P4 
       18.21        18.90        28.77        40.41        39.78        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG 
       18.48        30.08        18.90        13.94        14.43        34.55 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD 
       22.09        34.03        17.49        15.22        31.30        33.21 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
      216.76        79.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DO TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-HN-A2NL TCGA-LD-A9QF 
       85.35        43.73        69.30        66.38         2.60        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 
       24.95        29.23        14.50        12.36        19.59        36.30 
TCGA-OL-A5D8 TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       31.99        24.72        22.32        26.70        23.47        65.62 
TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PL-A8LX TCGA-PL-A8LY 
       42.77        14.07        40.11        47.01         0.16         0.26 
TCGA-S3-AA10 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ TCGA-XX-A89A 
       19.27        18.87        17.39        17.26        66.84        16.04 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.03              0.03 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           282.90            216.76 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           25.975            31.150 
[1] "0.0 - 282.9 (26.0)" "0.0 - 216.8 (31.1)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q GAIN MUTATED        48       47        2        6       242       168
  1Q GAIN WILD-TYPE      41       38        4        0       111        84
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           1         96         23         48       12
  1Q GAIN WILD-TYPE         1         58          6         17        8
                   vv
clus                STAGE TIS STAGE X
  1Q GAIN MUTATED           1       8
  1Q GAIN WILD-TYPE         0       5
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 48                41
  STAGE IA                47                38
  STAGE IB                 2                 4
  STAGE II                 6                 0
  STAGE IIA              242               111
  STAGE IIB              168                84
  STAGE III                1                 1
  STAGE IIIA              96                58
  STAGE IIIB              23                 6
  STAGE IIIC              48                17
  STAGE IV                12                 8
  STAGE TIS                1                 0
  STAGE X                  8                 5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED   153 433  88  30
  1Q GAIN WILD-TYPE 123 191  48  10
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1             153               123
  T2             433               191
  T3              88                48
  T4              30                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q GAIN MUTATED   330 236  72  56
  1Q GAIN WILD-TYPE 177 122  47  21
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0             330               177
  N1             236               122
  N2              72                47
  N3              56                21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   576  13
  1Q GAIN WILD-TYPE 313   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    576   13
  1Q GAIN WILD-TYPE  313    9
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0             576               313
  1              13                 9
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   699   7
  1Q GAIN WILD-TYPE 369   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    699    7
  1Q GAIN WILD-TYPE  369    5
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE             699               369
  MALE                 7                 5
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED   279 340
  1Q GAIN WILD-TYPE 150 178
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED    279  340
  1Q GAIN WILD-TYPE  150  178
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO              279               150
  YES             340               178
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q GAIN MUTATED                            1                           485
  1Q GAIN WILD-TYPE                          0                           285
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q GAIN MUTATED                              156                   4
  1Q GAIN WILD-TYPE                             44                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1Q GAIN MUTATED                       4                               16
  1Q GAIN WILD-TYPE                     5                               13
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1Q GAIN MUTATED                    8             32
  1Q GAIN WILD-TYPE                  9             15
D2V9, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                485               285
  INFILTRATING LOBULAR CARCINOMA               156                44
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)              16                13
  MUCINOUS CARCINOMA                             8                 9
  OTHER  SPECIFY                                32                15
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  1    33
  1Q GAIN WILD-TYPE                                0    27
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                         111   500
  1Q GAIN WILD-TYPE                        70   245
D2V11, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         33                27
  BLACK OR AFRICAN AMERICAN                    111                70
  WHITE                                        500               245
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V12, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    20 572
  1Q GAIN WILD-TYPE  19 303
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     20  572
  1Q GAIN WILD-TYPE   19  303
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  20                19
  NOT HISPANIC OR LATINO             572               303
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED   100  20
  2P GAIN WILD-TYPE 817 127
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              120               944 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               20               127 
$`2P GAIN MUTATED`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SO TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0SX 
      131.67        42.81        28.01        56.81        67.33        50.43 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XS 
       17.13         8.38        18.21        18.61        19.20        33.93 
TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
       50.37        26.96        30.61        35.67        31.73        20.19 
TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X 
       21.73        21.17        12.10         1.02        17.98        31.00 
TCGA-A8-A075 TCGA-A8-A07U TCGA-A8-A08R TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y 
       17.03        24.99         0.99        12.00         5.72        17.42 
TCGA-AC-A6IW TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FX TCGA-AO-A0J2 TCGA-AO-A0JD 
       13.58         1.78         0.16         0.33        32.78        72.00 
TCGA-AO-A124 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR TCGA-AR-A0TS TCGA-AR-A0TX 
      115.27        64.04        48.36        70.39        84.10        64.83 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A24Q TCGA-B6-A0I2 TCGA-B6-A0RE TCGA-B6-A0RU 
       65.36        83.87       104.28       143.38       255.68       282.90 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AW TCGA-BH-A0BG 
      206.86       245.10        70.16        18.84        20.45        61.51 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DL TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A18T 
       41.75        44.02        78.28         9.63        46.19         7.36 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FC 
       51.16        67.50        12.00        31.53        97.48       114.15 
TCGA-BH-A1FM TCGA-BH-A203 TCGA-BH-A5IZ TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V 
       45.63        38.60        18.64        11.77        12.66        12.66 
TCGA-C8-A131 TCGA-C8-A1HK TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A8HP 
       13.51        12.03        12.95         9.53         9.50        13.02 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JK TCGA-D8-A1XF 
       20.88        14.17        19.20        14.17        20.12        15.22 
TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A109 TCGA-E2-A10C 
       19.92        12.99        13.48        10.09        46.59        40.11 
TCGA-E2-A14P TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1II TCGA-E2-A1LE 
       40.96        14.79        25.05        23.34        33.70        28.90 
TCGA-E2-A1LK TCGA-E2-A574 TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A2JS TCGA-E9-A5FL 
        8.75        38.76         6.58        46.59        29.72         0.79 
TCGA-EW-A1IY TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DD 
        8.48         6.15        55.00       109.87        79.10        75.02 
TCGA-GM-A2DF TCGA-HN-A2NL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-OL-A5RW 
       70.85         2.60        14.70        14.79        19.53        36.36 
TCGA-OL-A66I TCGA-OL-A66P TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA10 TCGA-UL-AAZ6 
       23.47        14.07        28.21         9.93        19.27        17.03 

$`2P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 
       77.19        75.25         5.19        98.99       107.93        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        61.58        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      118.45        79.76        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        44.88        44.28        17.52        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        49.48        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT 
       18.15       105.34        10.59        36.23        39.65        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        32.75        56.28        47.31        35.93        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        14.50        17.92        14.73        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       53.06        29.03        26.01         1.02        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W 
       32.05         9.99        10.98         8.98         7.99         9.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        30.97        17.95        41.98         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95        22.95 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       15.48        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX 
       19.33        14.96        11.44        13.71        18.67        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        2.96         1.71         9.96         7.36         7.46         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.90         7.04         0.33         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        58.95        29.13        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        76.77        65.10        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33        71.80        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        98.27        57.30        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        61.87         0.53        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
      130.09         5.65        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       140.55        98.33         5.26       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       98.93        55.86       107.24       133.22       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      125.16       108.36       101.00       103.86        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       96.00        86.07        93.90        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27        77.69       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       98.76        98.66        89.00        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       71.05        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 
       73.35        33.30        38.96        10.59        77.62       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       275.87       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       233.62        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      129.07       140.88        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       21.47       113.79       129.70        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        85.35        68.12       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       59.84        25.55        63.09        81.44        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.16        70.22        81.63        84.13        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        43.53        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        77.95        49.05        89.06        90.97        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       77.98        23.44        38.01        29.98        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA 
       16.27         4.41        15.68        14.30        44.81        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        53.26        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       35.93        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EO 
       30.28        55.63        37.55        66.05        51.39        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE 
       25.81        89.16        24.62       120.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        26.14        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 
       12.66        12.66        48.53        12.56         3.16         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.92         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34        11.28         0.16        10.42        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.53        12.36         8.28         9.67 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ 
        0.03        24.56        14.43        33.99        12.95        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        56.81        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        21.14        17.49        16.50        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.15        18.90        12.03        53.00        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       23.90        27.58        18.15        12.39        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       21.80        14.50        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.31        16.64        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43        48.03        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        1.61        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        40.41        37.51        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15C 
       69.96        23.24        19.43        21.04        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       56.94        14.07        51.39        76.57        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        50.07       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        26.99        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       22.29        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        38.37        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.12         0.69        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       12.33         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        23.84        26.70        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV 
       10.52        14.43        34.55        19.96        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        10.16        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        83.34        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       15.32        14.47        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        12.36        19.59        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       40.08        34.92        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26        18.81        18.48        21.07        20.68 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S 
       13.84        18.87        17.39        17.26        13.94         3.81 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       66.84        11.41        52.96        29.03        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.16              0.03 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           282.90            281.29 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           23.405            28.355 
[1] "0.2 - 282.9 (23.4)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P GAIN MUTATED         6        8        0        1        46        33
  2P GAIN WILD-TYPE      83       77        6        5       307       219
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           0         14          3          7        1
  2P GAIN WILD-TYPE         2        140         26         58       19
                   vv
clus                STAGE TIS STAGE X
  2P GAIN MUTATED           0       1
  2P GAIN WILD-TYPE         1      12
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  6                83
  STAGE IA                 8                77
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               46               307
  STAGE IIB               33               219
  STAGE III                0                 2
  STAGE IIIA              14               140
  STAGE IIIB               3                26
  STAGE IIIC               7                58
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED    26  79  12   5
  2P GAIN WILD-TYPE 250 545 124  35
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              26               250
  T2              79               545
  T3              12               124
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P GAIN MUTATED    57  41  15   8
  2P GAIN WILD-TYPE 450 317 104  69
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              57               450
  N1              41               317
  N2              15               104
  N3               8                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   105   2
  2P GAIN WILD-TYPE 784  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    105    2
  2P GAIN WILD-TYPE  784   20
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0             105               784
  1               2                20
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED   123   0
  2P GAIN WILD-TYPE 945  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED    123    0
  2P GAIN WILD-TYPE  945   12
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE             123               945
  MALE                 0                12
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    42  61
  2P GAIN WILD-TYPE 387 457
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     42   61
  2P GAIN WILD-TYPE  387  457
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               42               387
  YES              61               457
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P GAIN MUTATED                            1                           109
  2P GAIN WILD-TYPE                          0                           661
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P GAIN MUTATED                                5                   2
  2P GAIN WILD-TYPE                            195                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2P GAIN MUTATED                       3                                0
  2P GAIN WILD-TYPE                     6                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2P GAIN MUTATED                    0              3
  2P GAIN WILD-TYPE                 17             44
D3V9, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                109               661
  INFILTRATING LOBULAR CARCINOMA                 5               195
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 3                44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  1    10
  2P GAIN WILD-TYPE                                0    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          32    69
  2P GAIN WILD-TYPE                       149   676
D3V11, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         10                50
  BLACK OR AFRICAN AMERICAN                     32               149
  WHITE                                         69               676
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V12, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     0 105
  2P GAIN WILD-TYPE  39 770
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      0  105
  2P GAIN WILD-TYPE   39  770
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                39
  NOT HISPANIC OR LATINO             105               770
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    62   9
  2Q GAIN WILD-TYPE 855 138
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               71               993 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9               138 
$`2Q GAIN MUTATED`
TCGA-3C-AALI TCGA-A1-A0SO TCGA-A2-A04W TCGA-A2-A0CX TCGA-A2-A0SX TCGA-A2-A0YE 
      131.67        28.01       101.98        56.81        50.43        18.21 
TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA 
       18.61        19.20        50.37        26.96        30.61        35.67 
TCGA-A7-A13D TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A07U 
       31.73        21.73        21.17        17.98        31.00        24.99 
TCGA-A8-A097 TCGA-AC-A23H TCGA-AC-A62Y TCGA-AN-A04C TCGA-AO-A124 TCGA-AO-A12D 
       12.00         5.72        17.42         1.78       115.27        64.04 
TCGA-AO-A12F TCGA-AR-A24Q TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A402 TCGA-BH-A0AW 
       48.36       104.28       206.86       245.10        70.16        20.45 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DL TCGA-BH-A0E9 TCGA-BH-A18T 
       61.51        74.89        44.02        78.28        46.19         7.36 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1F2 TCGA-BH-A203 TCGA-C8-A12P TCGA-C8-A12U 
       51.16        67.50        31.53        38.60        11.77        12.66 
TCGA-C8-A12V TCGA-C8-A131 TCGA-C8-A26Y TCGA-C8-A274 TCGA-C8-A8HP TCGA-D8-A147 
       12.66        13.51        12.95         9.53        13.02        19.20 
TCGA-D8-A1J8 TCGA-D8-A1XU TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P 
       14.17        12.99        13.48        46.59        40.11        40.96 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1LE TCGA-E2-A574 TCGA-E9-A5FL TCGA-EW-A1IY 
       25.05        23.34        28.90        38.76         0.79         8.48 
TCGA-EW-A1PC TCGA-EW-A2FR TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-LL-A5YN TCGA-LL-A5YP 
        6.15        55.00       109.87        79.10        14.70        14.79 
TCGA-LL-A73Y TCGA-OL-A5RW TCGA-OL-A66I TCGA-PL-A8LZ TCGA-S3-AA10 
       15.68        36.36        23.47         9.93        19.27 

$`2Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        87.25        63.12        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       77.19        75.25         5.19        98.99       107.93        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       118.45        79.76        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        27.12        44.88        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
        8.38        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        50.47        21.90        21.67        49.48 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       19.33        48.46        31.73        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       56.28        47.31        35.93        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E 
       34.29        35.47        37.45        33.11        29.79        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       25.15        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
        0.99        38.01        28.96        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       37.05         9.99        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
      112.08        43.00        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       49.05        45.07        29.98        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        22.95        73.91         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       29.26        16.80        14.53        19.33        14.96        11.44 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       13.71        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        9.96         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         7.04         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G 
      106.78       108.03        90.58        98.27        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       32.52         2.56        32.91        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       55.86       107.24        65.36       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
      107.21       125.16       108.36       101.00       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       98.33        96.00        86.07        93.90        99.32        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        94.29        61.28        86.53        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76       112.77        97.84       105.27        77.69       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       32.58        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       281.29        12.13       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       165.76       129.07       140.88       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      129.70        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       73.51       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       68.12        18.84       103.63        71.15        62.93        59.84 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        63.09        81.44        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       70.22        81.63        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       18.21        43.53        21.70        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        53.95        45.57        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        41.75        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP 
       23.44        38.01        29.98        13.91        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
        4.41        15.68        14.30         9.63        44.81        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        53.26        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       35.93        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EO 
       30.28        55.63        37.55        66.05        51.39        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        89.16        97.48        24.62       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       109.28        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12W 
       11.93        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53        12.56         3.16         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.28         0.16        12.03        10.42        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.53        12.36         8.28         9.67 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         9.50        24.56        14.43        33.99        12.95 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 
       20.58        13.97        14.17        13.48        21.14        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        55.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       53.00        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       18.15        12.39        17.16        15.22        14.73        21.80 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.31        16.64        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43        48.03        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        1.61        10.09        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       34.42        27.52        40.41        37.51        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        44.68        38.24        38.60        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       43.33        34.26        32.02        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       63.62        69.96        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       14.79        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       50.79        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        87.22        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        60.36        73.64        19.66        24.59        75.81 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       50.07       106.75       102.61         8.75        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 
       34.55        43.56         8.28        30.61        34.92        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       17.69        34.82        32.88        36.82        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.20        36.56        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        40.24         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        38.37        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.12         0.69        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.33        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       30.44        23.90        23.84        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       27.85        12.20        39.72        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       16.57        15.68        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS 
       13.94        10.52        14.43        34.55        19.96        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       15.22        16.77        24.99        31.30        33.21         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       13.55        18.12         2.60        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
       32.75        29.23        25.05        17.06        15.32        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       22.26         2.63        16.08         7.46        14.50        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       28.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26        18.81        18.48        21.07        20.68 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        18.87        17.39        17.26        13.94        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
        3.81        66.84        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.79              0.03 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            245.1             282.9 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            26.96             27.91 
[1] "0.8 - 245.1 (27.0)" "0.0 - 282.9 (27.9)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q GAIN MUTATED         5        4        0        1        28        23
  2Q GAIN WILD-TYPE      84       81        6        5       325       229
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           0          5          2          4        0
  2Q GAIN WILD-TYPE         2        149         27         61       20
                   vv
clus                STAGE TIS STAGE X
  2Q GAIN MUTATED           0       0
  2Q GAIN WILD-TYPE         1      13
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  5                84
  STAGE IA                 4                81
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               28               325
  STAGE IIB               23               229
  STAGE III                0                 2
  STAGE IIIA               5               149
  STAGE IIIB               2                27
  STAGE IIIC               4                61
  STAGE IV                 0                20
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    14  50   7   2
  2Q GAIN WILD-TYPE 262 574 129  38
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              14               262
  T2              50               574
  T3               7               129
  T4               2                38
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q GAIN MUTATED    37  24   6   4
  2Q GAIN WILD-TYPE 470 334 113  73
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              37               470
  N1              24               334
  N2               6               113
  N3               4                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    64   1
  2Q GAIN WILD-TYPE 825  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     64    1
  2Q GAIN WILD-TYPE  825   21
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              64               825
  1               1                21
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    73   0
  2Q GAIN WILD-TYPE 995  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     73    0
  2Q GAIN WILD-TYPE  995   12
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              73               995
  MALE                 0                12
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    24  38
  2Q GAIN WILD-TYPE 405 480
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     24   38
  2Q GAIN WILD-TYPE  405  480
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               24               405
  YES              38               480
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q GAIN MUTATED                            0                            64
  2Q GAIN WILD-TYPE                          1                           706
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q GAIN MUTATED                                3                   0
  2Q GAIN WILD-TYPE                            197                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2Q GAIN MUTATED                       3                                0
  2Q GAIN WILD-TYPE                     6                               29
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2Q GAIN MUTATED                    0              3
  2Q GAIN WILD-TYPE                 17             44
D4V9, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 64               706
  INFILTRATING LOBULAR CARCINOMA                 3               197
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               0                29
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 3                44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     8
  2Q GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          17    42
  2Q GAIN WILD-TYPE                       164   703
D4V11, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     17               164
  WHITE                                         42               703
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     0  63
  2Q GAIN WILD-TYPE  39 812
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      0   63
  2Q GAIN WILD-TYPE   39  812
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                39
  NOT HISPANIC OR LATINO              63               812
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED   112  21
  3P GAIN WILD-TYPE 805 126
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              133               931 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               21               126 
$`3P GAIN MUTATED`
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T2 
       24.79        77.19        98.99        27.12        50.43         8.38 
TCGA-A2-A0T7 TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CD 
       20.75        31.73        17.36        33.93        24.39        38.30 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13F TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE 
       35.67        33.11        25.15        14.70        14.50        21.17 
TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A08B TCGA-A8-A08C 
       10.29        13.02         1.02         9.01        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 
       33.01        12.00        37.05        31.00        33.01        17.95 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09Q 
       12.00         9.99        12.00        49.05        29.98        25.02 
TCGA-A8-A09R TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A5XU TCGA-AN-A03Y 
        8.98         5.72        26.04        14.66        14.96         0.33 
TCGA-AN-A0AS TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03O 
        0.33         0.36         0.33         0.33        12.33        81.63 
TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AQ-A04H TCGA-AQ-A54N 
       52.18        20.32       106.78        64.04        24.79         2.56 
TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K 
       32.91        84.10       108.36       101.00        37.81        50.89 
TCGA-AR-A24V TCGA-AR-A2LL TCGA-B6-A0IA TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RP 
      105.30        66.15       275.87       140.88       255.68       102.77 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A401 TCGA-B6-A408 
      100.70       282.90        79.63        43.59        85.35        68.12 
TCGA-BH-A0AU TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0C0 
       62.93        81.63        74.89        76.60        45.57        41.75 
TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY 
        2.56        46.19        24.49        20.38        27.25        50.79 
TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A5J0 
       37.74        51.39       114.15        26.14        38.60        23.51 
TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A1HI TCGA-C8-A27B 
       11.77        12.66        12.66        12.66        11.28        14.43 
TCGA-D8-A13Z TCGA-D8-A147 TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A1Y2 
       20.88        19.20        27.58        16.41        15.16        14.24 
TCGA-D8-A27R TCGA-D8-A73X TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14O 
       10.09        25.22        46.59        37.51        47.15        44.68 
TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1AZ 
       75.98        18.51        19.43        20.71        18.21        76.57 
TCGA-E2-A1IH TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF 
       33.73        50.07       102.61        32.09        40.24         6.58 
TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1P8 TCGA-EW-A1PH TCGA-GM-A2DF 
       23.84        26.40        28.77         7.86        19.96        70.85 
TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-OL-A5RW TCGA-OL-A6VO 
       69.30        15.32        14.79        16.08        36.36        28.21 
TCGA-S3-A6ZF 
       18.81 

$`3P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       39.32        28.01        19.20        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
       78.41       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX 
       88.60       107.93        75.25         5.19       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       99.19        54.64        44.88        44.28        17.52        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.21        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       19.33        48.46        23.77        23.47        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        91.07        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       35.93        50.37        50.83         7.30        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       30.61        37.45        29.79        31.73        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       13.41        11.97        14.93        13.74        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        11.05         9.37        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y 
       13.02        17.98        53.06        29.03        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 
        8.98         7.99        24.99         9.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08O 
       36.95        13.02         0.99        19.96         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 
        0.99        33.01       112.08        43.00        40.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M 
       41.98         9.99         1.02        50.04        45.07        33.07 
TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        1.02        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        22.95        73.91         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       74.14        33.04        19.33        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       14.83        22.19        24.13        25.05        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       19.79        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       14.53        19.33        11.44        13.71        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         2.30         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.62         2.96         1.78         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         5.36         0.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       61.35        66.77        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       29.13        32.78        21.40        26.04        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       65.10        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
      115.27        99.25       108.72       108.03        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        70.39         0.53        17.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
        5.65        15.62        32.52        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      125.16       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        17.23        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73       160.90        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       77.69        32.58        98.76        98.66        89.00        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       93.30        85.64        71.05        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        54.21        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       281.29        12.13       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      165.76       129.07        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       263.28       162.05       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        18.35        21.47       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       245.10        28.27        68.94        58.88       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 
       73.51       139.17       170.17        37.87         7.07        70.16 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       18.84       103.63        71.15        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       63.09        81.44        40.83        39.55        39.16        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       61.51        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        49.94        77.95        49.05        44.02        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        45.83        77.98        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT 
       13.91        78.28        17.26        15.65         3.22        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
        9.63        44.81        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       36.85        12.89        51.32         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q 
       20.12        90.84        26.66        72.56        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        51.16        67.50        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       109.28        20.88        18.64         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.16        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.08        12.33        10.92        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       10.42        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.50        24.56        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        56.81        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        21.14        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       55.50        15.78        18.15        18.90        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        55.30        15.85        16.31        16.64        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       43.04        16.54        15.32        15.52         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         4.80         1.61        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U 
       28.87        40.96        38.24        38.60        33.17        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 
       34.26        32.02        31.96        69.34        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       23.24        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        21.63        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO 
       33.70        28.44        59.18         3.88        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        60.36        73.64        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       75.81        28.90       106.75         8.75        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
       34.55        43.56         8.28        30.61        34.92        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       34.16        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02        11.15        48.23 
TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       45.01         1.12        46.65        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       41.03        41.72        40.73        40.50        20.12         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       38.99         1.94         7.13        24.56        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70         0.79        25.81        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       17.49        10.16        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        75.02        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       43.73        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       17.06        14.70        14.47        22.26         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        7.46        14.50        19.53        12.36        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       26.04        17.36        14.07        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       18.48        21.07        20.68        19.27        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.39        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.33              0.03 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           282.90            281.29 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            27.58             27.91 
[1] "0.3 - 282.9 (27.6)" "0.0 - 281.3 (27.9)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P GAIN MUTATED        11        9        0        1        54        21
  3P GAIN WILD-TYPE      78       76        6        5       299       231
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           0         18          7          6        4
  3P GAIN WILD-TYPE         2        136         22         59       16
                   vv
clus                STAGE TIS STAGE X
  3P GAIN MUTATED           0       2
  3P GAIN WILD-TYPE         1      11
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 11                78
  STAGE IA                 9                76
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               54               299
  STAGE IIB               21               231
  STAGE III                0                 2
  STAGE IIIA              18               136
  STAGE IIIB               7                22
  STAGE IIIC               6                59
  STAGE IV                 4                16
  STAGE TIS                0                 1
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED    32  83  10   9
  3P GAIN WILD-TYPE 244 541 126  31
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              32               244
  T2              83               541
  T3              10               126
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P GAIN MUTATED    68  36  18  10
  3P GAIN WILD-TYPE 439 322 101  67
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              68               439
  N1              36               322
  N2              18               101
  N3              10                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   124   4
  3P GAIN WILD-TYPE 765  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    124    4
  3P GAIN WILD-TYPE  765   18
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0             124               765
  1               4                18
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED   134   1
  3P GAIN WILD-TYPE 934  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED    134    1
  3P GAIN WILD-TYPE  934   11
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE             134               934
  MALE                 1                11
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    54  69
  3P GAIN WILD-TYPE 375 449
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     54   69
  3P GAIN WILD-TYPE  375  449
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               54               375
  YES              69               449
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P GAIN MUTATED                            0                           114
  3P GAIN WILD-TYPE                          1                           656
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P GAIN MUTATED                                7                   2
  3P GAIN WILD-TYPE                            193                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3P GAIN MUTATED                       2                                4
  3P GAIN WILD-TYPE                     7                               25
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3P GAIN MUTATED                    1              5
  3P GAIN WILD-TYPE                 16             42
D5V9, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                114               656
  INFILTRATING LOBULAR CARCINOMA                 7               193
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 5                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  0     8
  3P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          25    83
  3P GAIN WILD-TYPE                       156   662
D5V11, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     25               156
  WHITE                                         83               662
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V12, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     5 102
  3P GAIN WILD-TYPE  34 773
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      5  102
  3P GAIN WILD-TYPE   34  773
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO             102               773
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   180  28
  3Q GAIN WILD-TYPE 737 119
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              208               856 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               28               119 
$`3Q GAIN MUTATED`
TCGA-A1-A0SI TCGA-A2-A04U TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0D0 
       20.88        87.25        24.79        77.19        98.99        67.33 
TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       63.29        27.12        50.43        17.13         8.38        49.84 
TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 
       20.75        21.90        31.73        17.36        22.45        19.20 
TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB 
       33.93        24.39        38.30        30.61        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D 
       31.73        25.15        23.80        14.50        21.17        14.73 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A079 TCGA-A8-A07J 
       10.29        10.42        13.02         1.02         9.01        12.00 
TCGA-A8-A07L TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       32.05        24.99         9.99        38.01        28.96        33.01 
TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B 
       12.00        31.00        33.01        17.95         9.99        12.00 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-AC-A23H 
       49.05        29.98        33.07        25.02         8.98         5.72 
TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A6IW TCGA-AN-A03Y 
       26.04        14.66        14.96        13.71        13.58         0.33 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL 
        0.23         0.62         9.96         0.16         0.33         7.59 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A03O 
        0.36         0.33         0.33        12.33        80.28        81.63 
TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12D TCGA-AO-A1KR TCGA-AQ-A54N 
       52.18        20.32       106.78        64.04        70.39         2.56 
TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AS TCGA-AR-A24K 
       32.91        84.10       108.36       101.00        37.81        50.89 
TCGA-AR-A24M TCGA-AR-A24V TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LL TCGA-AR-A5QP 
      120.33       105.30        71.05        93.83        66.15        38.96 
TCGA-B6-A0I2 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RP 
      143.38       275.87       233.62        18.77       140.88       102.77 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A401 
      100.70       282.90        79.63        43.59       101.52        85.35 
TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT 
       68.12        62.93        81.63        74.89        76.60        45.57 
TCGA-BH-A0C0 TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 
       41.75        78.28         2.56        46.19        24.49        23.08 
TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18N TCGA-BH-A18Q 
       20.38        12.89        27.25        50.79        37.74        55.63 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1FC TCGA-BH-A1FN TCGA-BH-A202 
       51.39        51.16        12.00       114.15        72.07        26.14 
TCGA-BH-A203 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12M TCGA-C8-A12Q TCGA-C8-A12U 
       38.60        18.64        23.51        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A1HI TCGA-C8-A26W TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP 
       12.66        11.28        12.53        14.43        12.95        13.02 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ 
       20.88        14.17        19.20        18.58        27.58        21.80 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1Y2 
       14.50        19.92        16.41        12.99        15.16        14.24 
TCGA-D8-A27R TCGA-D8-A73X TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A14O 
       10.09        25.22        46.59        37.51        47.15        44.68 
TCGA-E2-A14Z TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1AZ 
       18.51        19.43        25.05        20.71        18.21        76.57 
TCGA-E2-A1IE TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       77.65        33.73        33.70        50.07       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1RB TCGA-E9-A1RC 
       43.04        34.92        34.16        35.24        32.09        40.24 
TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1J6 
        6.58        46.59        23.84         0.79        26.40        28.77 
TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PH 
       22.82        29.82         7.86        19.99         6.15        19.96 
TCGA-EW-A2FS TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL 
       52.73         7.40        79.10        70.85        72.10        69.30 
TCGA-HN-A2NL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A8F5 
        2.60        15.32        14.79        16.08        15.68        19.59 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF 
       36.36        20.38        28.21        86.96         9.93        18.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-UU-A93S 
       21.07        20.68        19.27         3.81 

$`3Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        73.84        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 
       75.25         5.19       107.93        56.81        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72        89.36        80.28       118.45 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       79.76        74.40        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY 
       61.94        24.72        99.19        54.64        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       17.52        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        50.47        21.67        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G4 
       48.46        23.77        23.47        60.72        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
      105.34        10.59        36.23        39.65        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A13E 
       35.31        34.29        35.47        37.45        29.79        20.19 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I 
       23.61        29.56        31.36        24.26        23.74        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       13.41        14.70        11.97        14.93        13.74        17.92 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       12.10        10.72        11.05         9.37         8.75        13.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03        53.98        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07Z 
       14.01         9.99        10.98         8.98         7.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08J 
       15.06        36.95        13.02         0.99        19.96        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00         0.99        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C 
       40.01        30.97        41.98        12.00         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       50.04        45.07         1.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95        22.95        73.91 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        1.48        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       60.92        87.12        74.14        33.04        19.33        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       29.26        16.80        14.53        19.33        11.44        17.42 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       18.67        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A 
        1.12         1.32         2.30         0.33         0.33         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT 
        1.78         1.71         7.36         7.46         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.00         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP 
        7.04         0.33         0.33         5.36         0.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       61.35        66.77        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       29.13        32.78        21.40        26.04        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       65.10        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
      115.27        99.25       108.72       108.03        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
        5.65        15.62        32.52        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      125.16       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        99.32        17.23        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O 
       86.43        33.73       160.90        94.22        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28       112.77        97.84       105.27        77.69 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       32.58        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       85.64       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        57.27        73.35        33.30 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       10.59        77.62       281.29        12.13       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       65.72       146.50       112.37       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      129.07       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       263.28       162.05       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        18.35        21.47       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI 
      129.70       245.10        28.27        68.94        58.88        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 
      139.17       170.17        37.87         7.07        70.16        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
      103.63        71.15        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 
       81.44        40.83        39.55        39.16        70.22        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS 
       21.70        61.68        72.23        75.48        74.14        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       49.94        77.95        49.05        44.02        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         3.22        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.58        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        53.26        24.56        41.00        52.96        26.50 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX 
        5.85         2.50        13.61        36.85        51.32         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO 
       30.28        37.55        66.05         7.36        67.50        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
      113.82        82.85        42.28        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.62       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 
       45.63       144.59        72.07        28.14        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W 
        9.44        11.93        11.77        12.66        11.77        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56         3.16        13.51         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.92         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.34         0.16        12.03        10.42        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.36        12.95         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A8HQ 
        9.53         0.03         9.50        24.56        33.99        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        56.81        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        21.14        14.17        17.49        16.50        55.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       15.78        18.15        18.90        12.03        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       25.74        23.90        18.15        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       14.73        17.69        55.30        15.85        16.31        16.64 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       43.04        16.54        15.32        15.52         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         4.80         1.61        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       28.87        40.96        38.24        38.60        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       43.33        34.26        32.02        31.96        69.34        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       69.96        23.24        21.04        23.87        14.79        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       22.82        17.29        21.63        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        16.47        37.25        37.41        70.36        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       60.36        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        26.99        34.55        43.56         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       22.29        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02        11.15        48.23        45.01 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        1.12        46.65        21.27        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO 
       32.91        30.18        30.44        23.90        26.70        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       30.08        18.90        13.94        10.52        14.43        34.55 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       55.00        25.91        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       23.51        15.22        16.77        24.99        31.30        33.21 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI 
      109.87        59.57       216.76        83.34        75.02        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       17.06        14.70        14.47        22.26         2.63         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        19.53        12.36        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       34.92        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX 
       19.73        40.11         8.91        47.01        64.21         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
        0.26        18.48        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.16              0.03 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           282.90            281.29 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           25.185            28.470 
[1] "0.2 - 282.9 (25.2)" "0.0 - 281.3 (28.5)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q GAIN MUTATED        15       15        1        1        82        42
  3Q GAIN WILD-TYPE      74       70        5        5       271       210
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           0         27         11         10        5
  3Q GAIN WILD-TYPE         2        127         18         55       15
                   vv
clus                STAGE TIS STAGE X
  3Q GAIN MUTATED           0       1
  3Q GAIN WILD-TYPE         1      12
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                15                70
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA               82               271
  STAGE IIB               42               210
  STAGE III                0                 2
  STAGE IIIA              27               127
  STAGE IIIB              11                18
  STAGE IIIC              10                55
  STAGE IV                 5                15
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED    45 133  21  13
  3Q GAIN WILD-TYPE 231 491 115  27
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              45               231
  T2             133               491
  T3              21               115
  T4              13                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q GAIN MUTATED   110  60  24  14
  3Q GAIN WILD-TYPE 397 298  95  63
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0             110               397
  N1              60               298
  N2              24                95
  N3              14                63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   185   5
  3Q GAIN WILD-TYPE 704  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    185    5
  3Q GAIN WILD-TYPE  704   17
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0             185               704
  1               5                17
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED   211   1
  3Q GAIN WILD-TYPE 857  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED    211    1
  3Q GAIN WILD-TYPE  857   11
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE             211               857
  MALE                 1                11
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    85 106
  3Q GAIN WILD-TYPE 344 412
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     85  106
  3Q GAIN WILD-TYPE  344  412
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               85               344
  YES             106               412
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q GAIN MUTATED                            0                           180
  3Q GAIN WILD-TYPE                          1                           590
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q GAIN MUTATED                               10                   4
  3Q GAIN WILD-TYPE                            190                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3Q GAIN MUTATED                       4                                6
  3Q GAIN WILD-TYPE                     5                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3Q GAIN MUTATED                    1              7
  3Q GAIN WILD-TYPE                 16             40
D6V9, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                180               590
  INFILTRATING LOBULAR CARCINOMA                10               190
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 7                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  1    13
  3Q GAIN WILD-TYPE                                0    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          47   128
  3Q GAIN WILD-TYPE                       134   617
D6V11, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         13                47
  BLACK OR AFRICAN AMERICAN                     47               134
  WHITE                                        128               617
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V12, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     6 169
  3Q GAIN WILD-TYPE  33 706
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6  169
  3Q GAIN WILD-TYPE   33  706
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                33
  NOT HISPANIC OR LATINO             169               706
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    65  10
  4P GAIN WILD-TYPE 852 137
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               75               989 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               10               137 
$`4P GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0ET TCGA-A2-A0YM TCGA-A2-A0YT 
       13.68        75.25         5.19        35.05        31.73        23.77 
TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A8-A06O TCGA-A8-A075 
       20.25        26.96        13.74        21.17        13.02        17.03 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T 
        9.01        18.97         9.99        19.96        33.01       112.08 
TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A0A9 TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3W5 
       33.01        29.98        27.02        33.04        14.66        16.57 
TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0JD TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW 
        1.78         0.33        72.00        32.91        84.10        98.93 
TCGA-AR-A2LL TCGA-B6-A0RG TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI TCGA-BH-A0DL 
       66.15        68.45        62.93        25.55        29.98        78.28 
TCGA-BH-A0HX TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A1EN TCGA-BH-A1EW TCGA-BH-A1EX 
       27.25        26.66        37.74        67.50        55.69        49.58 
TCGA-BH-A1FM TCGA-BH-A202 TCGA-C8-A1HN TCGA-C8-A1HO TCGA-D8-A1J8 TCGA-D8-A1JD 
       45.63        26.14        12.95        12.33        14.17        18.15 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JT TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R 
       53.00        14.01        13.32        15.32        13.48        10.09 
TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14S TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A1LA 
       12.26        46.59        33.17        69.96        20.71        24.59 
TCGA-E2-A56Z TCGA-E9-A1N9 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A22D 
        8.28        36.20        11.15        40.24        46.65        41.03 
TCGA-E9-A247 TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A6SA 
       38.99        26.40        29.82        52.73        25.91        16.77 
TCGA-LL-A5YN TCGA-S3-A6ZG TCGA-Z7-A8R5 
       14.70        18.48       108.07 

$`4P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      121.94        73.84        87.25        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       88.60       107.93        77.19        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       21.67        49.48        18.61        19.33        48.46        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        36.23        39.65        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD 
       11.28        13.41        14.70        11.97        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42         8.75        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 
       53.06        29.03        31.00        26.01         1.02        53.98 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99        24.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        0.99        43.00        40.01        30.97        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       49.05        45.07        33.07         1.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04         0.99        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       22.95        73.91         5.72         1.48        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       74.14        19.33        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 
       22.19        24.13        25.05        14.99        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       23.24        24.79        29.26        16.80        14.53        19.33 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       14.96        11.44        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.32         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         9.96         7.36         7.46 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        0.16         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        61.35        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       95.70        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       26.93       130.09         5.65        15.62        32.52         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       140.55        98.33         5.26       109.02        75.22 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       97.68        98.33        96.00        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        94.29        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       33.73       160.90        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       77.69       105.30        32.58        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        54.21        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
        7.07        85.35        70.16        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       71.15        59.84        20.45        63.09        81.44        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        70.22        81.63        84.13        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.95        45.57        49.94        77.95        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       38.01        13.91        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05        32.91         4.90        35.93        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       90.84        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        12.00        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.62       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
      122.89        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        38.60        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       18.64        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56         3.16        13.51         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V 
       11.28         0.16        12.03        10.42        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         9.50        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE 
       19.20        17.49        16.50        55.50        15.78        18.90 
TCGA-D8-A1JF TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        21.01        12.20        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        15.16        43.04        16.54        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       14.43        48.03        16.41         4.80         1.61        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       25.22        43.00        34.42        27.52        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        75.98        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       31.96        69.34        18.51        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        51.39        76.57        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        75.81        28.90        50.07       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
        8.75        43.04        26.99        34.55        43.56        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       34.92        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        22.29        34.16        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       28.27        34.95         2.56         6.12         3.02        48.23 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       45.01        32.09         1.12         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.72        40.73        40.50        20.12         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       38.07        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70         0.79        25.81        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 
       14.43        34.55        19.96        55.00        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        10.16        23.51        15.22        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       33.21         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       83.34        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       25.05        17.06        15.32        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       21.07        20.68        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.26        13.94        17.03         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       107.05 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.33              0.03 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           112.08            282.90 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            26.66             28.21 
[1] "0.3 - 112.1 (26.7)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.4"
D7V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P GAIN MUTATED         3        4        0        2        31        15
  4P GAIN WILD-TYPE      86       81        6        4       322       237
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0         10          5          4        2
  4P GAIN WILD-TYPE         2        144         24         61       18
                   vv
clus                STAGE TIS STAGE X
  4P GAIN MUTATED           0       0
  4P GAIN WILD-TYPE         1      13
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  3                86
  STAGE IA                 4                81
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA               31               322
  STAGE IIB               15               237
  STAGE III                0                 2
  STAGE IIIA              10               144
  STAGE IIIB               5                24
  STAGE IIIC               4                61
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED    13  46  11   6
  4P GAIN WILD-TYPE 263 578 125  34
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              13               263
  T2              46               578
  T3              11               125
  T4               6                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P GAIN MUTATED    38  26   5   5
  4P GAIN WILD-TYPE 469 332 114  72
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              38               469
  N1              26               332
  N2               5               114
  N3               5                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    67   2
  4P GAIN WILD-TYPE 822  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     67    2
  4P GAIN WILD-TYPE  822   20
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              67               822
  1               2                20
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    74   2
  4P GAIN WILD-TYPE 994  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     74    2
  4P GAIN WILD-TYPE  994   10
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              74               994
  MALE                 2                10
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    28  40
  4P GAIN WILD-TYPE 401 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     28   40
  4P GAIN WILD-TYPE  401  478
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               28               401
  YES              40               478
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P GAIN MUTATED                            0                            59
  4P GAIN WILD-TYPE                          1                           711
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P GAIN MUTATED                                4                   1
  4P GAIN WILD-TYPE                            196                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4P GAIN MUTATED                       3                                3
  4P GAIN WILD-TYPE                     6                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4P GAIN MUTATED                    1              5
  4P GAIN WILD-TYPE                 16             42
D7V9, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 59               711
  INFILTRATING LOBULAR CARCINOMA                 4               196
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 5                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     2
  4P GAIN WILD-TYPE                                1    58
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           9    52
  4P GAIN WILD-TYPE                       172   693
D7V11, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          2                58
  BLACK OR AFRICAN AMERICAN                      9               172
  WHITE                                         52               693
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V12, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  59
  4P GAIN WILD-TYPE  36 816
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   59
  4P GAIN WILD-TYPE   36  816
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO              59               816
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    60  12
  4Q GAIN WILD-TYPE 857 135
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               72               992 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               12               135 
$`4Q GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A0YT 
       13.68        75.25         5.19        49.84        31.73        23.77 
TCGA-A2-A1G0 TCGA-A2-A4S1 TCGA-A7-A4SB TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A079 
       20.25        26.96        13.74        13.02        29.03         9.01 
TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 
       18.97         9.99        19.96        33.01       112.08        33.01 
TCGA-A8-A0A9 TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AN-A04C TCGA-AN-A0FY TCGA-AO-A0J3 
       27.02        14.66        16.57         1.78         0.33        21.40 
TCGA-AQ-A54O TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A250 TCGA-AR-A2LL TCGA-B6-A0RG 
       32.91        84.10        98.93        89.00        66.15        68.45 
TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0DI TCGA-BH-A0HX TCGA-BH-A18L 
       18.84        62.93        25.55        29.98        27.25        26.66 
TCGA-BH-A18N TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1FC TCGA-BH-A1FM TCGA-C8-A1HO 
       37.74        55.69        49.58       114.15        45.63        12.33 
TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JT TCGA-D8-A1XA 
       14.17        18.15        53.00        14.01        13.32        27.58 
TCGA-D8-A1XF TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 
       15.22        15.32        13.48        10.09        12.26        46.59 
TCGA-E2-A14S TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15O TCGA-E2-A1LA TCGA-E9-A1R6 
       33.17        69.96        20.71        50.79        24.59        11.15 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A247 TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A2FS 
       40.24        46.65        38.99        26.40        29.82        52.73 
TCGA-EW-A2FV TCGA-LL-A5YN TCGA-OL-A66I TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-Z7-A8R5 
       25.91        14.70        23.47        18.48        19.27       108.07 

$`4Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      121.94        73.84        87.25        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       88.60       107.93        77.19        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       21.67        49.48        18.61        19.33        48.46        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        36.23        39.65        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD 
       11.28        13.41        14.70        11.97        14.93        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       17.98        53.06        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       53.98        43.00        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        33.01        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 
       31.00         0.99        43.00        40.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB 
       12.00        19.04        13.02        21.04         0.99        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95        22.95        73.91         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       87.12        26.04        74.14        33.04        19.33        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X 
       16.80        14.53        19.33        14.96        11.44        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        9.96         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         7.04         0.33         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         5.36         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        65.10        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       115.27        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.03        90.58        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        40.57        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        32.52         2.56        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26       109.02        75.22        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       86.07        93.90        99.32        17.23        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       61.28        86.53        86.43        33.73       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27        77.69       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.76        98.66        99.62        93.30        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM 
       93.83       166.42        20.25        86.53        54.21        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        57.27        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      275.87       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      233.62        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      140.88       255.68       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      170.17        37.87         7.07        85.35        70.16        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        71.15        59.84        20.45        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        70.22        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        74.89        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       23.44        38.01        13.91        78.28        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        53.26        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       36.85        12.89        51.32        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q 
       35.93        20.12        90.84        72.56        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       37.55        66.05         7.36        51.39        51.16        67.50 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY 
       91.99       113.82        82.85        42.28        12.00        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.62       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       13.51         1.87        12.59        12.92         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42        12.33        12.95        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       24.56        14.43        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       13.97        14.17        13.48        21.14        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       16.50        55.50        15.78        18.90        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        18.15        12.39        17.16        14.73        21.80 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.31        16.64        12.99        15.16        43.04        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43        48.03        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        1.61        13.08        12.53        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18        12.66        25.22        43.00        34.42        27.52 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        38.60        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        69.34        18.51        63.62 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        17.29        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       56.94        14.07        51.39        76.57        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       73.64        19.66        75.81        28.90        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
        6.12         3.02        48.23        45.01        32.09         1.12 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       40.73        40.50        20.12         0.69         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       19.96        55.00        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       23.51        15.22        16.77        24.99        31.30        33.21 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        15.32        14.47        14.79        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       16.08        15.68         7.46        14.50        19.53        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J 
       28.87        24.72        22.32        20.38        26.70        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26         9.93        18.81        21.07        20.68 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        18.87        17.39        17.26        13.94        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
        3.81        66.84        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.33              0.03 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           114.15            282.90 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            26.53             28.27 
[1] "0.3 - 114.2 (26.5)" "0.0 - 282.9 (28.3)"
[1] "hr=" "1.7"
D8V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q GAIN MUTATED         4        5        1        0        29        14
  4Q GAIN WILD-TYPE      85       80        5        6       324       238
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          9          5          4        2
  4Q GAIN WILD-TYPE         2        145         24         61       18
                   vv
clus                STAGE TIS STAGE X
  4Q GAIN MUTATED           0       0
  4Q GAIN WILD-TYPE         1      13
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  4                85
  STAGE IA                 5                80
  STAGE IB                 1                 5
  STAGE II                 0                 6
  STAGE IIA               29               324
  STAGE IIB               14               238
  STAGE III                0                 2
  STAGE IIIA               9               145
  STAGE IIIB               5                24
  STAGE IIIC               4                61
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED    18  40   9   6
  4Q GAIN WILD-TYPE 258 584 127  34
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              18               258
  T2              40               584
  T3               9               127
  T4               6                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q GAIN MUTATED    34  27   5   5
  4Q GAIN WILD-TYPE 473 331 114  72
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              34               473
  N1              27               331
  N2               5               114
  N3               5                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    65   2
  4Q GAIN WILD-TYPE 824  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     65    2
  4Q GAIN WILD-TYPE  824   20
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              65               824
  1               2                20
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    72   1
  4Q GAIN WILD-TYPE 996  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     72    1
  4Q GAIN WILD-TYPE  996   11
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              72               996
  MALE                 1                11
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    28  37
  4Q GAIN WILD-TYPE 401 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     28   37
  4Q GAIN WILD-TYPE  401  481
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               28               401
  YES              37               481
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q GAIN MUTATED                            0                            57
  4Q GAIN WILD-TYPE                          1                           713
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q GAIN MUTATED                                4                   2
  4Q GAIN WILD-TYPE                            196                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4Q GAIN MUTATED                       2                                2
  4Q GAIN WILD-TYPE                     7                               27
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4Q GAIN MUTATED                    1              5
  4Q GAIN WILD-TYPE                 16             42
D8V9, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 57               713
  INFILTRATING LOBULAR CARCINOMA                 4               196
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               2                27
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 5                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                1    59
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                          11    49
  4Q GAIN WILD-TYPE                       170   696
D8V11, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          1                59
  BLACK OR AFRICAN AMERICAN                     11               170
  WHITE                                         49               696
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V12, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  57
  4Q GAIN WILD-TYPE  36 818
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   57
  4Q GAIN WILD-TYPE   36  818
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO              57               818
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   267  45
  5P GAIN WILD-TYPE 650 102
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              312               752 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               45               102 
$`5P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04W 
      129.14       131.67        13.68        39.32        19.20       101.98 
TCGA-A2-A0CX TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
       56.81        89.36        80.28        79.76        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EX TCGA-A2-A0SW TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE 
       31.82        24.72        44.88        18.90        20.75        18.21 
TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A25B 
       21.90        23.77        17.36        60.72        20.25        42.44 
TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD 
       29.98        50.37        24.39        26.96        21.14        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26J 
       30.61        33.11        29.79        31.73        25.15        20.61 
TCGA-A7-A2KD TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF 
       22.32        14.70        14.93        13.74        14.50        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O 
       14.73        12.10        10.29         9.37        10.42        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07U 
        1.02        17.98        29.03         1.02        18.97        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G 
        9.99        45.07        13.02        38.01        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       12.00        31.00         0.99        17.95        41.98        12.00 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09X 
        9.99        12.00         1.02        25.02         8.98        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FE 
       12.00        13.02        27.02        22.95        73.91        86.66 
TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A5EI TCGA-AC-A62V TCGA-AC-A7VC TCGA-AC-A8OP 
       14.66        16.31        14.53        11.44         0.03        20.19 
TCGA-AC-A8OQ TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        1.12         0.33         1.78         9.96         0.16         0.33 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XO 
        7.96         7.00         0.33         0.33         5.36        12.33 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 
        0.33        80.28        61.35        81.63        32.78        21.40 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM 
       20.32        53.03        50.86        76.77        55.33        71.80 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KR TCGA-AO-A1KS 
      106.78        90.58        98.27        57.30        70.39         0.53 
TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TV 
       24.79         5.65         2.56        32.91         5.26        75.22 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24R TCGA-AR-A24U 
      108.36       103.86        61.28        33.73       112.77        77.69 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL 
      105.30        32.58        85.64        71.05        54.21        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0IJ TCGA-B6-A0IQ 
       57.27        73.35        38.96        77.62       233.62       140.88 
TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A409 
       79.63       113.79        73.51        37.87        68.12        18.84 
TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 
      103.63        62.93        59.84        20.45        63.09        39.55 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       70.22        84.13        37.22        43.53        21.70        74.89 
TCGA-BH-A0BP TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EB 
       75.48        44.02        29.98        15.65         2.56        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX 
       31.00        24.43        23.08        13.61        36.85        27.25 
TCGA-BH-A0HY TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
       50.79        42.35        44.81        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV 
       37.74        51.39        67.50        91.99        42.28        12.00 
TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A203 
       55.69        31.53        97.48        45.63        26.14        38.60 
TCGA-BH-A208 TCGA-BH-A2L8 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-C8-A12L 
       57.83        20.12         9.63         5.26         9.70        11.93 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HI TCGA-C8-A1HK 
       11.77        12.66         3.16        12.92        11.28        12.03 
TCGA-C8-A1HM TCGA-C8-A27B TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       12.33        14.43        13.97        21.14        14.17        17.49 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       18.90        53.00        14.01        20.09        20.12        20.09 
TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XL TCGA-D8-A1XS 
       13.32        17.79        27.58        18.15        19.92        16.31 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27H 
       12.99        43.04        16.54        15.52        14.24        13.05 
TCGA-D8-A27I TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A10B 
       14.43        12.53        12.26        25.22        34.42        37.51 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14Y TCGA-E2-A14Z 
       44.68        40.96        33.17        75.98        69.34        18.51 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A15E TCGA-E2-A15G 
       69.96        23.24        21.04        14.79        20.71        18.21 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BD 
       20.58        11.05        53.62        33.01        32.35        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
       33.73        33.70        22.19        11.08        54.18        19.66 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 
       50.07       106.75        26.99        38.76        17.69        22.29 
TCGA-E9-A1NA TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       36.56         9.86         2.56         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RH 
       48.23        32.09        40.24         1.12        21.27        46.59 
TCGA-E9-A243 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A54X TCGA-E9-A54Y 
       20.12         7.13        12.33        38.07        23.90        23.84 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1P4 
        0.79        26.40         8.48        16.57        28.77        29.82 
TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A423 TCGA-EW-A6SD TCGA-GM-A2DC 
       23.11         6.15        13.94        10.16        33.21        83.34 
TCGA-GM-A2DH TCGA-GM-A3NW TCGA-GM-A3XN TCGA-GM-A5PV TCGA-HN-A2OB TCGA-LD-A66U 
       72.10       110.50        66.38        13.55        62.47        21.24 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
       15.32        14.79         2.63        19.59        17.49        22.39 
TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LX 
       20.38        26.04         8.91        47.01        86.96         0.16 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UU-A93S TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       18.48        21.07         3.81        11.41       108.07       107.05 

$`5P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        31.79         7.96        28.01        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
       18.02        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       98.99       107.93        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW 
       25.22       101.72       118.45        74.40        72.00        61.94 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        27.12        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       32.55        25.28        50.47        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G1 
       19.33        48.46        31.73        23.47        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
      105.34        10.59        36.23        39.65        33.93        91.07 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW 
       32.75        56.28        47.31        35.93        50.83         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.30        23.21        21.90        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       37.45        35.67        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.74        23.80        21.73        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SE TCGA-A7-A5ZW 
       10.29        11.28        13.41        11.97        21.17        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       11.05         8.75        13.02        53.06        31.00        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08J 
        7.99        15.06        36.95         0.99        28.96        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00        33.01       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
       33.01        30.97         9.99        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       29.98        33.07         1.02        19.04        15.02         0.99 
TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        21.04         0.99        17.03        38.04         0.95 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
        5.72         1.48        73.05        99.35        40.57        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45         6.48        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y 
       29.26        16.80        19.33        14.96        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR 
       18.67        13.58        12.26         1.68         8.22         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        2.30         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         7.36         7.46         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        5.65         7.59         7.17         6.90         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.36         0.33         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R 
        0.33         5.33         5.59        66.77        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        58.95        29.13        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       22.36        21.53        50.70        72.00        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 
       50.24        62.04       115.27        99.25       108.72       108.03 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       61.87        17.79        26.93       130.09        15.62        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
       19.20       140.55        98.33        84.10       109.02        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM 
      134.14       107.21       125.16       101.00        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       96.00        86.07        93.90        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       94.29        86.53        86.43       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
      120.33        99.78       118.59         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
      105.27        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 
       39.39        40.54        33.30        10.59       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       275.87       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      112.37        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
      282.90       157.41        97.48       188.68        18.35        21.47 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 
       43.59       101.52       139.17       170.17         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       70.16        71.15        25.55        81.44        40.83        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM 
       81.63        51.68        32.02        18.21        61.51        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       72.23        74.14        76.60        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       77.95        49.05        41.75        89.06        90.97        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       77.98        23.44        38.01        13.91        78.28        17.26 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA 
       12.89        51.32         5.59        23.93        24.95        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18Q 
       32.91         4.90        35.93        20.12        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05         7.36        51.16       113.82        82.85 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB 
       49.58        17.69        25.81        89.16        24.62       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 
       55.00        72.07       144.59        72.07        28.14        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
      130.16        10.65         6.44        10.52       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
       18.64        23.51        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       48.53        12.56        13.51         1.87        12.59         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL 
        4.08        12.33        10.92        11.34         0.16        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         9.53         0.03         9.50        24.56 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       56.81        20.88        13.25        20.58        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF 
       19.20        16.50        55.50        15.78        18.15        12.03 
TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU 
       18.97        19.40        20.38        21.01        12.20        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        16.73        25.74        23.90        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        21.80        14.50        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y1 
       16.41        15.85        16.64        15.16        15.32         9.93 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27L 
       14.14        17.42        16.04        13.45        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 
       13.48         4.80         1.61        10.09        13.08        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A108 
       18.51        21.67        16.18        12.66        43.00        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        40.11        28.44        28.87        47.15 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.24        38.60        43.33        34.26        32.02        31.96 
TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       63.62        19.43        23.87        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       17.29        21.63        12.92        55.63        53.92         9.04 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       50.79        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       87.22        28.50        16.47        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L8 
       28.44        59.18         3.88        60.99        60.36        73.64 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       24.59        75.81        28.90       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 
       34.55        43.56         8.28        30.61        34.92        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       34.82        32.88        36.82        34.16        36.20        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ 
       41.62        35.77        35.24        25.84        18.94        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1RA TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RI 
       28.27        34.95        45.01        46.65         6.58        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 
       41.03        41.72        40.73        40.50         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
        1.94        24.56        29.72         9.47        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       30.44        26.70        25.81        27.85        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        18.90        13.25        15.68        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE 
       18.48        30.08         7.86        18.90        19.99        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA 
       22.09        34.03        17.49        23.51        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        75.02        70.85        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62        85.35        38.20        43.73        69.30 
TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U 
       72.03        18.12         2.60        11.84        11.57        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR 
       25.05        17.06        14.70        14.47        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 
       15.68         7.46        14.50        19.53        12.36        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       34.92        36.36        28.87        24.72        22.32        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       23.47        65.62        41.92        42.77        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ 
       28.21        19.73        40.11        64.21         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       18.81        20.68        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB41 TCGA-WT-AB44 
       17.26        13.94        17.03        66.84        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A 
       15.35        16.04 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.03              0.03 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           233.62            282.90 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           23.870            29.785 
[1] "0.0 - 233.6 (23.9)" "0.0 - 282.9 (29.8)"
[1] "hr=" "1.5"
D9V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P GAIN MUTATED        29       19        1        1       110        68
  5P GAIN WILD-TYPE      60       66        5        5       243       184
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           1         50          9         17        7
  5P GAIN WILD-TYPE         1        104         20         48       13
                   vv
clus                STAGE TIS STAGE X
  5P GAIN MUTATED           0       3
  5P GAIN WILD-TYPE         1      10
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 29                60
  STAGE IA                19                66
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA              110               243
  STAGE IIB               68               184
  STAGE III                1                 1
  STAGE IIIA              50               104
  STAGE IIIB               9                20
  STAGE IIIC              17                48
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED    74 183  45  13
  5P GAIN WILD-TYPE 202 441  91  27
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1              74               202
  T2             183               441
  T3              45                91
  T4              13                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P GAIN MUTATED   161  87  45  18
  5P GAIN WILD-TYPE 346 271  74  59
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             161               346
  N1              87               271
  N2              45                74
  N3              18                59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   273   7
  5P GAIN WILD-TYPE 616  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    273    7
  5P GAIN WILD-TYPE  616   15
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             273               616
  1               7                15
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   311   5
  5P GAIN WILD-TYPE 757   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    311    5
  5P GAIN WILD-TYPE  757    7
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE             311               757
  MALE                 5                 7
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   120 159
  5P GAIN WILD-TYPE 309 359
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    120  159
  5P GAIN WILD-TYPE  309  359
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO              120               309
  YES             159               359
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P GAIN MUTATED                            1                           229
  5P GAIN WILD-TYPE                          0                           541
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P GAIN MUTATED                               56                   2
  5P GAIN WILD-TYPE                            144                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5P GAIN MUTATED                       7                                8
  5P GAIN WILD-TYPE                     2                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5P GAIN MUTATED                    2             11
  5P GAIN WILD-TYPE                 15             36
D9V9, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                229               541
  INFILTRATING LOBULAR CARCINOMA                56               144
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          7                 2
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                11                36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0    11
  5P GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          47   223
  5P GAIN WILD-TYPE                       134   522
D9V11, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     47               134
  WHITE                                        223               522
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11 254
  5P GAIN WILD-TYPE  28 621
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11  254
  5P GAIN WILD-TYPE   28  621
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                28
  NOT HISPANIC OR LATINO             254               621
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   185  24
  5Q GAIN WILD-TYPE 732 123
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              209               855 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               24               123 
$`5Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A0CX TCGA-A2-A0EN TCGA-A2-A0ET 
      129.14        13.68        39.32        56.81        89.36        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG 
       34.29        31.82        18.90        20.75        18.21        21.90 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A3XU TCGA-A2-A4RX TCGA-A2-A4S1 
       17.36        60.72        20.25        29.98        24.39        26.96 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J 
       21.14        38.30        33.11        29.79        25.15        20.61 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q 
       14.70        13.74        14.50        10.29        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06Z TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 
       17.98         1.02        18.97         9.99        45.07        13.02 
TCGA-A8-A08G TCGA-A8-A08R TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09B 
       19.96         0.99        17.95        41.98        12.00        12.00 
TCGA-A8-A09C TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A9 
        1.02         8.98        14.01        12.00        13.02        27.02 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FE TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A5EI 
       22.95        73.91        86.66        14.66        16.31        14.53 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        0.03        20.19         0.33         9.96         0.16         0.33 
TCGA-AN-A0FK TCGA-AN-A0FX TCGA-AN-A0XO TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J2 
        7.00         0.33        12.33        80.28        81.63        32.78 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A12A 
       20.32        53.03        50.86        76.77        71.80        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AR-A0TR TCGA-AR-A1AI 
       98.27        57.30         0.53         5.65         5.26       108.36 
TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A254 
      103.86        61.28       112.77       105.30        32.58        85.64 
TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0WV 
       71.05        54.21        66.15        73.35        38.96        79.63 
TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AU 
      113.79        73.51        68.12        18.84       103.63        62.93 
TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL 
       63.09        70.22        84.13        37.22        21.70        74.89 
TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0EB TCGA-BH-A0EE 
       44.02        29.98        15.65         2.56        24.49        31.00 
TCGA-BH-A0H7 TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K 
       23.08        36.85        27.25        42.35        44.81        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       26.66        72.56        37.74        51.39        67.50        91.99 
TCGA-BH-A1EU TCGA-BH-A1F6 TCGA-BH-A202 TCGA-BH-A2L8 TCGA-BH-A6R8 TCGA-BH-A6R9 
       42.28        97.48        26.14        20.12         9.63         5.26 
TCGA-BH-A8FY TCGA-C8-A12P TCGA-C8-A135 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        9.70        11.77        12.92        11.34        11.28        12.03 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JT 
       21.14        14.17        18.90        14.01        20.09        13.32 
TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XY 
       17.79        27.58        18.15        16.31        12.99        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27I TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A73X 
       15.52        14.24        14.43        12.53        12.26        25.22 
TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A14O TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A152 
       34.42        37.51        44.68        33.17        75.98        69.96 
TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BD 
       23.24        20.71        18.21        33.01        32.35        37.25 
TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LG 
       33.73        22.19        11.08        54.18        19.66        50.07 
TCGA-E2-A1LH TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1NI TCGA-E9-A1R3 
      106.75         8.28        17.69        22.29         9.86         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RG 
        6.12         3.02        11.15        40.24         1.12        21.27 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UP 
        7.13        12.33        29.72        23.90         0.79        26.40 
TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A423 
        8.48        16.57        28.77        23.11         6.15        10.16 
TCGA-GM-A2DC TCGA-GM-A3NW TCGA-GM-A3XN TCGA-GM-A5PV TCGA-LD-A66U TCGA-LL-A6FQ 
       83.34       110.50        66.38        13.55        21.24         2.63 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DE 
       19.59        17.49        22.39        26.04         8.91        86.96 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-W8-A86G TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       18.48        21.07        11.41       108.07       107.05 

$`5Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        20.88        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 
       77.19        75.25         5.19        98.99       107.93        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       34.55        33.76        61.58        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
      118.45        79.76        74.40        72.00        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       63.29        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       17.46        32.55        25.28        50.47        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        91.07        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 
       35.93        50.37        50.83         7.30        21.30        23.21 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.67        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        23.80        21.73        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U 
        9.37        10.42         8.75        13.02        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A084 TCGA-A8-A085 
       10.98         8.98         7.99        24.99        15.06        36.95 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J 
        0.99        38.01        28.96        33.01        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D 
       40.01        33.01        30.97         9.99         9.99        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       49.05        45.07        29.98        33.07         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 
       19.04        15.02         0.99        19.04        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95         5.72         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       99.35        40.57        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3OD 
       74.14        33.04        19.33        32.45         6.48        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XS 
       15.48        23.24        24.79        29.26        16.80        19.33 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       14.96        11.44        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         7.36         7.46         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        5.65         7.96         7.59         7.17         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         5.36         0.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.59        61.35        66.77        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        21.40        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       22.36        21.53        50.70        72.00        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      106.78       108.03        64.04        48.36        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       26.93       130.09        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       140.55        98.33        84.10       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL 
       83.87       134.14       107.21       125.16       101.00        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       98.33        96.00        86.07        93.90        99.32        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       37.81        94.29        86.53        86.43        33.73       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z 
      104.28        97.84       105.27        77.69        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       89.00        99.62        93.30        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       86.53        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       33.30        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      275.87       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      233.62        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
       89.46       282.90       157.41        97.48       188.68        18.35 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.88        43.59       101.52       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
        7.07        85.35        70.16        71.15        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 
       25.55        81.44        40.83        39.55        39.16        81.63 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM 
       51.68        32.02        18.21        43.53        61.51        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 
       49.94        77.95        49.05        41.75        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        77.98        23.44        38.01        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       17.26         3.22        38.47        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY 
        5.85         2.50        13.61        12.89        51.32        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
        5.59        23.93        24.95        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       35.93        20.12        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW 
        7.36        51.16       113.82        82.85        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        89.16        24.62 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       28.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
        6.44        10.52       109.28        20.88        18.64        23.51 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56         3.16        13.51         1.87        12.59 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HL 
        4.11         4.08        12.33        10.92         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       24.56        14.43        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        14.17        13.48        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JI 
       55.50        15.78        18.15        12.03        53.00        18.97 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.12        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       14.70        18.58        16.73        25.74        23.90        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV 
       17.69        55.30        16.41        15.85        16.64        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       43.04        15.32         9.93        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.45        13.05        48.03        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        1.61        10.09        13.08        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       16.18        12.66        43.00        27.52        46.59        40.41 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       38.60        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       18.51        63.62        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H 
       25.05        23.34        22.82        17.29        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       87.22        28.50        16.47        77.65        37.41        70.36 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L7 
       33.70        28.44        59.18         3.88        60.99        60.36 
TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LK 
       73.64        24.59        75.81        28.90       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 
       43.04        26.99        34.55        43.56        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       38.76        34.29        34.82        32.88        36.82        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.20        36.56        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R7 
       25.84        18.94        24.82        28.27        34.95        48.23 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI 
       45.01        32.09        46.65         6.58        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       41.03        41.72        40.73        40.50        20.12         0.69 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       38.99         1.94        24.56         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE 
       30.18        30.44        23.84        26.70        25.81        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 
       12.20        39.72        18.21        18.90        13.25        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        29.82        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       33.21         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      106.06       101.62        85.35        38.20        43.73        69.30 
TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       72.03        18.12         2.60        62.47        11.84        11.57 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       29.23        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.79        22.26        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       19.53        12.36        27.91         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       24.72        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       41.92        42.77        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       40.11        47.01        64.21         0.16         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       18.81        20.68        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB41 
       17.26        13.94        17.03         3.81        66.84        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       29.03        15.35        16.04 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.03              0.03 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           129.14            282.90 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            22.19             29.82 
[1] "0.0 - 129.1 (22.2)" "0.0 - 282.9 (29.8)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q GAIN MUTATED        19       16        1        1        67        48
  5Q GAIN WILD-TYPE      70       69        5        5       286       204
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           1         36          5         14        1
  5Q GAIN WILD-TYPE         1        118         24         51       19
                   vv
clus                STAGE TIS STAGE X
  5Q GAIN MUTATED           0       2
  5Q GAIN WILD-TYPE         1      11
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 19                70
  STAGE IA                16                69
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA               67               286
  STAGE IIB               48               204
  STAGE III                1                 1
  STAGE IIIA              36               118
  STAGE IIIB               5                24
  STAGE IIIC              14                51
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED    55 113  36   7
  5Q GAIN WILD-TYPE 221 511 100  33
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1              55               221
  T2             113               511
  T3              36               100
  T4               7                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q GAIN MUTATED   107  59  29  14
  5Q GAIN WILD-TYPE 400 299  90  63
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0             107               400
  N1              59               299
  N2              29                90
  N3              14                63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   180   1
  5Q GAIN WILD-TYPE 709  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    180    1
  5Q GAIN WILD-TYPE  709   21
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0             180               709
  1               1                21
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   210   2
  5Q GAIN WILD-TYPE 858  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    210    2
  5Q GAIN WILD-TYPE  858   10
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE             210               858
  MALE                 2                10
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    78 109
  5Q GAIN WILD-TYPE 351 409
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     78  109
  5Q GAIN WILD-TYPE  351  409
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               78               351
  YES             109               409
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q GAIN MUTATED                            0                           141
  5Q GAIN WILD-TYPE                          1                           629
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q GAIN MUTATED                               47                   1
  5Q GAIN WILD-TYPE                            153                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5Q GAIN MUTATED                       6                                6
  5Q GAIN WILD-TYPE                     3                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5Q GAIN MUTATED                    2              9
  5Q GAIN WILD-TYPE                 15             38
D10V9, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                141               629
  INFILTRATING LOBULAR CARCINOMA                47               153
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          6                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                 9                38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     7
  5Q GAIN WILD-TYPE                                1    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                          20   162
  5Q GAIN WILD-TYPE                       161   583
D10V11, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                53
  BLACK OR AFRICAN AMERICAN                     20               161
  WHITE                                        162               583
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V12, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     7 170
  5Q GAIN WILD-TYPE  32 705
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7  170
  5Q GAIN WILD-TYPE   32  705
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             170               705
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED   177  32
  6P GAIN WILD-TYPE 740 115
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              209               855 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               32               115 
$`6P GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A04X TCGA-A2-A0CM 
        9.96        31.79        28.01        73.84        55.43        24.79 
TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0T2 
       33.76        79.76        35.05        31.82        63.29         8.38 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FX 
       18.21        21.90        18.61        31.73        23.77        60.72 
TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       17.19        33.93        32.75        47.31        35.93        50.83 
TCGA-A2-A4S1 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13F 
       26.96        38.30        30.61        35.67        29.79        25.15 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       21.73        20.61        14.70        14.50        21.17        17.92 
TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07F 
       10.29        17.98        31.00        17.03        53.98        18.97 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R 
        8.98        24.99         9.99        38.01        28.96         0.99 
TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09Q TCGA-AC-A23E 
       33.01        30.97        12.00        49.05        25.02        22.95 
TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A7VC TCGA-AC-A8OQ 
       33.04        16.57        14.96        13.71         0.03         1.12 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW 
        0.33         0.23         9.96         0.16         7.00         0.36 
TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JL 
        0.33         0.33        80.28        66.77        81.63        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KS 
       71.80       115.27       108.03        98.27        48.36         0.53 
TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0U0 
        5.65        19.20         5.26        84.10        75.22        65.36 
TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LL 
       61.28       104.28        98.66        89.00        71.05        66.15 
TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RU 
       57.27       143.38        12.13        84.59       165.76       282.90 
TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A400 TCGA-B6-A402 
      113.79       245.10        43.59       101.52         7.07        70.16 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
       68.12        18.84        71.15        59.84        20.45        25.55 
TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT 
       39.55        81.63        37.22        61.51        74.89        45.57 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DH TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A0WA 
       49.05        44.02        38.01        24.49        36.85        23.05 
TCGA-BH-A18K TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EV 
       90.84        55.63         7.36        67.50        91.99        12.00 
TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V 
       31.53       114.15        38.60        57.83       130.16        20.88 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A1HJ TCGA-C8-A1HM 
       18.64        11.93        12.66         3.16         0.16        12.33 
TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 TCGA-D8-A1JJ 
       12.36        20.88        13.97        14.17        14.17        20.09 
TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XY 
       20.09        21.80        14.50        19.92        16.41        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27R TCGA-D8-A27V TCGA-E2-A10C 
       15.32        14.14        16.04        10.09        12.53        40.11 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M TCGA-E2-A15S 
       31.96        18.51        63.62        25.05        11.05        14.07 
TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1LG TCGA-E2-A1LH 
       53.62        33.70         3.88        22.19        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N9 
      102.61        26.99         8.28        34.92        38.76        36.20 
TCGA-E9-A1ND TCGA-E9-A1RF TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A54Y 
       41.62         6.58        12.33        38.07        30.18        23.84 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       25.94        22.82        29.82        18.48        30.08         7.86 
TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DF TCGA-HN-A2NL 
       25.91        10.16        24.99       109.87        70.85         2.60 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 
        7.10        32.75        14.70        16.08        15.68        14.50 
TCGA-LL-A7T0 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PE-A5DE 
       12.36        58.62        36.36        20.38        23.47        86.96 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-Z7-A8R5 
        9.93        18.81        20.68        19.27       108.07 

$`6P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       18.21       143.15        18.02        78.41       121.94        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12       101.98        36.13       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       98.99       107.93        56.81        67.33        34.55        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72        89.36        80.28       118.45        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       72.00        34.29        61.94        24.72        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       27.12        44.88        50.43        44.28        17.52        17.13 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       25.28        50.47        21.67        49.48        19.33        48.46 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        17.36        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        42.44        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW 
       10.59        36.23        39.65        91.07        29.98        56.28 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.37         7.30        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       21.90        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        20.19        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.74        23.80        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D 
       11.28        13.41        11.97        14.93        13.74        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        11.05         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y 
       13.02        13.02         1.02        53.06        29.03        26.01 
TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
        1.02         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07Z 
       12.00        32.05         9.99        10.98         7.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F TCGA-A8-A08G 
       15.06        36.95        13.02         0.99        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08T 
       12.00        37.05         9.99        31.00        31.00       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       43.00        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99         1.02        50.04        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
       27.02        17.03        38.04         0.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        1.48        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        26.04        74.14        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       25.05        14.99        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       29.26        16.80        14.53        19.33        11.44        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP 
       18.67        13.58        12.26         1.68         8.22        20.19 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        1.32         2.30         0.33         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        1.78         1.71         7.36         7.46         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL 
        6.90         7.04         0.33         0.33         0.33         5.36 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        61.35        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D 
       62.04        99.25       108.72       106.78        90.58        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 
       70.39        17.79        24.79        26.93       130.09        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT 
       32.52         2.56        32.91       140.55        98.33       109.02 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       98.93        64.83        55.86       107.24       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       97.68        98.33        96.00        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        37.81        94.29        86.53        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76       112.77        97.84       105.27        77.69       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 
       32.58        98.76        99.62        93.30        85.64        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       281.29       275.87       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP 
      146.50       112.37       233.62        18.77       127.33       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       21.47       206.86       129.70        28.27        68.94        58.88 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A40B 
       73.51       139.17       170.17        37.87        85.35       103.63 
TCGA-BH-A0AU TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       62.93        63.09        81.44        40.83        39.16        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       84.13        51.68        32.02        18.21        43.53        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        77.95        41.75        89.06        90.97        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       77.98        23.44        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       46.19        32.58        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        53.26        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       20.12        26.66        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05        51.39        51.16       113.82        82.85        42.28 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 
       55.69        49.58        17.69        25.81        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.62       120.62        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       28.14        26.14        83.31        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
       10.52       109.28        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.56        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK 
        4.08        12.33        10.92        11.34        11.28        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       10.42        12.95        12.33        20.25        12.53        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         9.53         0.03         9.50        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 
       19.46        56.81        13.25        20.58        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       19.20        17.49        16.50        55.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK 
       18.90        12.03        53.00        14.01        18.97        20.12 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       19.40        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       18.58        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XM 
       18.15        12.39        17.16        15.22        14.73        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       55.30        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G 
       43.04        15.52         9.93        14.24        17.42        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43        48.03        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        1.61        13.08        12.26        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18        12.66        25.22        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        37.51        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       44.68        40.96        38.24        38.60        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 
       43.33        34.26        32.02        69.34        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        50.79        19.56        56.94 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        76.57        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       28.44        59.18        60.99        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK 
       73.64        19.66        24.59        75.81        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU 
       43.04        34.55        43.56        30.61        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA 
       34.82        32.88        36.82        22.29        34.16        36.56 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       39.55        35.77        35.24        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
       11.15        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       46.65        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 
        7.13        24.56        29.72         9.47        32.91        30.44 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        26.70         0.79        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        28.77        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PB 
       41.13        39.78        52.96        23.11        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       55.00        52.73        22.09        34.03        17.49        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       15.22        16.77        31.30        33.21         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        83.34        75.02        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       18.12        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        10.62        24.95        29.23        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       15.32        14.47        14.79        22.26         2.63         7.46 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       19.53        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       36.30        58.52        31.99        40.08        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       24.72        22.32        26.70        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG 
        8.91        47.01        64.21         0.16         0.26        18.48 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       21.07        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       17.03         3.81        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.03              0.03 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           282.90            281.29 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            25.91             28.27 
[1] "0.0 - 282.9 (25.9)" "0.0 - 281.3 (28.3)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P GAIN MUTATED        15       10        1        1        80        52
  6P GAIN WILD-TYPE      74       75        5        5       273       200
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           0         28          7         10        3
  6P GAIN WILD-TYPE         2        126         22         55       17
                   vv
clus                STAGE TIS STAGE X
  6P GAIN MUTATED           0       1
  6P GAIN WILD-TYPE         1      12
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                10                75
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA               80               273
  STAGE IIB               52               200
  STAGE III                0                 2
  STAGE IIIA              28               126
  STAGE IIIB               7                22
  STAGE IIIC              10                55
  STAGE IV                 3                17
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED    40 136  26   7
  6P GAIN WILD-TYPE 236 488 110  33
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1              40               236
  T2             136               488
  T3              26               110
  T4               7                33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P GAIN MUTATED   104  63  26  11
  6P GAIN WILD-TYPE 403 295  93  66
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0             104               403
  N1              63               295
  N2              26                93
  N3              11                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   173   4
  6P GAIN WILD-TYPE 716  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    173    4
  6P GAIN WILD-TYPE  716   18
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0             173               716
  1               4                18
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED   208   1
  6P GAIN WILD-TYPE 860  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED    208    1
  6P GAIN WILD-TYPE  860   11
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE             208               860
  MALE                 1                11
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    73 113
  6P GAIN WILD-TYPE 356 405
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     73  113
  6P GAIN WILD-TYPE  356  405
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               73               356
  YES             113               405
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P GAIN MUTATED                            0                           168
  6P GAIN WILD-TYPE                          1                           602
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P GAIN MUTATED                               20                   4
  6P GAIN WILD-TYPE                            180                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6P GAIN MUTATED                       4                                3
  6P GAIN WILD-TYPE                     5                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6P GAIN MUTATED                    1              8
  6P GAIN WILD-TYPE                 16             39
D11V9, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                168               602
  INFILTRATING LOBULAR CARCINOMA                20               180
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 8                39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     8
  6P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                          50   132
  6P GAIN WILD-TYPE                       131   613
D11V11, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     50               131
  WHITE                                        132               613
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V12, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     9 165
  6P GAIN WILD-TYPE  30 710
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9  165
  6P GAIN WILD-TYPE   30  710
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                30
  NOT HISPANIC OR LATINO             165               710
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED   127  23
  6Q GAIN WILD-TYPE 790 124
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              150               914 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               23               124 
$`6Q GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D2 
       13.68        31.79        19.20        55.43        24.79        33.76 
TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ 
       79.76        63.29         8.38        18.21        21.90        18.61 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CD 
       60.72        19.20        47.31        35.93        26.96        38.30 
TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A4SE 
       30.61        35.67        29.79        14.70        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07F 
       17.92        10.29        17.98        31.00        17.03        18.97 
TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A09B 
        8.98        38.01        28.96         0.99        33.01        12.00 
TCGA-A8-A09Q TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A7VC 
       25.02        22.95        33.04        14.96        13.71         0.03 
TCGA-AN-A03Y TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AO-A03O TCGA-AO-A124 
        0.33         0.16         7.00         0.33        81.63       115.27 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A7U7 
      108.03        98.27        48.36         0.53         5.65        19.20 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A1AI TCGA-AR-A1AV 
       84.10       109.02        75.22        65.36       108.36        61.28 
TCGA-AR-A24Q TCGA-AR-A24Z TCGA-AR-A2LL TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0I9 
      104.28        98.66        66.15        57.27       143.38        12.13 
TCGA-B6-A0IO TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY 
      165.76         7.07        70.16        18.84        59.84        25.55 
TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT 
       39.55        81.63        37.22        61.51        74.89        45.57 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A18Q TCGA-BH-A1EO 
       49.05        44.02        24.49        36.85        55.63        91.99 
TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V 
       12.00        31.53        38.60        57.83       130.16        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A1HJ 
       18.64        23.51        11.93        12.66         3.16         0.16 
TCGA-C8-A1HM TCGA-C8-A26X TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1J8 
       12.33        12.36        20.88        13.97        14.17        14.17 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1X5 TCGA-D8-A1XJ TCGA-D8-A1XK 
       20.09        20.09        21.01        18.58        21.80        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27V 
       16.41        16.54        15.32        14.14        16.04        12.53 
TCGA-E2-A10C TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15M 
       40.11        31.96        18.51        63.62        25.05        11.05 
TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 
       53.62        33.70       106.75        26.99        34.92        38.76 
TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1OV TCGA-EW-A1P4 
       36.20        35.24        30.18        23.84        25.94        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A423 TCGA-GI-A2C9 TCGA-GM-A2DH 
       18.48        30.08         7.86        10.16       109.87        72.10 
TCGA-HN-A2NL TCGA-LD-A7W5 TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7T0 
        2.60         7.10        14.70        16.08        15.68        12.36 
TCGA-OL-A5DA TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-Z7-A8R5 
       58.62        86.96         9.93        20.68        19.27       108.07 

$`6Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       14.27        47.24        20.88         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       87.25        63.12       101.98        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
        5.19        98.99       107.93        56.81        67.33        34.55 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72        89.36        80.28       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52        17.13        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       49.48        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       17.36        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        50.37        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       23.21        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       37.45        33.11        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A56D TCGA-A7-A5ZV 
       13.41        11.97        14.93        13.74        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       10.72        11.05         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z 
       13.02         1.02        53.06        29.03        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I 
       53.98         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        15.06        36.95        13.02         0.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       33.01        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       31.00       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       17.95        41.98        12.00         9.99         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        73.91         5.72         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       26.04        74.14        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       16.57        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       16.80        14.53        19.33        11.44        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ 
       13.58        12.26         1.68         8.22        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         7.46 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.90         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       80.28        61.35        66.77        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        55.33        71.80        99.25       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        64.04        57.30        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        61.87        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TP 
      130.09        15.62        32.52         2.56        32.91       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       98.33         5.26        98.93        64.83        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
      133.22        83.87       134.14       107.21       125.16       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      103.86        97.68        98.33        96.00        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX 
       99.32        17.23        37.81        94.29        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       33.73       160.90        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       112.77        97.84       105.27        77.69 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
      105.30        32.58        98.76        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM 
       54.21        63.62        38.17        39.39        40.54        73.35 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0IA 
       33.30        38.96        10.59        77.62       281.29       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
       18.77       127.33        84.59       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.88        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       37.87        85.35        68.12       103.63        71.15        62.93 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       20.45        63.09        81.44        40.83        39.16        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       84.13        51.68        32.02        18.21        43.53        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        77.95        41.75        89.06        90.97        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        23.44        38.01        29.98        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.16        67.50       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       28.14        26.14        83.31        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       10.52       109.28         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       13.51         1.87        12.59        12.92         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34        11.28        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z 
       12.95        12.33        20.25        12.53        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       56.81        13.25        20.58        13.48        21.14        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       17.49        16.50        55.50        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JM 
       12.03        53.00        14.01        18.97        20.12        19.40 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.38        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       15.22        14.73        19.92        17.69        55.30        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.31        16.64        12.99        15.16        43.04        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
        9.93        14.24        17.42        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       48.03        16.41        13.48         4.80         1.61        10.09 
TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       13.08        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       12.66        25.22        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        37.51        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       34.26        32.02        69.34        69.96        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        76.57        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        60.36        73.64        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       28.90        50.07       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       43.56         8.28        30.61        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        22.29        34.16        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       41.62        35.77        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       32.91        30.44        23.90        26.70         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW 
       18.90        13.25        16.57        15.68        28.77        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P5 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       23.11        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA 
       22.09        34.03        17.49        23.51        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30        33.21         7.40        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
       79.10        83.34        75.02        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z 
       15.32        14.47        14.79        22.26         2.63         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        19.53        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        58.52        31.99        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       64.21         0.16         0.26        18.81        18.48        21.07 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        18.87        17.39        17.26        13.94        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
        3.81        66.84        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.03              0.03 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           165.76            282.90 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           24.905            28.355 
[1] "0.0 - 165.8 (24.9)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.4"
D12V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q GAIN MUTATED        12        8        1        0        60        34
  6Q GAIN WILD-TYPE      77       77        5        6       293       218
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           0         19          5          8        2
  6Q GAIN WILD-TYPE         2        135         24         57       18
                   vv
clus                STAGE TIS STAGE X
  6Q GAIN MUTATED           0       0
  6Q GAIN WILD-TYPE         1      13
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 12                77
  STAGE IA                 8                77
  STAGE IB                 1                 5
  STAGE II                 0                 6
  STAGE IIA               60               293
  STAGE IIB               34               218
  STAGE III                0                 2
  STAGE IIIA              19               135
  STAGE IIIB               5                24
  STAGE IIIC               8                57
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED    27  97  21   5
  6Q GAIN WILD-TYPE 249 527 115  35
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1              27               249
  T2              97               527
  T3              21               115
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q GAIN MUTATED    85  38  17   9
  6Q GAIN WILD-TYPE 422 320 102  68
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              85               422
  N1              38               320
  N2              17               102
  N3               9                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED   127   2
  6Q GAIN WILD-TYPE 762  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    127    2
  6Q GAIN WILD-TYPE  762   20
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0             127               762
  1               2                20
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED   149   1
  6Q GAIN WILD-TYPE 919  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED    149    1
  6Q GAIN WILD-TYPE  919   11
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE             149               919
  MALE                 1                11
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    57  75
  6Q GAIN WILD-TYPE 372 443
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     57   75
  6Q GAIN WILD-TYPE  372  443
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               57               372
  YES              75               443
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q GAIN MUTATED                            0                           120
  6Q GAIN WILD-TYPE                          1                           650
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q GAIN MUTATED                               14                   4
  6Q GAIN WILD-TYPE                            186                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6Q GAIN MUTATED                       4                                3
  6Q GAIN WILD-TYPE                     5                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6Q GAIN MUTATED                    1              4
  6Q GAIN WILD-TYPE                 16             43
D12V9, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                120               650
  INFILTRATING LOBULAR CARCINOMA                14               186
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 4                43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     7
  6Q GAIN WILD-TYPE                                1    53
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                          34    95
  6Q GAIN WILD-TYPE                       147   650
D12V11, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          7                53
  BLACK OR AFRICAN AMERICAN                     34               147
  WHITE                                         95               650
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V12, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7 117
  6Q GAIN WILD-TYPE  32 758
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7  117
  6Q GAIN WILD-TYPE   32  758
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             117               758
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   266  42
  7P GAIN WILD-TYPE 651 105
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              308               756 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               42               105 
$`7P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SN 
      129.14       131.67        48.10        20.88        13.68        39.32 
TCGA-A2-A04W TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EV TCGA-A2-A0EY 
      101.98        98.99       107.93        67.33        31.82        63.29 
TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ 
       44.88        17.13         8.38        18.21        21.90        18.61 
TCGA-A2-A1FV TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       23.47        20.25        19.56        42.44        33.93        91.07 
TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       50.37        26.96        35.31        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26H 
       31.73        20.19        25.15        23.61        24.26        23.80 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       14.70        13.74        14.50        21.17        17.92        12.10 
TCGA-A7-A6VV TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       10.29         1.02        17.98        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A07F TCGA-A8-A07U TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08P 
       53.98        18.97        24.99        28.96        19.96        31.00 
TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       43.00        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23G TCGA-AC-A23H 
       29.98        33.07        14.01        12.00        73.91         5.72 
TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A5EI TCGA-AC-A5XU TCGA-AC-A62V 
       26.04        14.66        16.57        14.53        14.96        11.44 
TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS 
       17.42         1.68         0.03        20.19         1.12         2.30 
TCGA-AN-A049 TCGA-AN-A0AL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XL 
        0.62         7.46         7.04         0.36         0.33         5.36 
TCGA-AO-A03N TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JL 
       66.77        21.40        37.48        50.70        72.00        55.33 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      115.27        99.25       106.78        98.27        64.04        57.30 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AR-A0TR 
       61.87        70.39        15.62        32.52        32.91         5.26 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24H 
       65.36        83.87       134.14        17.23        61.28       160.90 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A2LR TCGA-AR-A5QM 
       50.89       104.28        32.58        89.00        57.27        73.35 
TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC 
       38.96       143.38       281.29        12.13       129.57        50.70 
TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RV 
      112.37       127.33        84.59       255.68       234.28       157.41 
TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY 
       79.63       206.86        85.35        62.93        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B4 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP 
       63.09        39.16        37.22        21.70        74.89        75.48 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DO 
       45.57        49.05        44.02        45.83        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 
       15.65         2.56        38.47         4.41         9.63        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0HP TCGA-BH-A0HQ 
       32.58        24.49        30.35        23.08        13.61        36.85 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18V TCGA-BH-A1EN 
       50.79         5.59        44.81        90.84        51.16        67.50 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F6 TCGA-BH-A1FD TCGA-BH-A1FN 
       91.99        12.00        49.58        97.48        33.17        72.07 
TCGA-BH-A202 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L 
       26.14        18.64        23.51         9.63         5.26        11.93 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A131 TCGA-C8-A138 
       11.77        12.66        12.66        48.53        13.51         4.08 
TCGA-C8-A1HI TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 
       11.28        12.36        12.95         8.28         9.67        33.99 
TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG 
       14.17        21.14        14.17        18.15        12.03        53.00 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1X9 TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XR 
       20.12        20.09        23.90        15.22        19.92        15.85 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A3Z5 
       12.99        16.54        15.32         9.93        48.03        33.37 
TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14R 
       18.51        34.42        37.51        40.11        40.96        38.60 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       75.98        34.26        32.02        69.96        23.24        19.43 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I 
       25.05        23.34        17.29        20.71        18.21        55.63 
TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IH 
       11.05        56.94        76.57        32.35        37.25        33.73 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LL 
       33.70        60.99        19.66        28.90       102.61        43.04 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N8 
        8.28        30.61        34.92        17.69        34.82        34.16 
TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 
       36.20        41.62        35.24        24.82         2.56         6.12 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 TCGA-E9-A22E 
       48.23        45.01        32.09        40.24        34.45        41.72 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A3HO TCGA-E9-A3X8 
       38.99         7.13        24.56        12.33        38.07        30.44 
TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P3 
       23.90         8.48        28.77        22.82        41.13        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A423 
       29.82        23.11         7.86        18.90        19.99        10.16 
TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DL 
        7.40        79.10        83.34        75.02        70.85       115.69 
TCGA-GM-A3XN TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       66.38         2.60        11.84        10.62        24.95        32.75 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A9Q3 
       15.32        22.26         2.63        16.08        14.50        17.49 
TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H 
       58.52        34.92        36.36        28.87        22.32        26.70 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A97C TCGA-PE-A5DE 
       41.92        26.04        14.07        28.21         8.91        86.96 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
        0.16        18.81        21.07        13.94        17.03         3.81 
TCGA-W8-A86G TCGA-WT-AB44 
       11.41        29.03 

$`7P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK 
        8.52        14.37        43.43        14.27        47.24        31.79 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        28.01        19.20        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X 
       78.41       121.94        73.84        87.25        63.12        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX 
       88.60       107.93        77.19        75.25         5.19        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       118.45        79.76        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       34.29        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW 
       49.48        19.33        48.46        31.73        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       60.72        22.45        19.20        16.47        52.47       107.70 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        32.75        56.28        47.31        35.93        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A13H 
       38.30        34.29        35.47        30.61        29.79        29.56 
TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       31.36        23.74        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        10.72        11.05         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A079 
       13.02        13.02        53.06        29.03        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99         9.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F 
       15.06        36.95        13.02         0.99        38.01        33.01 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S 
       12.00        37.05         9.99        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09C 
      112.08        40.01        33.01        30.97         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       50.04        49.05        45.07         1.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       19.04        15.02         0.99        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95        22.95 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        1.48        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       60.92        87.12        74.14        33.04        19.33        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       16.80        19.33        13.71        18.67        13.58        12.26 
TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        8.22         1.32         0.33         0.33         0.23         0.33 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM 
        2.96         1.78         1.71         9.96         7.36         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX 
        7.00         7.59         7.17         6.90         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        52.18        26.04        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       21.53        50.86        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12F 
       62.04        71.80       108.72       108.03        90.58        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT 
       41.62        40.57        14.73        82.62         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 
       24.79        26.93       130.09         5.65         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      140.55        98.33        84.10       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH 
       64.83        55.86       107.24       133.22       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       86.07        93.90        99.32        37.81        94.29        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       86.43        33.73        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V 
        2.76       112.77        97.84       105.27        77.69       105.30 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.76        98.66        99.62        93.30        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       93.83       166.42        20.25        86.53        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QQ 
       63.62        38.17        39.39        40.54        33.30        10.59 
TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK 
       77.62       275.87        65.72       146.50       233.62        18.77 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL 
      165.76       129.07       140.88        68.45       212.25        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       282.90        97.48       188.68        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        70.16        68.12        18.84       103.63        71.15 
TCGA-BH-A0AV TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 
       59.84        81.44        40.83        39.55        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       84.13        51.68        32.02        18.21        43.53        61.51 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        72.23        74.14        76.60        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG 
       77.95        41.75        89.06        90.97        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       38.01        29.98        13.91         3.22        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI 
       16.27        15.68        14.30        44.81        31.00        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        53.26        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HU 
       52.96        26.50        20.38         5.85         2.50        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA 
       51.32        27.25        23.93        24.95        42.35        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M 
       32.91         4.90        35.93        20.12        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY 
       51.39       113.82        82.85        42.28        55.69        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        24.62       120.62       114.15 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
      144.59        72.07        28.14        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
       20.88         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        12.66        12.56 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
        3.16         1.87        12.59        12.92         4.11        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34         0.16        12.03        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A274 TCGA-C8-A275 
       12.95        12.33        20.25        12.53         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.50        24.56        14.43        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.97        13.48        19.20        17.49        16.50        55.50 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       15.78        18.90        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.80        14.50        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.41        16.31        16.64        15.16        43.04        15.52 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43        16.41        13.48         4.80         1.61        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       13.08        12.53        12.26        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E 
       25.22        43.00        27.52        46.59        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14U 
       28.87        47.15        44.68        38.24        33.17        43.33 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 
       31.96        69.34        18.51        63.62        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K 
       14.79        22.82        21.63        12.92        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        50.79        19.56        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF 
       87.22        33.01        28.50        16.47        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       70.36        28.44        59.18         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG 
       54.18        60.36        73.64        24.59        75.81        50.07 
TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A574 
      106.75         8.75        26.99        34.55        43.56        38.76 
TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC 
       34.29        32.88        36.82        22.29        36.56        39.55 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        25.84        18.94         9.86        28.27        34.95 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
        3.02        11.15         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.03        40.73        40.50        20.12         0.69 
TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y 
        1.94        29.72         9.47        32.91        30.18        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       26.70         0.79        25.81        26.40        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P6 
       25.94        29.95        29.85        40.41        39.78        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       30.08         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI 
       33.21       109.87        59.57       216.76        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       86.96       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       43.73        69.30        72.03        13.55        18.12        62.47 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A442 
       11.57        21.24        13.22         7.10        13.28        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y 
       25.05        17.06        14.70        14.47        14.79        15.68 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        19.53        12.36        19.59        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RY 
        2.10        36.30        31.99        58.62        40.08        24.72 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VQ 
       20.38        23.47        65.62        42.77        17.36        19.73 
TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG 
       40.11        47.01        64.21         0.26         9.93        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-V7-A7HQ TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       66.84        52.96        15.35        16.04       108.07       107.05 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.03              0.03 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           281.29            282.90 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           28.490            27.715 
[1] "0.0 - 281.3 (28.5)" "0.0 - 282.9 (27.7)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P GAIN MUTATED        19       22        3        2       111        68
  7P GAIN WILD-TYPE      70       63        3        4       242       184
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED           0         41          8         22        7
  7P GAIN WILD-TYPE         2        113         21         43       13
                   vv
clus                STAGE TIS STAGE X
  7P GAIN MUTATED           0       5
  7P GAIN WILD-TYPE         1       8
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 19                70
  STAGE IA                22                63
  STAGE IB                 3                 3
  STAGE II                 2                 4
  STAGE IIA              111               242
  STAGE IIB               68               184
  STAGE III                0                 2
  STAGE IIIA              41               113
  STAGE IIIB               8                21
  STAGE IIIC              22                43
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED    72 182  40  13
  7P GAIN WILD-TYPE 204 442  96  27
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              72               204
  T2             182               442
  T3              40                96
  T4              13                27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P GAIN MUTATED   145  99  31  25
  7P GAIN WILD-TYPE 362 259  88  52
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             145               362
  N1              99               259
  N2              31                88
  N3              25                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   244   7
  7P GAIN WILD-TYPE 645  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    244    7
  7P GAIN WILD-TYPE  645   15
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             244               645
  1               7                15
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   302   7
  7P GAIN WILD-TYPE 766   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    302    7
  7P GAIN WILD-TYPE  766    5
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             302               766
  MALE                 7                 5
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   115 156
  7P GAIN WILD-TYPE 314 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    115  156
  7P GAIN WILD-TYPE  314  362
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              115               314
  YES             156               362
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P GAIN MUTATED                            1                           237
  7P GAIN WILD-TYPE                          0                           533
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P GAIN MUTATED                               42                   1
  7P GAIN WILD-TYPE                            158                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7P GAIN MUTATED                       5                                7
  7P GAIN WILD-TYPE                     4                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7P GAIN MUTATED                    2             14
  7P GAIN WILD-TYPE                 15             33
D13V9, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                237               533
  INFILTRATING LOBULAR CARCINOMA                42               158
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          5                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                14                33
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  1    16
  7P GAIN WILD-TYPE                                0    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          57   212
  7P GAIN WILD-TYPE                       124   533
D13V11, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         16                44
  BLACK OR AFRICAN AMERICAN                     57               124
  WHITE                                        212               533
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V12, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     9 249
  7P GAIN WILD-TYPE  30 626
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9  249
  7P GAIN WILD-TYPE   30  626
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                30
  NOT HISPANIC OR LATINO             249               626
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   232  33
  7Q GAIN WILD-TYPE 685 114
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              265               799 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               33               114 
$`7Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SF TCGA-A1-A0SI TCGA-A1-A0SN TCGA-A2-A04W 
      129.14       131.67        48.10        20.88        39.32       101.98 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0EV TCGA-A2-A0EY 
       98.99       107.93        67.33        33.76        31.82        63.29 
TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FV 
       44.88         8.38        18.21        21.90        18.61        23.47 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ 
       20.25        19.56        42.44        33.93        91.07        50.37 
TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       26.96        35.31        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A425 TCGA-A7-A4SB 
       20.19        25.15        23.61        24.26        14.70        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A8-A06Q 
       14.50        21.17        17.92        12.10        10.29         1.02 
TCGA-A8-A06R TCGA-A8-A06Y TCGA-A8-A07F TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       17.98        26.01        18.97        24.99         9.99        45.07 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       28.96        33.01        19.96        37.05        31.00         0.99 
TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09A TCGA-A8-A09B 
       43.00        33.01        17.95        41.98         9.99        12.00 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM 
       33.07        25.02        14.01        73.91         5.72        26.04 
TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A5EI TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y 
       14.66        16.57        14.53        14.96        13.71        17.42 
TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A0FL 
        1.68         0.03        20.19         1.12         2.30         7.59 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.36         0.33         5.36        66.77        32.78        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12B TCGA-AO-A12D 
       37.48        72.00       115.27        99.25        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       57.30        48.36        61.87        70.39        15.62        32.52 
TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A1AI TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A24K 
       32.91         5.26       108.36        17.23        61.28        50.89 
TCGA-AR-A24Q TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP 
      104.28        93.83        39.39        57.27        73.35        38.96 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
      143.38       281.29        12.13       112.37       233.62       127.33 
TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A401 
      255.68       234.28       157.41        79.63       206.86        85.35 
TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B4 TCGA-BH-A0BA 
       70.16        18.84        62.93        20.45        39.16        37.22 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 
       21.70        74.89        75.48        45.57        49.05        44.02 
TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       45.83        78.28        17.26        15.65         2.56        38.47 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0HQ 
        4.41         9.63        46.19        32.58        24.49        36.85 
TCGA-BH-A0RX TCGA-BH-A18K TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1EX 
        5.59        90.84        51.16        67.50        91.99        49.58 
TCGA-BH-A1F6 TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12Q TCGA-C8-A12V 
       97.48        18.64         9.63         5.26        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A134 TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y 
       48.53        12.59        11.28        12.95        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A3M7 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD 
        8.28         9.67        33.99        21.14        14.17        18.15 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XF TCGA-D8-A1XY 
       12.03        53.00        20.12        20.09        15.22        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27K TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-E2-A107 
       15.32         9.93        48.03        33.37        18.51        34.42 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V 
       37.51        40.11        40.96        38.60        75.98        34.26 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15D 
       69.96        23.24        19.43        25.05        23.34        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BD 
       20.71        18.21        55.63        56.94        76.57        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       33.73        33.70        19.66         8.28        30.61        34.92 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1QZ 
       17.69        34.82        34.16        39.55        41.62        24.82 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A226 TCGA-E9-A22E TCGA-E9-A247 
       45.01        32.09        40.24        34.45        41.72        38.99 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 
        7.13        12.33        30.44        23.90         8.48        28.77 
TCGA-EW-A1OW TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       22.82        52.96        23.11         7.86        18.90        19.99 
TCGA-EW-A423 TCGA-EW-A6SB TCGA-GI-A2C8 TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
       10.16        24.99         7.40        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-GM-A3XN TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A9QF 
       70.85        69.30        66.38         2.60        11.84        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       24.95        32.75        15.32        22.26         2.63        16.08 
TCGA-LL-A740 TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       14.50        17.49        58.52        34.92        36.36        28.87 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A97C 
       22.32        26.70        41.92        26.04        28.21         8.91 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-UU-A93S TCGA-W8-A86G 
       86.96         0.16        18.81        21.07         3.81        11.41 
TCGA-WT-AB44 
       29.03 

$`7Q GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ 
        8.52        14.37        43.43        14.27        47.24        13.68 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        28.01        19.20        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
       18.02        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       56.81        34.55        61.58        25.22       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       80.28       118.45        79.76        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       34.29        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 
       50.43        44.28        17.52        17.13        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        49.48        19.33        48.46        31.73        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 
       17.36        60.72        22.45        19.20        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       50.83         7.30        24.39        21.30        23.21        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DC 
       21.90        38.30        34.29        35.47        30.61        29.79 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       11.97        14.93        14.73        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U 
       10.42         8.75        13.02        13.02        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00         1.02        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       10.98         8.98         7.99        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S 
        0.99        38.01        12.00         9.99        31.00        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C 
      112.08        40.01        30.97        12.00         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09R 
       50.04        49.05        45.07        29.98         1.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02         0.99        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       22.95         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        60.92        87.12        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       25.05        14.99        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW 
       29.26        16.80        19.33        11.44        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
       12.26         8.22         1.32         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.00         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO 
        7.04         0.33         0.33         0.33         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        80.28        61.35        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 
       47.87        58.95        29.13        21.40        26.04        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE 
       22.36        53.03        21.53        50.70        50.86        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       65.10        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12G TCGA-AO-A12H 
      108.72       106.78       108.03        90.58        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62         0.53        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
      130.09         5.65         2.56        19.20       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      125.16       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       86.07        93.90        99.32        37.81        94.29        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73       160.90        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       112.77        97.84       105.27        77.69 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
      105.30        32.58        98.76        98.66        89.00        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       93.30        85.64        71.05       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QN 
       54.21        66.15        63.62        38.17        40.54        33.30 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
       10.59        77.62       275.87       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
      146.50        18.77        84.59       165.76       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       212.25        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS 
      102.77       140.48       100.70        89.46       282.90        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        18.35        21.47       113.79       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A408 TCGA-B6-A40B 
      139.17       170.17        37.87         7.07        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       71.15        59.84        25.55        63.09        81.44        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        70.22        81.63        84.13        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       18.21        43.53        61.51        61.68        72.23        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       76.60        53.95        49.94        77.95        41.75        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
        3.22        67.86        70.88        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       44.81        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        53.26        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU 
       26.50        20.38         5.85         2.50        13.61        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        27.25        50.79        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05        32.91         4.90        35.93        20.12 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       66.05         7.36        51.39       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        17.69        25.81        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.62       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07        28.14        26.14        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       20.88        23.51         9.70        18.87        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U 
       11.93        11.77        11.77        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        12.56         3.16        13.51         1.87 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        10.42        12.33        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       12.53         9.53         0.03         9.50        24.56        14.43 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE 
       19.20        17.49        16.50        55.50        15.78        18.90 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        18.97        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.80        14.50        19.92        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       43.04        15.52        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.45        13.05        14.43        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A4Z1 
        1.61        10.09        13.08        12.53        12.26        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       16.18        12.66        25.22        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q 
       40.41        28.44        28.87        47.15        44.68        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       33.17        43.33        32.02        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15F 
       63.62        21.04        23.87        14.79        22.82        21.63 
TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       12.92        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        14.07        51.39        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        73.64        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       50.07       106.75       102.61         8.75        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.55        43.56        38.76        34.29        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       22.29        36.20        36.56        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       18.94         9.86        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        3.02        11.15        48.23         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       21.27        46.59        47.64        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        38.37        41.03        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        0.69         1.94        24.56        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       32.91        30.18        23.84        26.70         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
       26.40        27.85        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        29.82        18.48        30.08 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C9 
       23.51        15.22        16.77        31.30        33.21       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       59.57       216.76        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        62.47        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.22         7.10        13.28        29.23        25.05        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7SZ 
       14.70        14.47        14.79        15.68         7.46        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       12.36        19.59        27.91        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66I 
       31.99        58.62        40.08        24.72        20.38        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR 
       65.62        42.77        17.36        14.07        19.73        40.11 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z 
       47.01        64.21         0.26         9.93        18.48        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       19.27        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       17.03        66.84        52.96        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.03              0.03 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           281.29            282.90 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            28.96             27.25 
[1] "0.0 - 281.3 (29.0)" "0.0 - 282.9 (27.2)"
[1] "hr=" "1.1"
D14V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q GAIN MUTATED        15       21        3        2        97        57
  7Q GAIN WILD-TYPE      74       64        3        4       256       195
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED           0         31          9         20        7
  7Q GAIN WILD-TYPE         2        123         20         45       13
                   vv
clus                STAGE TIS STAGE X
  7Q GAIN MUTATED           0       3
  7Q GAIN WILD-TYPE         1      10
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 15                74
  STAGE IA                21                64
  STAGE IB                 3                 3
  STAGE II                 2                 4
  STAGE IIA               97               256
  STAGE IIB               57               195
  STAGE III                0                 2
  STAGE IIIA              31               123
  STAGE IIIB               9                20
  STAGE IIIC              20                45
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED    63 155  31  15
  7Q GAIN WILD-TYPE 213 469 105  25
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              63               213
  T2             155               469
  T3              31               105
  T4              15                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q GAIN MUTATED   129  80  26  23
  7Q GAIN WILD-TYPE 378 278  93  54
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             129               378
  N1              80               278
  N2              26                93
  N3              23                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   209   7
  7Q GAIN WILD-TYPE 680  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    209    7
  7Q GAIN WILD-TYPE  680   15
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             209               680
  1               7                15
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   261   5
  7Q GAIN WILD-TYPE 807   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    261    5
  7Q GAIN WILD-TYPE  807    7
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             261               807
  MALE                 5                 7
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   103 132
  7Q GAIN WILD-TYPE 326 386
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    103  132
  7Q GAIN WILD-TYPE  326  386
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              103               326
  YES             132               386
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q GAIN MUTATED                            1                           203
  7Q GAIN WILD-TYPE                          0                           567
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q GAIN MUTATED                               37                   2
  7Q GAIN WILD-TYPE                            163                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7Q GAIN MUTATED                       5                                6
  7Q GAIN WILD-TYPE                     4                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7Q GAIN MUTATED                    2             10
  7Q GAIN WILD-TYPE                 15             37
D14V9, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                203               567
  INFILTRATING LOBULAR CARCINOMA                37               163
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          5                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                10                37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  0    14
  7Q GAIN WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          58   171
  7Q GAIN WILD-TYPE                       123   574
D14V11, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                46
  BLACK OR AFRICAN AMERICAN                     58               123
  WHITE                                        171               574
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V12, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     7 213
  7Q GAIN WILD-TYPE  32 662
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7  213
  7Q GAIN WILD-TYPE   32  662
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             213               662
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   241  44
  8P GAIN WILD-TYPE 676 103
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              285               779 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               44               103 
$`8P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SJ 
      129.14       131.67         9.96        43.43        14.27        13.68 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
      143.15       121.94        24.79        75.25        98.99        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ER 
       67.33        33.76        61.58        80.28        79.76        74.40 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       27.12        44.88         8.38        17.46        18.90        20.75 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A259 TCGA-A2-A3XS 
       18.21        18.61        20.25        19.20        52.47        33.93 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 
       47.31        35.93        50.83        24.39        26.96        21.14 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26F 
       38.30        30.61        35.67        29.79        25.15        24.26 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD 
       23.80        21.73        10.29        11.97        14.93        14.50 
TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Y TCGA-A8-A06Z 
       10.72        10.29        10.42         8.75        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A086 TCGA-A8-A08C 
       53.98         9.01        43.00        18.97        13.02        28.96 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09B 
        0.99       112.08        30.97        17.95         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A9 
        1.02        49.05        33.07        14.01        19.04        27.02 
TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2BM TCGA-AC-A2FE TCGA-AC-A2FM 
       17.03        22.95        73.91        99.35        86.66        26.04 
TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3YI TCGA-AC-A5EI TCGA-AC-A62V TCGA-AC-A62X 
       14.66         6.48        23.24        14.53        11.44        13.71 
TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AN-A03X TCGA-AN-A0AJ TCGA-AN-A0FK 
       13.58         1.68         0.03         0.33         9.96         7.00 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03R TCGA-AO-A03T 
        7.04         0.36         0.33         0.33        68.75        47.87 
TCGA-AO-A0J7 TCGA-AO-A0JI TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
       20.32        50.24       108.03        98.27        57.30        48.36 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       82.62        61.87         0.53        32.52         2.56        32.91 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A1AY 
       65.36       107.21       125.16       108.36        99.32        33.73 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A254 
      104.28       112.77        97.84        32.58        99.62        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LR 
       71.05        93.83        20.25        54.21        66.15        57.27 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH 
       33.30        38.96       281.29       275.87       129.57       112.37 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RP TCGA-B6-A0RV 
      255.68       212.25        81.17        78.02       102.77       157.41 
TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A400 
       21.47       245.10        43.59       101.52       170.17         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B4 
       85.35        70.16        62.93        20.45        39.55        39.16 
TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DP 
       37.22        18.21        61.51        49.05        44.02        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GY 
        2.56        38.47        15.68        14.30        44.81        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HQ TCGA-BH-A0HU 
       10.78        15.16        24.56        26.50        36.85        12.89 
TCGA-BH-A0RX TCGA-BH-A0W7 TCGA-BH-A18L TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU 
        5.59        44.81        26.66        91.99       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE 
       12.00        49.58        89.16       120.62       114.15        74.73 
TCGA-BH-A1FG TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A5J0 TCGA-BH-A6R8 
      122.89        45.63        26.14        83.31        23.51         9.63 
TCGA-C8-A12O TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       12.66        12.66        12.66        12.66        12.66         3.16 
TCGA-C8-A135 TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A142 
       12.92        12.36         9.67         0.03        20.58        13.97 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JP TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1XB 
       12.03        14.01        21.01        14.70        17.79        18.15 
TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY 
       15.22        14.50        19.92        12.99        43.04        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27V TCGA-E2-A107 
       15.32         9.93        14.14        14.43        12.53        34.42 
TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14U TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A154 
       46.59        44.68        43.33        69.34        69.96        19.43 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15S TCGA-E2-A1AZ 
       14.79        25.05        17.29        21.63        14.07        76.57 
TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IN TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A576 
       28.50        37.25        22.19        26.99        34.92        34.29 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NE TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 
       36.82        22.29        35.77        34.95         2.56        11.15 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22G 
       45.01        32.09        40.24        42.25        38.37        40.73 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3X8 TCGA-E9-A54X 
       20.12        38.99        12.33        29.72        30.44        23.90 
TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1P0 
       26.70        26.40         8.48        18.90        28.77        41.13 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A6SA TCGA-GM-A2DC 
       23.11        18.48        19.99         6.15        16.77        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DO TCGA-HN-A2NL TCGA-LL-A5YO TCGA-LL-A73Y 
       75.02        70.85        85.35         2.60        14.47        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
        7.46        14.50        19.53        58.52        31.99        58.62 
TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VR TCGA-S3-A6ZG TCGA-S3-AA10 
       23.47        26.04        28.21        40.11        18.48        19.27 
TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB41 
       18.87        11.41        52.96 

$`8P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM 
       14.37        48.10        47.24        20.88        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        19.20        18.21        18.02        78.41 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EM 
       77.19         5.19       107.93        34.55        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       89.36       118.45        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX 
       61.94        24.72        63.29        99.19        54.64        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0YC 
       44.28        17.52        17.13        49.84        20.52        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       48.46        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       22.45        19.56        16.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT 
       18.15       105.34        10.59        36.23        39.65        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY 
       29.98        32.75        56.28        50.37         7.30        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       23.21        21.90        35.31        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 
       23.74        20.61        22.32        11.34        10.59        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       13.41        14.70        13.74        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       12.10        11.05         9.37        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07E 
       17.98        53.06        29.03        31.00        17.03        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 
        8.98         7.99        24.99         9.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
       36.95         0.99        38.01        33.01        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X 
       37.05         9.99        31.00        31.00        33.01        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D 
       40.01        33.01        41.98        12.00         9.99        50.04 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98         1.02        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       15.02         0.99        12.00        13.02        21.04         0.99 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB 
       38.04         0.95         5.72         1.48        73.05        40.57 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        60.92        87.12        74.14        33.04        19.33 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        16.57        19.79        15.48        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       16.80        19.33        14.96        17.42        18.67        12.26 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03Y 
        8.22        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.23         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.59         7.17         6.90 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03U 
       80.28        61.35        66.77        81.63        95.70        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        65.10        26.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D 
      115.27        99.25       108.72       106.78        90.58        64.04 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       41.62        40.57        14.73        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TP 
       26.93       130.09         5.65        15.62        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       98.33         5.26        84.10       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24       133.22        83.87       134.14 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        17.23        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43       160.90        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X 
      118.59         2.76       105.27        77.69       105.30        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM 
       98.66        89.00        93.30       166.42        86.53        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 
       38.17        39.39        40.54        73.35        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ 
      143.38        12.13        50.70        65.72       146.50       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS 
       68.45       234.28       263.28       162.05       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       282.90        97.48       188.68        79.63        18.35 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      113.79       206.86       129.70        28.27        68.94        58.88 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
       73.51       139.17        37.87        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       71.15        59.84        25.55        63.09        81.44        40.83 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF 
       70.22        81.63        84.13        51.68        32.02        43.53 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        74.89        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 
       76.60        53.95        45.57        49.94        77.95        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       89.06        90.97        45.83        77.98        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV 
       29.98        13.91        78.28        17.26         3.22        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
       70.88        16.27         4.41         9.63        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H7 
       24.49        31.00        24.43        37.78        53.26        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        20.38         5.85         2.50        13.61 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        27.25        50.79        23.93        24.95        42.35 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EW 
        7.36        51.39        51.16        67.50        82.85        55.69 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD 
       17.69        25.81        31.53        97.48        24.62        33.17 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        55.00        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       28.14        38.60        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 
       20.12        10.52       109.28        20.88        18.64         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       11.77        11.77        12.66        48.53        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.87        12.59         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.28         0.16        12.03        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z 
       12.95        12.33        20.25        12.53        12.95         8.28 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         9.50        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        14.17        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       17.49        16.50        55.50        15.78        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       53.00        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 
       20.38        12.20        13.32        18.58        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        27.58        12.39        17.16        14.73        21.80 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XV TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.16        15.52        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       13.05        48.03        16.41        13.48         4.80         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       10.09        13.08        12.26        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A 
       16.18        12.66        25.22        43.00        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       37.51        40.11        28.44        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.17        75.98        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       31.96        18.51        63.62        23.24        21.04        23.87 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       23.34        22.82        20.71        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       56.94        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       16.47        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18         3.88        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       60.36        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       50.07       106.75       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 
       43.56         8.28        30.61        38.76        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       32.88        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        6.12         3.02        48.23         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 
       21.27        46.59        47.64        34.45        32.05        37.74 
TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A248 
       39.09        41.03        41.72        40.50         0.69         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
        7.13        24.56         9.47        38.07        32.91        30.18 
TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       23.84         0.79        25.81        27.85        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        13.25        16.57        15.68        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.95        29.85        40.41        39.78        52.96        29.82 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        18.90        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB 
       34.03        17.49        10.16        23.51        15.22        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       79.10        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       72.03        13.55        18.12        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       32.75        29.23        25.05        17.06        15.32        14.70 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LL-A8F5 
       14.79        22.26         2.63        16.08        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RU 
       17.49        27.91        22.39         2.10        36.30        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       26.70        65.62        41.92        42.77        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       19.73         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26         9.93        18.81        21.07        20.68        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.39        17.26        13.94        17.03         3.81        66.84 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.03              0.16 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           281.29            282.90 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            26.96             28.27 
[1] "0.0 - 281.3 (27.0)" "0.2 - 282.9 (28.3)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P GAIN MUTATED        22       26        2        2        95        70
  8P GAIN WILD-TYPE      67       59        4        4       258       182
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           2         34          9         15        7
  8P GAIN WILD-TYPE         0        120         20         50       13
                   vv
clus                STAGE TIS STAGE X
  8P GAIN MUTATED           0       5
  8P GAIN WILD-TYPE         1       8
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 22                67
  STAGE IA                26                59
  STAGE IB                 2                 4
  STAGE II                 2                 4
  STAGE IIA               95               258
  STAGE IIB               70               182
  STAGE III                2                 0
  STAGE IIIA              34               120
  STAGE IIIB               9                20
  STAGE IIIC              15                50
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED    78 162  38   9
  8P GAIN WILD-TYPE 198 462  98  31
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              78               198
  T2             162               462
  T3              38                98
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P GAIN MUTATED   136 102  26  19
  8P GAIN WILD-TYPE 371 256  93  58
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             136               371
  N1             102               256
  N2              26                93
  N3              19                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   238   8
  8P GAIN WILD-TYPE 651  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    238    8
  8P GAIN WILD-TYPE  651   14
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             238               651
  1               8                14
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   285   5
  8P GAIN WILD-TYPE 783   7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    285    5
  8P GAIN WILD-TYPE  783    7
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE             285               783
  MALE                 5                 7
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   110 141
  8P GAIN WILD-TYPE 319 377
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    110  141
  8P GAIN WILD-TYPE  319  377
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              110               319
  YES             141               377
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P GAIN MUTATED                            0                           221
  8P GAIN WILD-TYPE                          1                           549
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P GAIN MUTATED                               39                   3
  8P GAIN WILD-TYPE                            161                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8P GAIN MUTATED                       5                                8
  8P GAIN WILD-TYPE                     4                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8P GAIN MUTATED                    3             11
  8P GAIN WILD-TYPE                 14             36
D15V9, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                221               549
  INFILTRATING LOBULAR CARCINOMA                39               161
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          5                 4
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                11                36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0    13
  8P GAIN WILD-TYPE                                1    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                          60   192
  8P GAIN WILD-TYPE                       121   553
D15V11, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                47
  BLACK OR AFRICAN AMERICAN                     60               121
  WHITE                                        192               553
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V12, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     9 230
  8P GAIN WILD-TYPE  30 645
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      9  230
  8P GAIN WILD-TYPE   30  645
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   9                30
  NOT HISPANIC OR LATINO             230               645
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   444  75
  8Q GAIN WILD-TYPE 473  72
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              519               545 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               75                72 
$`8Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
      129.14       131.67         9.96        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04N 
       14.27        13.68        31.79        39.32        19.20       143.15 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CP 
       78.41       121.94        36.13        99.12        24.79        92.48 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       75.25        98.99        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX 
       61.58        25.22        80.28        79.76        34.29        24.72 
TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T1 
       63.29        27.12        44.88        50.43        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YE 
        8.38        49.84        17.46        18.90        20.75        18.21 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       21.90        21.67        18.61        31.73        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A259 
       17.36        60.72        20.25        19.20        19.56        52.47 
TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU 
       42.44        18.15       105.34        39.65        33.93        29.98 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 
       47.31        35.93        50.83        24.39        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D 
       21.90        38.30        30.61        35.67        29.79        31.73 
TCGA-A7-A13F TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       25.15        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE 
       22.32        10.29        11.97        14.93        14.50        21.17 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       12.10        10.72        10.29        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       13.02        17.98        53.06        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07O 
       53.98         9.01        43.00        18.97        14.01         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A086 TCGA-A8-A08C 
       10.98         8.98        24.99         9.99        13.02        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
       33.01        19.96        12.00        37.05        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       33.01       112.08        43.00        33.01        30.97        17.95 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
        9.99        12.00         1.02        49.05        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A09X 
        1.02        25.02         8.98        19.04         0.99        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A23G 
       19.04         0.99        27.02        17.03        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FE TCGA-AC-A2FM TCGA-AC-A2QH 
        5.72        73.05        99.35        86.66        26.04        33.04 
TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3YI TCGA-AC-A5EI TCGA-AC-A62V TCGA-AC-A62X 
       14.66         6.48        23.24        14.53        11.44        13.71 
TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A03Y 
       13.58         1.68         0.03        20.19         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        0.62         1.78         1.71         9.96         0.16         0.33 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.00         7.59         7.04         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XS TCGA-AO-A03O TCGA-AO-A03R 
        0.33         5.36         0.33         0.33        81.63        68.75 
TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 
       47.87        29.13        21.40        52.18        26.04        20.32 
TCGA-AO-A0JI TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
       50.24       106.78       108.03        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       48.36        41.62        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       17.79        24.79       130.09        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
       32.91       140.55        98.33        84.10       109.02        98.93 
TCGA-AR-A0U0 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AP 
       65.36       107.21       108.36       101.00       103.86        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24Q 
       99.32        94.29        86.53        86.43        33.73       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
      112.77        97.84        77.69       105.30        32.58        98.66 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LK 
       99.62        85.64        71.05        93.83        20.25        54.21 
TCGA-AR-A2LL TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       66.15        39.39        57.27        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IH 
       77.62       143.38       281.29       275.87       129.57       112.37 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM 
      127.33        84.59       255.68       212.25        81.17        78.02 
TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      102.77       282.90       157.41        18.35        21.47       113.79 
TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A400 
      245.10        58.88        43.59       101.52       170.17         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       85.35        70.16        18.84        62.93        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA 
       25.55        40.83        39.55        39.16        81.63        37.22 
TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ 
       18.21        61.51        74.89        75.48        45.57        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DS 
       41.75        44.02        45.83        78.28        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0GZ 
       38.47        16.27        15.68        14.30        44.81        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HQ TCGA-BH-A0HU 
       15.16        24.56        23.08        26.50        36.85        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       27.25        50.79         5.59        42.35        44.81        23.05 
TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       35.93        26.66        37.74        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 
      113.82        42.28        12.00        55.69        49.58        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        97.48       120.62       114.15        74.73       122.89 
TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42V 
       45.63        72.07        26.14        83.31       130.16        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       23.51         9.63        18.87        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        12.66         3.16        13.51 
TCGA-C8-A135 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       12.92        11.34        12.03        12.33        12.95        12.33 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A8HR 
       12.36         8.28         9.67         0.03        24.56        13.41 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1JC TCGA-D8-A1JD 
       20.58        13.97        14.17        19.20        15.78        18.15 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        53.00        14.01        20.09        20.12        20.09 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XB 
       21.01        13.32        14.70        18.58        17.79        18.15 
TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU 
       15.22        14.50        19.92        16.41        16.31        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       43.04        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R 
       14.14        13.05        14.43        16.41        13.48        10.09 
TCGA-D8-A27V TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14O 
       12.53        34.42        27.52        40.11        47.15        44.68 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y 
       38.60        33.17        75.98        43.33        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 
       18.51        69.96        23.24        19.43        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15J 
       23.34        22.82        17.29        20.71        21.63        53.92 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        50.79        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1II TCGA-E2-A1IN 
       53.62        32.35        28.50        37.25        33.70        22.19 
TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       60.99        60.36        24.59       106.75       102.61         8.75 
TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       26.99         8.28        34.92        38.76        34.29        17.69 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI 
       36.82        22.29        36.20        35.77        35.24         9.86 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
       34.95         2.56        11.15        45.01        32.09        40.24 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       46.65        21.27        39.09        38.37        41.72        40.73 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3QA 
       20.12        38.99         1.94        12.33        29.72        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1IY 
       30.44        23.90        23.84        26.70        26.40         8.48 
TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       18.90        28.77        22.82        29.85        40.41        41.13 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC 
       52.96        23.11        18.48         7.86        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD 
       13.94        19.96        25.91        16.77        24.99        33.21 
TCGA-GI-A2C9 TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DO TCGA-GM-A3XL 
      109.87        83.34        75.02        70.85        85.35        69.30 
TCGA-GM-A5PV TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A5YM 
       13.55         2.60        11.84        11.57         7.10        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       14.70        14.47        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       19.53        12.36        17.49        58.52        31.99        58.62 
TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VR TCGA-PE-A5DC TCGA-S3-A6ZF 
       23.47        26.04        28.21        40.11        47.01        18.81 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA12 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       18.48        19.27        18.87        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-Z7-A8R6 
       11.41        52.96       107.05 

$`8Q GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04P 
       47.24        20.88         7.96        28.01        18.21        18.02 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK 
       73.84        87.25        63.12       101.98        55.43       136.73 
TCGA-A2-A0CO TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW 
      114.81        88.60       107.93        77.19         5.19       107.93 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
      101.72        89.36       118.45        74.40        72.00        35.05 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T4 
       31.82        61.94        99.19        54.64        44.28        20.52 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       32.55        25.28        50.47        49.48        19.33        48.46 
TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25F TCGA-A2-A3KC 
       22.45        16.47       107.70        17.19        10.59        36.23 
TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY 
       91.07        32.75        56.28        50.37         7.30        21.30 
TCGA-A2-A4S0 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       23.21        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A3IY TCGA-A7-A3IZ 
       20.19        23.61        29.56        31.36        11.34        10.59 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       11.28        13.41        14.70        13.74        17.92        14.73 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A07E 
       11.05         9.37         1.02        29.03        31.00        19.99 
TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07S TCGA-A8-A07Z TCGA-A8-A084 
       18.97        12.00        32.05         7.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08Z 
       36.95         0.99        38.01         9.99        31.00        40.01 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09V 
       41.98        12.00         9.99        50.04        45.07        15.02 
TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A2B8 
       12.00        13.02        21.04        38.04         0.95         1.48 
TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI 
       40.57        90.71        60.92        87.12        74.14        19.33 
TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        16.57        19.79        15.48        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       16.80        19.33        14.96        17.42        18.67        12.26 
TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A041 TCGA-AN-A046 
        8.22         1.12         1.32         2.30         0.23         0.33 
TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        2.96         7.36         7.46         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XO 
        5.65         7.96         7.17         6.90         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.30         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A0J2 
       80.28        61.35        66.77        95.70        58.95        32.78 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12H 
       71.80       115.27        99.25       108.72        90.58        40.57 
TCGA-AO-A1KO TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TV 
       14.73        26.93         5.65        19.20         5.26        75.22 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24       133.22        83.87       134.14 
TCGA-AR-A1AH TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AR 
      125.16        97.68        98.33        96.00        86.07        17.23 
TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       37.81        61.28       160.90        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24X TCGA-AR-A250 
       99.78       118.59         2.76       105.27        98.76        89.00 
TCGA-AR-A252 TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ 
       93.30       166.42        86.53        63.62        38.17        40.54 
TCGA-AR-A5QM TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ 
       73.35        12.13        50.70        65.72       146.50       233.62 
TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI 
       18.77       165.76       129.07       140.88        68.45       234.28 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS 
      263.28       162.05       140.48       100.70        89.46        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
      188.68        79.63       206.86       129.70        28.27        68.94 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       73.51       139.17        37.87        68.12       103.63        71.15 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       63.09        81.44        70.22        84.13        51.68        32.02 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       43.53        21.70        61.68        72.23        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       53.95        49.94        77.95        89.06        90.97        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ 
       23.44        38.01        29.98        13.91        17.26         3.22 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA 
       67.86        70.88         4.41         9.63        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.49        31.00        24.43        30.35        37.78        53.26 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        20.38         5.85         2.50        13.61 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J 
       51.32        23.93        24.95        32.91         4.90        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       90.84        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F8 
        7.36        67.50        82.85        17.69        25.81        24.62 
TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR 
       33.17        36.92        63.35        55.00        72.07       144.59 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       28.14        38.60        57.83        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 
       10.52       109.28        18.64         5.26         9.70        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12Y TCGA-C8-A12Z 
        9.44        11.93        11.77        12.66        48.53        12.56 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.87        12.59         4.11         4.08        12.33        10.92 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       11.28         0.16        10.42        20.25        12.53        12.95 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.53         9.50        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A145 
       12.49        19.46        56.81        20.88        13.25        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JE 
       21.14        14.17        17.49        16.50        55.50        18.90 
TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1X7 TCGA-D8-A1X8 
       18.97        19.40        20.38        12.20        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        27.58        12.39        17.16        14.73        21.80 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A27E 
       17.69        55.30        15.85        16.64        15.16        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T 
       16.04        13.45        48.03         4.80         1.61        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       25.22        43.00        46.59        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A150 
       28.87        40.96        38.24        34.26        32.02        63.62 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K 
       21.04        23.87        18.21        12.92        55.63         9.04 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1IE 
       20.58        19.56        87.22        33.01        16.47        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       11.08        54.18        73.64        19.66        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N3 
       50.07        43.04        34.55        43.56        30.61        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG 
       32.88        34.16        36.56        39.55        41.62        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       18.94        24.82        28.27         6.12         3.02        48.23 
TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        1.12         6.58        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A249 
       42.25        37.74        41.03        40.50         0.69         7.13 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A5FL TCGA-E9-A5UO 
       24.56         9.47        38.07        32.91         0.79        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       27.85        12.20        39.72        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P7 
       15.68        25.94        29.95        39.78        29.82        30.08 
TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS 
       18.90        10.52        14.43        34.55        55.00        52.73 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        10.16        23.51        15.22 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DH 
       31.30         7.40        59.57       216.76        79.10        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2OB 
       38.20        43.73        66.38        72.03        18.12        62.47 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       21.24        13.22        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       29.23        25.05        17.06        14.79        22.26         2.63 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5RU 
       19.59        27.91        22.39         2.10        36.30        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       26.70        65.62        41.92        42.77        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
       19.73         8.91        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        9.93        21.07        20.68        13.84        17.39        17.26 
TCGA-S3-AA17 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       13.94        29.03        15.35        16.04       108.07 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.03              0.16 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           282.90            263.28 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            26.04             29.23 
[1] "0.0 - 282.9 (26.0)" "0.2 - 263.3 (29.2)"
[1] "hr=" "1.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q GAIN MUTATED        45       38        3        3       182       108
  8Q GAIN WILD-TYPE      44       47        3        3       171       144
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED           2         77         15         33       11
  8Q GAIN WILD-TYPE         0         77         14         32        9
                   vv
clus                STAGE TIS STAGE X
  8Q GAIN MUTATED           0       9
  8Q GAIN WILD-TYPE         1       4
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 45                44
  STAGE IA                38                47
  STAGE IB                 3                 3
  STAGE II                 3                 3
  STAGE IIA              182               171
  STAGE IIB              108               144
  STAGE III                2                 0
  STAGE IIIA              77                77
  STAGE IIIB              15                14
  STAGE IIIC              33                32
  STAGE IV                11                 9
  STAGE TIS                0                 1
  STAGE X                  9                 4
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED   139 309  58  20
  8Q GAIN WILD-TYPE 137 315  78  20
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1             139               137
  T2             309               315
  T3              58                78
  T4              20                20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q GAIN MUTATED   249 162  65  40
  8Q GAIN WILD-TYPE 258 196  54  37
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             249               258
  N1             162               196
  N2              65                54
  N3              40                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   447  12
  8Q GAIN WILD-TYPE 442  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    447   12
  8Q GAIN WILD-TYPE  442   10
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             447               442
  1              12                10
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   521   8
  8Q GAIN WILD-TYPE 547   4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    521    8
  8Q GAIN WILD-TYPE  547    4
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             521               547
  MALE                 8                 4
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   196 264
  8Q GAIN WILD-TYPE 233 254
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    196  264
  8Q GAIN WILD-TYPE  233  254
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              196               233
  YES             264               254
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q GAIN MUTATED                            1                           418
  8Q GAIN WILD-TYPE                          0                           352
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q GAIN MUTATED                               58                   5
  8Q GAIN WILD-TYPE                            142                   1
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8Q GAIN MUTATED                       6                               12
  8Q GAIN WILD-TYPE                     3                               17
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8Q GAIN MUTATED                    4             24
  8Q GAIN WILD-TYPE                 13             23
D16V9, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                418               352
  INFILTRATING LOBULAR CARCINOMA                58               142
  MEDULLARY CARCINOMA                            5                 1
  METAPLASTIC CARCINOMA                          6                 3
  MIXED HISTOLOGY (PLEASE SPECIFY)              12                17
  MUCINOUS CARCINOMA                             4                13
  OTHER  SPECIFY                                24                23
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  1    28
  8Q GAIN WILD-TYPE                                0    32
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                         104   340
  8Q GAIN WILD-TYPE                        77   405
D16V11, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         28                32
  BLACK OR AFRICAN AMERICAN                    104                77
  WHITE                                        340               405
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V12, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    14 424
  8Q GAIN WILD-TYPE  25 451
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     14  424
  8Q GAIN WILD-TYPE   25  451
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  14                25
  NOT HISPANIC OR LATINO             424               451
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED   116  23
  9P GAIN WILD-TYPE 801 124
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              139               925 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               23               124 
$`9P GAIN MUTATED`
TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM 
       11.44        31.79        73.84        87.25       101.98        24.79 
TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YM 
       77.19        98.99        50.43         8.38        49.84        31.73 
TCGA-A2-A1FV TCGA-A2-A25D TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A3J0 
       23.47        18.15        21.14        33.11        20.19        10.29 
TCGA-A7-A425 TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A07F TCGA-A8-A07R 
       14.70        14.50        14.73        10.42        18.97         8.98 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08X TCGA-A8-A093 
       24.99        45.07        38.01        28.96        43.00        17.95 
TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A3W5 
       14.01        22.95         5.72        73.05        26.04        16.57 
TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV 
       13.71         1.12         0.33         7.00         7.04         0.33 
TCGA-AN-A0FX TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JL TCGA-AO-A128 TCGA-AQ-A54N 
        0.33        20.32        53.03        55.33       106.78         2.56 
TCGA-AR-A0U0 TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 TCGA-B6-A0I2 
       65.36        33.73       160.90        89.00        93.83       143.38 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RS TCGA-B6-A0RU 
      112.37       233.62       140.88       255.68       100.70       282.90 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0B9 
      206.86       245.10        43.59        73.51        25.55        51.68 
TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0RX 
       37.22        61.51        45.57        32.58        31.00         5.59 
TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 
       32.91        55.63        51.16        42.28        12.00        25.81 
TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-C8-A132 
       97.48       114.15        26.14        18.64         5.26         1.87 
TCGA-C8-A138 TCGA-C8-A26Z TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 
        4.08         8.28        13.02        20.58        21.14        14.17 
TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF 
       16.50        18.15        18.90        13.32        18.15        15.22 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A27V TCGA-D8-A3Z6 
       14.50        19.92        12.99        43.04        12.53        18.51 
TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A1AZ 
       37.51        47.15        19.43        14.79        25.05        76.57 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A2P5 
       37.25        33.73        33.70        19.66        43.04        26.99 
TCGA-E2-A56Z TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY 
        8.28        17.69        22.29         0.69        38.07         8.48 
TCGA-EW-A1J1 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-GM-A2DF 
       18.90         7.86         6.15        34.55        19.96        70.85 
TCGA-GM-A2DH TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-LL-A5YM TCGA-LL-A6FR TCGA-MS-A51U 
       72.10        69.30        72.03        15.32        16.08        22.39 
TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF 
       36.36        23.47        28.21        86.96         9.93        18.81 
TCGA-S3-AA0Z 
       20.68 

$`9P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
       63.12        55.43        36.13       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       92.48        88.60       107.93        75.25         5.19       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       56.81        67.33        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY 
       63.29        99.19        54.64        27.12        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.52        17.13        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW 
       49.48        18.61        19.33        48.46        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        42.44        17.19       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CD 
       24.39        21.30        23.21        26.96        21.90        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       35.31        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        31.73        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       24.26        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       11.34        10.59        11.28        13.41        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        21.17        17.92        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       14.01        12.00        32.05         9.99        10.98         7.99 
TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F 
        9.99        15.06        36.95        13.02         0.99        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
        0.99        33.01       112.08        40.01        33.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
       25.02         8.98        19.04        15.02         0.99        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
       38.04         0.95        73.91         1.48        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 
       22.19        24.13        25.05        14.99        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       23.24        24.79        29.26        16.80        14.53        19.33 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        11.44        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
        1.68         8.22         0.03        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         7.46         0.16 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.33         0.33         6.44         5.65         7.96         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.17         6.90         0.36         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       32.78        21.40        52.18        26.04        37.48        22.36 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        62.04        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       70.39         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        32.52        32.91        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       98.33         5.26        84.10       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
      107.21       125.16       108.36       101.00       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       98.33        96.00        86.07        93.90        99.32        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K 
       37.81        94.29        61.28        86.53        86.43        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27        77.69       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 
       98.76        98.66        99.62        93.30        85.64        71.05 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        57.27        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        10.59        77.62       281.29        12.13       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM 
      129.57        50.70        65.72       146.50        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       165.76       129.07        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       21.47       113.79       129.70        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
      101.52       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       70.16        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       59.84        20.45        63.09        81.44        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        70.22        81.63        84.13        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       74.14        76.60        53.95        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       46.19        24.49        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        53.26        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        51.32        27.25        50.79        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        23.05         4.90        35.93        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       90.84        26.66        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        67.50        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       82.85        55.69        49.58        17.69        31.53        89.16 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       24.62       120.62        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       28.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
        6.44        20.12        10.52       109.28        20.88        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       13.51        12.59        12.92         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.28         0.16        12.03        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       33.99        12.95        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
       20.88        13.25        13.97        14.17        13.48        19.20 
TCGA-D8-A1J9 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       17.49        55.50        15.78        12.03        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58        12.39        17.16        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       21.80        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        15.16        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43        48.03        16.41        13.48         4.80         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U 
       10.09        13.08        12.26        33.37        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       12.66        25.22        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       40.41        40.11        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       32.02        31.96        69.34        18.51        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.24        21.04        23.87        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       20.71        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       14.07        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        16.47        77.65        37.41        70.36        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       60.36        73.64        24.59        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
      106.75       102.61         8.75        34.55        43.56        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        38.76        34.29        34.82        32.88        36.82 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       34.16        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02        11.15        48.23 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       45.01        32.09        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       12.33        29.72         9.47        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       23.90        23.84        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       27.85        12.20        39.72        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08        18.90        19.99        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       14.43        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       17.49        10.16        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        83.34        75.02        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        13.55        18.12         2.60        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
       24.95        32.75        29.23        25.05        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        14.79        22.26         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        19.53        12.36        19.59        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX 
       19.73        40.11         8.91        47.01        64.21         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        0.26        18.48        21.07        19.27        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.39        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.33              0.03 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           282.90            281.29 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            24.99             28.44 
[1] "0.3 - 282.9 (25.0)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.1"
D17V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P GAIN MUTATED         9        6        1        2        56        34
  9P GAIN WILD-TYPE      80       79        5        4       297       218
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           0         11          4         12        2
  9P GAIN WILD-TYPE         2        143         25         53       18
                   vv
clus                STAGE TIS STAGE X
  9P GAIN MUTATED           0       1
  9P GAIN WILD-TYPE         1      12
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  9                80
  STAGE IA                 6                79
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               56               297
  STAGE IIB               34               218
  STAGE III                0                 2
  STAGE IIIA              11               143
  STAGE IIIB               4                25
  STAGE IIIC              12                53
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED    28  90  14   8
  9P GAIN WILD-TYPE 248 534 122  32
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1              28               248
  T2              90               534
  T3              14               122
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P GAIN MUTATED    66  48  10  14
  9P GAIN WILD-TYPE 441 310 109  63
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              66               441
  N1              48               310
  N2              10               109
  N3              14                63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED   117   3
  9P GAIN WILD-TYPE 772  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    117    3
  9P GAIN WILD-TYPE  772   19
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0             117               772
  1               3                19
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED   141   0
  9P GAIN WILD-TYPE 927  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED    141    0
  9P GAIN WILD-TYPE  927   12
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE             141               927
  MALE                 0                12
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    54  74
  9P GAIN WILD-TYPE 375 444
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     54   74
  9P GAIN WILD-TYPE  375  444
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               54               375
  YES              74               444
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P GAIN MUTATED                            0                           110
  9P GAIN WILD-TYPE                          1                           660
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P GAIN MUTATED                               20                   2
  9P GAIN WILD-TYPE                            180                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9P GAIN MUTATED                       2                                1
  9P GAIN WILD-TYPE                     7                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9P GAIN MUTATED                    1              5
  9P GAIN WILD-TYPE                 16             42
D17V9, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                110               660
  INFILTRATING LOBULAR CARCINOMA                20               180
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 5                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     8
  9P GAIN WILD-TYPE                                1    52
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                          30    94
  9P GAIN WILD-TYPE                       151   651
D17V11, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          8                52
  BLACK OR AFRICAN AMERICAN                     30               151
  WHITE                                         94               651
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V12, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     5 115
  9P GAIN WILD-TYPE  34 760
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      5  115
  9P GAIN WILD-TYPE   34  760
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO             115               760
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    96  21
  9Q GAIN WILD-TYPE 821 126
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              117               947 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               21               126 
$`9Q GAIN MUTATED`
TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CS 
       42.81        11.44        31.79        73.84        87.25        77.19 
TCGA-A2-A0CV TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A25B 
       98.99         8.38        49.84        31.73        23.47        42.44 
TCGA-A2-A4S2 TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A6VX 
       21.14        33.11        20.19        10.29        14.70        10.42 
TCGA-A8-A07F TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A093 TCGA-A8-A09X 
       18.97        45.07        38.01        28.96        17.95        14.01 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A5XU TCGA-AN-A04A TCGA-AN-A0FK 
       22.95         5.72        26.04        14.96         2.96         7.00 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XR TCGA-AO-A0J7 TCGA-AO-A128 
        7.04         0.33         0.33         0.33        20.32       106.78 
TCGA-AQ-A04H TCGA-AR-A0TR TCGA-AR-A1AJ TCGA-AR-A24H TCGA-AR-A250 TCGA-AR-A256 
       24.79         5.26       101.00       160.90        89.00        93.83 
TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IQ 
       73.35       143.38       112.37       233.62        18.77       140.88 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WZ TCGA-B6-A1KI TCGA-BH-A0AY TCGA-BH-A0BA 
      100.70       282.90       206.86        73.51        25.55        37.22 
TCGA-BH-A0BG TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A18F TCGA-BH-A18V TCGA-BH-A1EU 
       61.51        46.19        32.58        32.91        51.16        42.28 
TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A5IZ TCGA-BH-A6R9 
       12.00        31.53       114.15        26.14        18.64         5.26 
TCGA-C8-A12M TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A26Y 
       11.77         1.87         4.08        11.34        12.03        12.95 
TCGA-C8-A275 TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD 
        0.03        13.02        20.58        21.14        14.17        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JT TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL 
       18.90        53.00        13.32        18.15        15.22        19.92 
TCGA-D8-A1XU TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14N TCGA-E2-A154 
       12.99        12.53        18.51        37.51        47.15        19.43 
TCGA-E2-A1BD TCGA-E2-A1II TCGA-E2-A1L9 TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z 
       37.25        33.70        19.66        43.04        26.99         8.28 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A3HO TCGA-EW-A1IY 
       17.69        22.29        41.72         0.69        38.07         8.48 
TCGA-EW-A1J1 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH 
       18.90        29.82         7.86         6.15        34.55        19.96 
TCGA-GI-A2C8 TCGA-GM-A2DF TCGA-GM-A3XL TCGA-MS-A51U TCGA-OL-A5RW TCGA-OL-A66I 
        7.40        70.85        69.30        22.39        36.36        23.47 
TCGA-PE-A5DE TCGA-S3-AA0Z TCGA-Z7-A8R6 
       86.96        20.68       107.05 

$`9Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14       131.67        40.14        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V 
       18.21       143.15        18.02        78.41       121.94        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48        88.60       107.93        75.25         5.19 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        56.81        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 
       50.43        44.28        17.52        17.13        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.77        17.36        60.72        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
      105.34        10.59        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        56.28        47.31        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.90        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       37.45        35.67        29.79        31.73        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        22.32        11.34        10.59        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        8.75        13.02        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08F 
        9.99        15.06        36.95        13.02         0.99        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK 
       17.03        38.04         0.95        73.91         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       74.14        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       16.57        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       16.80        14.53        19.33        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
       20.19         1.12         1.32         2.30         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.59         7.17         6.90 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         5.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.30         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
       80.28        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        37.48        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.03        90.58        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        40.57        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
        0.53        17.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       32.52         2.56        32.91        19.20       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
      107.24        65.36       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      125.16       108.36       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       86.07        93.90        99.32        17.23        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L 
       61.28        86.53        86.43        33.73        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE 
       98.66        99.62        93.30        85.64        71.05       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        57.27        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       281.29        12.13       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
       65.72       146.50       127.33        84.59       165.76       129.07 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
      263.28       162.05       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
      101.52       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       70.16        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       59.84        20.45        63.09        81.44        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.16        70.22        81.63        84.13        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        43.53        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       75.48        74.14        76.60        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        49.05        41.75        44.02        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       78.28        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
        9.63        44.81        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW 
       51.39        67.50        91.99       113.82        82.85        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        25.81        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       109.28        20.88        23.51         9.63 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 
       12.66        48.53        12.56         3.16        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.92         4.11        12.33        10.92        11.28         0.16 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       10.42        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A 
       12.36         8.28         9.67         9.53         9.50        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       14.43        33.99        12.95        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       56.81        20.88        13.25        13.97        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JF 
       19.20        17.49        16.50        55.50        15.78        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        21.01        12.20        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        21.80        14.50        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.31        16.64        15.16        43.04        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       13.48         4.80         1.61        10.09        13.08        12.26 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       33.37        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       18.51        63.62        69.96        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       28.50        16.47        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        73.64        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX 
       50.07       106.75       102.61         8.75        34.55        43.56 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        38.76        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.03        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       12.33        29.72         9.47        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       23.90        23.84        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       27.85        12.20        39.72        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        18.90        19.99        13.94        10.52        14.43 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       10.16        23.51        15.22        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       33.21       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       75.02        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        32.75        29.23        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       14.70        14.47        14.79        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       15.68         7.46        14.50        19.53        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       17.49        27.91         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       47.01        64.21         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       18.48        21.07        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.26        13.94        17.03         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       52.96        29.03        15.35        16.04       108.07 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.03              0.03 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           282.90            281.29 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            22.95             28.44 
[1] "0.0 - 282.9 (22.9)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q GAIN MUTATED         8        4        1        2        46        31
  9Q GAIN WILD-TYPE      81       81        5        4       307       221
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           0         12          5          7        2
  9Q GAIN WILD-TYPE         2        142         24         58       18
                   vv
clus                STAGE TIS STAGE X
  9Q GAIN MUTATED           0       0
  9Q GAIN WILD-TYPE         1      13
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  8                81
  STAGE IA                 4                81
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               46               307
  STAGE IIB               31               221
  STAGE III                0                 2
  STAGE IIIA              12               142
  STAGE IIIB               5                24
  STAGE IIIC               7                58
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED    23  77  13   6
  9Q GAIN WILD-TYPE 253 547 123  34
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1              23               253
  T2              77               547
  T3              13               123
  T4               6                34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q GAIN MUTATED    56  44   9   9
  9Q GAIN WILD-TYPE 451 314 110  68
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              56               451
  N1              44               314
  N2               9               110
  N3               9                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED   101   2
  9Q GAIN WILD-TYPE 788  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    101    2
  9Q GAIN WILD-TYPE  788   20
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0             101               788
  1               2                20
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED   119   0
  9Q GAIN WILD-TYPE 949  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED    119    0
  9Q GAIN WILD-TYPE  949   12
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE             119               949
  MALE                 0                12
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    46  63
  9Q GAIN WILD-TYPE 383 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     46   63
  9Q GAIN WILD-TYPE  383  455
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               46               383
  YES              63               455
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q GAIN MUTATED                            0                            90
  9Q GAIN WILD-TYPE                          1                           680
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q GAIN MUTATED                               18                   3
  9Q GAIN WILD-TYPE                            182                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9Q GAIN MUTATED                       2                                1
  9Q GAIN WILD-TYPE                     7                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9Q GAIN MUTATED                    1              4
  9Q GAIN WILD-TYPE                 16             43
D18V9, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 90               680
  INFILTRATING LOBULAR CARCINOMA                18               182
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 4                43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0    11
  9Q GAIN WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                          19    83
  9Q GAIN WILD-TYPE                       162   662
D18V11, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     19               162
  WHITE                                         83               662
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V12, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     4 101
  9Q GAIN WILD-TYPE  35 774
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4  101
  9Q GAIN WILD-TYPE   35  774
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                35
  NOT HISPANIC OR LATINO             101               774
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED   179  33
  10P GAIN WILD-TYPE 738 114
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               212                852 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                33                114 
$`10P GAIN MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U 
       43.43        48.10        28.01        18.02        78.41        87.25 
TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0EV TCGA-A2-A0SW TCGA-A2-A0SX 
       24.79        33.76        79.76        31.82        44.88        50.43 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YJ 
       17.13         8.38        49.84        20.75        21.90        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A7-A0DA 
       31.73        19.20        42.44        33.93        91.07        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SA TCGA-A7-A4SD 
       31.73        20.19        23.74        21.73        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06X 
       17.92        14.73        10.29        13.02         1.02        31.00 
TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A08B 
       17.03        43.00         8.98        24.99        45.07        38.01 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09A 
       19.96        37.05        31.00        43.00        30.97         9.99 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A2BK 
       50.04        49.05        25.02        14.01        22.95        73.05 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AS 
       11.44        13.71         1.12         1.78         1.71         0.33 
TCGA-AN-A0FZ TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 
        0.33        81.63        29.13        32.78        21.40        53.03 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A1KR TCGA-AO-A1KS 
       55.33       115.27       106.78        90.58        70.39         0.53 
TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TS TCGA-AR-A0TT 
      130.09         2.56        32.91        19.20        84.10       109.02 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AW 
      107.21       108.36       101.00       103.86        99.32        86.53 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V 
       33.73       160.90        50.89        97.84        77.69       105.30 
TCGA-AR-A251 TCGA-AR-A2LL TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       99.62        66.15       129.57        65.72       112.37       233.62 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0X1 
       84.59       165.76       140.88       255.68       162.05       245.10 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AW TCGA-BH-A0AY 
       43.59       101.52        70.16        18.84        20.45        25.55 
TCGA-BH-A0B6 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C0 TCGA-BH-A0DS TCGA-BH-A0DT 
       81.63        61.51        74.89        41.75         2.56        38.47 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H7 
        9.63        44.81        32.58        31.00        30.35        23.08 
TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN 
       12.89        50.79         5.59        26.66         7.36        67.50 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-C8-A12O 
       12.00        55.69        31.53        97.48       114.15        12.66 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A1HM TCGA-C8-A26X 
       11.77        12.66         3.16        13.51        12.33        12.36 
TCGA-C8-A274 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A147 
        9.53        14.43        13.02        20.88        13.97        19.20 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JL TCGA-D8-A1X5 TCGA-D8-A1X9 
       55.50        18.15        12.03        20.09        18.58        23.90 
TCGA-D8-A1XF TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A3Z6 TCGA-E2-A107 
       15.22        12.99        43.04        15.32        18.51        34.42 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A154 
       47.15        44.68        38.60        63.62        69.96        19.43 
TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A1AZ TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       25.05        18.21        76.57       106.75       102.61         8.75 
TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1RB 
       26.99        34.92        38.76        22.29        36.20        32.09 
TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3QA 
       46.59        41.03         0.69        38.99        12.33        30.18 
TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PB 
       26.40        28.77        25.94        22.82        40.41        19.99 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6SB 
        6.15        19.96        52.73        25.91        10.16        24.99 
TCGA-GI-A2C9 TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-JL-A3YW TCGA-LD-A7W5 
      109.87        79.10        70.85        72.10        11.84         7.10 
TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A8F5 
       10.62        15.32        14.47         2.63         7.46        19.59 
TCGA-MS-A51U TCGA-OL-A5S0 TCGA-OL-A6VO TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA17 
       22.39        20.38        28.21        20.68        19.27        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S 
       17.03         3.81 

$`10P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SH 
       48.36         9.96         8.52        14.37        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
       18.21       143.15       121.94        73.84        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        67.33        34.55        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       118.45        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       35.05        34.29        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 
       54.64        27.12        44.28        17.52        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        32.55        25.28        18.21        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       26.96        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F 
       35.47        30.61        37.45        33.11        29.79        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J 
       23.61        29.56        31.36        24.26        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.70        11.97        13.74        21.17        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R 
       11.05         9.37        10.42         8.75        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 
       53.06        29.03        26.01         1.02        53.98         9.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 
        9.99        10.98         7.99         9.99        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L 
       13.02         0.99        28.96        33.01        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        33.01       112.08        40.01        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98        12.00         9.99        12.00         1.02 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98        33.07         1.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02         0.99        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G 
        0.99        27.02        17.03        38.04         0.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72         1.48        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       23.24        24.79        29.26        16.80        14.53        19.33 
TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       14.96        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        8.22         0.03        20.19         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ 
        0.33         0.23         0.33         0.62         2.96         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         7.46         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J4 TCGA-AO-A0J5 
       95.70        68.75        47.87        58.95        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        20.32        22.36        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        65.10        26.24        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D 
       71.80        99.25       108.72       108.03        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       61.87        17.79        24.79        26.93         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TW 
       32.52       140.55        98.33         5.26        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      134.14       125.16        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX 
       93.90        17.23        37.81        94.29        61.28        86.43 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      112.77       105.27        32.58        98.76        98.66        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       93.30        85.64        71.05        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        54.21        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG 
      143.38       281.29        12.13       275.87        50.70       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       18.77       127.33       129.07        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       263.28       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
       18.35        21.47       113.79       206.86       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.88        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
        7.07        85.35        68.12       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       59.84        63.09        81.44        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       70.22        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       43.53        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        29.98        13.91        78.28        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
        3.22        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       14.30        46.19        24.49        24.43        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        53.26        24.56        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        36.85        51.32 
TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       27.25        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
       32.91         4.90        35.93        20.12        90.84        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       37.74        30.28        55.63        37.55        66.05        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX 
       51.16        91.99       113.82        82.85        42.28        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       17.69        25.81        89.16        24.62       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       48.53        12.56         1.87        12.59        12.92         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.08        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42        12.95        12.33        20.25        12.53 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
       12.95         8.28         9.67         0.03         9.50        24.56 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       33.99        12.95        12.49        13.41        19.46        56.81 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       13.25        20.58        14.17        13.48        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       17.49        16.50        15.78        18.90        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.12        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       12.20        13.32        14.70        17.79        16.73        25.74 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        18.15        12.39        17.16        14.73        21.80 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31        16.64        15.16        16.54        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43        48.03        16.41        13.48         4.80         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 
       10.09        13.08        12.53        12.26        33.37        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       16.18        12.66        25.22        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P 
       40.41        37.51        40.11        28.44        28.87        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       31.96        69.34        18.51        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       50.79        19.56        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       60.36        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       50.07        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 
       34.29        17.69        34.82        32.88        36.82        34.16 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
        6.12         3.02        11.15        48.23        45.01        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
        1.12        46.65         6.58        21.27        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
       32.05        42.25        37.74        39.09        38.37        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.73        40.50        20.12         1.94         7.13        24.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
       29.72         9.47        38.07        32.91        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       23.84        26.70         0.79        25.81        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       15.68        29.95        29.85        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FW 
       13.94        10.52        14.43        34.55        55.00        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC 
       34.03        17.49        23.51        15.22        16.77        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD 
       33.21         7.40        59.57       216.76        83.34        75.02 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12         2.60        62.47        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.22        13.28        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y 
       17.06        14.70        14.79        22.26        16.08        15.68 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 
       14.50        19.53        12.36        17.49        27.91         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         9.93        18.81        18.48        21.07 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ TCGA-W8-A86G 
       13.84        18.87        17.39        17.26        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.33               0.03 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            255.68             282.90 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            29.655             27.185 
[1] "0.3 - 255.7 (29.7)" "0.0 - 282.9 (27.2)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P GAIN MUTATED        17       12        1        1        79        41
  10P GAIN WILD-TYPE      72       73        5        5       274       211
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           0         29          7         13        7
  10P GAIN WILD-TYPE         2        125         22         52       13
                    vv
clus                 STAGE TIS STAGE X
  10P GAIN MUTATED           1       3
  10P GAIN WILD-TYPE         0      10
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  17                 72
  STAGE IA                 12                 73
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                79                274
  STAGE IIB                41                211
  STAGE III                 0                  2
  STAGE IIIA               29                125
  STAGE IIIB                7                 22
  STAGE IIIC               13                 52
  STAGE IV                  7                 13
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED    46 131  23  12
  10P GAIN WILD-TYPE 230 493 113  28
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               46                230
  T2              131                493
  T3               23                113
  T4               12                 28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P GAIN MUTATED   107  58  27  17
  10P GAIN WILD-TYPE 400 300  92  60
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0              107                400
  N1               58                300
  N2               27                 92
  N3               17                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   181   8
  10P GAIN WILD-TYPE 708  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    181    8
  10P GAIN WILD-TYPE  708   14
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0              181                708
  1                8                 14
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED   212   2
  10P GAIN WILD-TYPE 856  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED    212    2
  10P GAIN WILD-TYPE  856   10
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE              212                856
  MALE                  2                 10
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    84 106
  10P GAIN WILD-TYPE 345 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     84  106
  10P GAIN WILD-TYPE  345  412
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                84                345
  YES              106                412
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P GAIN MUTATED                            0                           183
  10P GAIN WILD-TYPE                          1                           587
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P GAIN MUTATED                               16                   4
  10P GAIN WILD-TYPE                            184                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10P GAIN MUTATED                       1                                4
  10P GAIN WILD-TYPE                     8                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10P GAIN MUTATED                    0              6
  10P GAIN WILD-TYPE                 17             41
D19V9, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 183                587
  INFILTRATING LOBULAR CARCINOMA                 16                184
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  6                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  1    11
  10P GAIN WILD-TYPE                                0    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                          53   129
  10P GAIN WILD-TYPE                       128   616
D19V11, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          11                 49
  BLACK OR AFRICAN AMERICAN                      53                128
  WHITE                                         129                616
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V12, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     7 168
  10P GAIN WILD-TYPE  32 707
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      7  168
  10P GAIN WILD-TYPE   32  707
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 32
  NOT HISPANIC OR LATINO              168                707
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED   101  21
  10Q GAIN WILD-TYPE 816 126
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
               122                942 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                21                126 
$`10Q GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A0CM 
       48.10        28.01        18.02        78.41        87.25        24.79 
TCGA-A2-A0EQ TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T7 TCGA-A2-A3XS TCGA-A7-A13E 
       79.76        50.43        17.13        20.75        33.93        20.19 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A8-A06O TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07Z 
       23.74        21.73        13.02        31.00        17.03        45.07 
TCGA-A8-A08B TCGA-A8-A08P TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09Q 
       38.01        31.00        30.97         9.99        50.04        25.02 
TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A62V TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A0FZ 
       14.01        22.95        11.44        13.71         1.78         0.33 
TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J9 TCGA-AO-A128 TCGA-AO-A12A 
       81.63        32.78        21.40        53.03       106.78        90.58 
TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AQ-A54N TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A1AI 
        0.53       130.09         2.56        84.10       109.02       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24S 
      101.00        99.32        86.53       160.90        50.89        97.84 
TCGA-AR-A24U TCGA-AR-A24V TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
       77.69       105.30       129.57        65.72       112.37       233.62 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A409 
      165.76       140.88       162.05        79.63        43.59        18.84 
TCGA-BH-A0AY TCGA-BH-A0B6 TCGA-BH-A0BL TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E6 
       25.55        81.63        74.89         2.56        38.47         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A18L TCGA-BH-A1EN TCGA-BH-A1EV 
       44.81        32.58        31.00        26.66        67.50        12.00 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HM TCGA-C8-A274 
       12.66        11.77        12.66         3.16        12.33         9.53 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF 
       13.02        20.88        19.20        55.50        18.15        12.03 
TCGA-D8-A1X9 TCGA-D8-A1XL TCGA-D8-A1XZ TCGA-E2-A107 TCGA-E2-A14O TCGA-E2-A150 
       23.90        19.92        15.32        34.42        44.68        63.62 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A15G TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1LI 
       69.96        19.43        18.21        14.07        76.57       102.61 
TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1RB TCGA-E9-A1RH 
       26.99        34.92        22.29        36.20        32.09        46.59 
TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5UP TCGA-EW-A1J6 
       41.03        38.99        12.33        30.18        26.40        28.77 
TCGA-EW-A1OV TCGA-EW-A1PC TCGA-EW-A423 TCGA-GM-A2DB TCGA-GM-A2DH TCGA-LD-A9QF 
       25.94         6.15        10.16        79.10        72.10        10.62 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-MS-A51U TCGA-OL-A5S0 
       15.32        14.47         2.63         7.46        22.39        20.38 
TCGA-S3-AA0Z TCGA-S3-AA10 
       20.68        19.27 

$`10Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG 
       48.36         9.96         8.52        14.37        43.43        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V 
       19.20        18.21       143.15       121.94        73.84        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO 
      101.98        55.43        36.13       136.73        99.12       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       98.99       107.93        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72        89.36        80.28       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       18.90        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       26.96        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       35.47        30.61        37.45        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z 
        1.02        17.98        53.06        29.03        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99        24.99         9.99        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00         0.99        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        33.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00         1.02        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
        1.02         8.98        19.04        15.02         0.99        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        73.91         5.72         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62Y 
       29.26        16.80        14.53        19.33        14.96        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
       20.19         1.12         1.32         2.30         0.33         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         2.96         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JA 
       52.18        26.04        37.48        20.32        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.72       108.03        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        40.57        14.73        82.62        61.87        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79        26.93         5.65        15.62        32.52 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV 
       32.91        19.20       140.55        98.33         5.26        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL 
       83.87       134.14       107.21       125.16       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS 
       98.33        96.00        86.07        93.90        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M 
       94.29        61.28        86.43        33.73        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       99.78       118.59         2.76       104.28       112.77       105.27 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       32.58        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG 
      143.38       281.29        12.13       275.87        50.70       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG 
       18.77       127.33        84.59       129.07       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
      212.25       234.28        81.17        78.02       263.28       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       282.90       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        18.35        21.47       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      245.10        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
      139.17       170.17        37.87         7.07        85.35        70.16 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       68.12       103.63        71.15        62.93        59.84        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       63.09        81.44        40.83        39.55        39.16        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       61.51        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
       15.65         3.22        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY 
       15.68        14.30        46.19        24.49        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
       32.91         4.90        35.93        20.12        90.84        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        51.16        91.99       113.82        82.85        42.28 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       55.69        49.58        17.69        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       97.48        24.62       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28        20.88        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.56        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.08        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
       12.36        12.95         8.28         9.67         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
       24.56        14.43        33.99        12.95        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       19.46        56.81        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC 
       13.48        21.14        14.17        17.49        16.50        15.78 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        53.00        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XA 
       14.70        18.58        17.79        16.73        25.74        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       18.15        12.39        17.16        15.22        14.73        21.80 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 
       16.64        12.99        15.16        43.04        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        9.93        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43        48.03        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        1.61        10.09        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       18.51        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       23.34        22.82        17.29        20.71        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        56.94        51.39        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        75.81        28.90        50.07       106.75 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       34.16        36.56        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02        11.15        48.23        45.01 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI 
       40.24         1.12        46.65         6.58        21.27        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       41.72        40.73        40.50        20.12         0.69         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        7.13        24.56        29.72         9.47        38.07        32.91 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.44        23.90        23.84        26.70         0.79        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 
       25.91        22.09        34.03        17.49        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
       59.57       216.76        83.34        75.02        70.85        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
       13.22         7.10        13.28        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR 
       25.05        17.06        14.70        14.79        22.26        16.08 
TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       15.68        14.50        19.53        12.36        19.59        17.49 
TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       18.81        18.48        21.07        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.26        13.94        17.03         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.33               0.03 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            233.62             282.90 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            29.475             27.550 
[1] "0.3 - 233.6 (29.5)" "0.0 - 282.9 (27.5)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q GAIN MUTATED         9        8        0        0        44        28
  10Q GAIN WILD-TYPE      80       77        6        6       309       224
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           0         18          5          5        3
  10Q GAIN WILD-TYPE         2        136         24         60       17
                    vv
clus                 STAGE TIS STAGE X
  10Q GAIN MUTATED           1       1
  10Q GAIN WILD-TYPE         0      12
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  8                 77
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                44                309
  STAGE IIB                28                224
  STAGE III                 0                  2
  STAGE IIIA               18                136
  STAGE IIIB                5                 24
  STAGE IIIC                5                 60
  STAGE IV                  3                 17
  STAGE TIS                 1                  0
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED    25  80  13   5
  10Q GAIN WILD-TYPE 251 544 123  35
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               25                251
  T2               80                544
  T3               13                123
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q GAIN MUTATED    62  37  15   6
  10Q GAIN WILD-TYPE 445 321 104  71
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               62                445
  N1               37                321
  N2               15                104
  N3                6                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED   109   3
  10Q GAIN WILD-TYPE 780  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    109    3
  10Q GAIN WILD-TYPE  780   19
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0              109                780
  1                3                 19
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED   123   1
  10Q GAIN WILD-TYPE 945  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED    123    1
  10Q GAIN WILD-TYPE  945   11
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE              123                945
  MALE                  1                 11
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    51  63
  10Q GAIN WILD-TYPE 378 455
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     51   63
  10Q GAIN WILD-TYPE  378  455
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                51                378
  YES               63                455
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q GAIN MUTATED                            0                           104
  10Q GAIN WILD-TYPE                          1                           666
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q GAIN MUTATED                               10                   3
  10Q GAIN WILD-TYPE                            190                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10Q GAIN MUTATED                       1                                3
  10Q GAIN WILD-TYPE                     8                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10Q GAIN MUTATED                    0              3
  10Q GAIN WILD-TYPE                 17             44
D20V9, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 104                666
  INFILTRATING LOBULAR CARCINOMA                 10                190
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  3                 44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  1     8
  10Q GAIN WILD-TYPE                                0    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                          25    79
  10Q GAIN WILD-TYPE                       156   666
D20V11, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      25                156
  WHITE                                          79                666
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V12, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     5  96
  10Q GAIN WILD-TYPE  34 779
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5   96
  10Q GAIN WILD-TYPE   34  779
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO               96                779
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED   121  17
  11P GAIN WILD-TYPE 796 130
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               138                926 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                130 
$`11P GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A2-A04U TCGA-A2-A04W 
      129.14        20.88        31.79         7.96        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU 
       55.43        24.79        75.25        67.33        80.28        34.29 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A1FW TCGA-A2-A1G1 
        8.38        49.84        20.75        18.21        17.36        19.20 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A26F 
       39.65        91.07        38.30        30.61        29.79        24.26 
TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SD 
       23.74        20.61        10.59        10.29        14.70        14.50 
TCGA-A7-A6VX TCGA-A8-A075 TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I 
       10.42        17.03        18.97         8.98        38.01        12.00 
TCGA-A8-A091 TCGA-A8-A09A TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A0A6 
       33.01         9.99        29.98        33.07        25.02        21.04 
TCGA-A8-A0A7 TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A3QQ TCGA-AC-A62V TCGA-AC-A62Y 
        0.99         0.95         5.72        24.13        11.44        17.42 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FY TCGA-AN-A0XL 
        1.78         9.96         0.33         7.00         0.33         5.36 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A0J3 TCGA-AO-A126 TCGA-AO-A12A TCGA-AO-A12B 
        0.33        80.28        21.40       108.72        90.58        98.27 
TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AR-A0TW TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A250 
      130.09        15.62        98.93        50.89       105.30        89.00 
TCGA-AR-A2LR TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0RS TCGA-B6-A0X0 
       57.27       143.38       129.57       112.37       100.70       129.70 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BT 
       73.51        68.12        62.93        61.51        21.70        45.57 
TCGA-BH-A0DG TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A18M 
       23.44        17.26        15.65        24.43        30.35        72.56 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A209 TCGA-C8-A12O 
       51.16        91.99        26.14        57.83       130.16        12.66 
TCGA-C8-A27A TCGA-D8-A140 TCGA-D8-A1JF TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XY 
       24.56        13.25        12.03        15.22        14.50        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A152 TCGA-E2-A15A 
       15.52        14.14        44.68        34.26        69.96        23.34 
TCGA-E2-A15M TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1BC TCGA-E2-A1II TCGA-E2-A1IU 
       11.05        56.94        76.57        16.47        33.70        11.08 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RB TCGA-E9-A1RE 
       38.76        34.16         6.12        11.15        32.09        46.65 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J1 
       20.12         0.69        38.99         7.13         0.79        18.90 
TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A3U0 TCGA-EW-A423 
       28.77        29.85        23.11        19.99        17.49        10.16 
TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GM-A2DB TCGA-GM-A2DH TCGA-HN-A2NL TCGA-LL-A441 
       24.99        33.21        79.10        72.10         2.60        32.75 
TCGA-LL-A73Y TCGA-OL-A66I TCGA-OL-A6VO TCGA-PL-A8LZ TCGA-S3-AA17 TCGA-UU-A93S 
       15.68        23.47        28.21         9.93        13.94         3.81 

$`11P GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        13.68        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V 
      143.15        18.02        78.41       121.94        73.84        63.12 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        99.12       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        77.19         5.19        98.99       107.93        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN 
       34.55        33.76        61.58        25.22       101.72        89.36 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV 
      118.45        79.76        74.40        72.00        35.05        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 
       44.88        50.43        44.28        17.52        17.13        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        32.55        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       23.77        23.47        60.72        22.45        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
      105.34        10.59        36.23        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A3RF 
       23.80        21.73        22.32        11.34        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01         1.02        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       19.99        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 
       10.98         7.99        24.99         9.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       36.95        13.02         0.99        28.96        33.01        19.96 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       37.05         9.99        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
      112.08        43.00        40.01        30.97        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
       12.00         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       45.07         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-A8-A0AB 
       14.01        12.00        19.04        13.02        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04        22.95        73.91         1.48        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       74.14        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       16.31        14.83        22.19        25.05        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       19.79        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW 
       14.53        19.33        14.96        13.71        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.32         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.62         2.96         1.71         7.36         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL 
        0.33         0.33         6.44         5.65         7.96         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         7.04         0.33         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        0.33         5.33         5.59        61.35        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       95.70        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
       99.25       106.78       108.03        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        40.57        14.73        82.62        61.87        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 
        0.53        17.79        24.79        26.93         5.65        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       84.10       109.02        75.22        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       86.07        93.90        99.32        17.23        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        86.53        86.43        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       97.84       105.27        77.69        32.58        98.76        98.66 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       77.62       281.29        12.13       275.87        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       233.62        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       113.79       206.86       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B 
       37.87         7.07        85.35        70.16        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        70.22        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BL 
       51.68        37.22        32.02        18.21        43.53        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        49.05        41.75        44.02        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        45.83        77.98        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       78.28         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 
       46.19        32.58        24.49        31.00        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA 
       37.78        53.26        24.56        23.08        41.00        52.96 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18P 
       35.93        20.12        90.84        26.66        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       55.63        37.55        66.05         7.36        51.39        67.50 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       63.35        55.00        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       28.14        38.60        83.31        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        48.53        12.56         3.16        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87        12.59        12.92         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       10.92        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       19.46        56.81        20.88        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       55.50        15.78        18.15        18.90        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.80        19.92        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       43.04        15.32         9.93        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         1.61        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        75.98        43.33        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        18.51        63.62        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        25.05        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        50.79        19.56        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BD TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.73        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       22.19        60.99        54.18        60.36        73.64        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        75.81        28.90        50.07       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        26.99        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        22.29        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA 
       28.27        34.95         2.56         3.02        48.23        45.01 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A248 TCGA-E9-A24A 
       41.03        41.72        40.73        40.50         1.94        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.33        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       30.44        23.90        23.84        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 
       27.85        12.20        39.72         8.48        18.21        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ 
       16.57        15.68        25.94        22.82        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 
       34.03        23.51        15.22        16.77        31.30         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
      109.87        59.57       216.76        83.34        75.02        70.85 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 
       13.22         7.10        13.28        10.62        24.95        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       25.05        17.06        15.32        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       22.26         2.63        16.08         7.46        14.50        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.16         0.26        18.81        18.48        21.07        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 
       19.27        13.84        18.87        17.39        17.26        17.03 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       66.84        11.41        52.96        29.03        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.33               0.03 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            143.38             282.90 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            24.345             28.440 
[1] "0.3 - 143.4 (24.3)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P GAIN MUTATED        10       15        1        2        52        28
  11P GAIN WILD-TYPE      79       70        5        4       301       224
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           0         15          3          6        4
  11P GAIN WILD-TYPE         2        139         26         59       16
                    vv
clus                 STAGE TIS STAGE X
  11P GAIN MUTATED           0       2
  11P GAIN WILD-TYPE         1      11
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 15                 70
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA                52                301
  STAGE IIB                28                224
  STAGE III                 0                  2
  STAGE IIIA               15                139
  STAGE IIIB                3                 26
  STAGE IIIC                6                 59
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED    34  84  15   4
  11P GAIN WILD-TYPE 242 540 121  36
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               34                242
  T2               84                540
  T3               15                121
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P GAIN MUTATED    75  41  10   9
  11P GAIN WILD-TYPE 432 317 109  68
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               75                432
  N1               41                317
  N2               10                109
  N3                9                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED   115   4
  11P GAIN WILD-TYPE 774  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    115    4
  11P GAIN WILD-TYPE  774   18
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0              115                774
  1                4                 18
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED   136   2
  11P GAIN WILD-TYPE 932  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED    136    2
  11P GAIN WILD-TYPE  932   10
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE              136                932
  MALE                  2                 10
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    50  70
  11P GAIN WILD-TYPE 379 448
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     50   70
  11P GAIN WILD-TYPE  379  448
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                50                379
  YES               70                448
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P GAIN MUTATED                            0                           113
  11P GAIN WILD-TYPE                          1                           657
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P GAIN MUTATED                               12                   1
  11P GAIN WILD-TYPE                            188                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11P GAIN MUTATED                       2                                1
  11P GAIN WILD-TYPE                     7                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11P GAIN MUTATED                    2              7
  11P GAIN WILD-TYPE                 15             40
D21V9, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 113                657
  INFILTRATING LOBULAR CARCINOMA                 12                188
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  7                 40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     5
  11P GAIN WILD-TYPE                                1    55
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                          22    97
  11P GAIN WILD-TYPE                       159   648
D21V11, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 55
  BLACK OR AFRICAN AMERICAN                      22                159
  WHITE                                          97                648
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V12, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     7 111
  11P GAIN WILD-TYPE  32 764
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      7  111
  11P GAIN WILD-TYPE   32  764
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 32
  NOT HISPANIC OR LATINO              111                764
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    77  17
  11Q GAIN WILD-TYPE 840 130
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                94                970 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                17                130 
$`11Q GAIN MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EU TCGA-A2-A0EY 
       20.88        31.79        67.33        80.28        34.29        63.29 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A0CD TCGA-A7-A26F 
       18.21        18.61        19.20        91.07        38.30        24.26 
TCGA-A7-A26G TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A6VX TCGA-A8-A075 TCGA-A8-A07F 
       23.74        10.59        10.29        10.42        17.03        18.97 
TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A09A TCGA-A8-A09Q 
       18.97         8.98        38.01        12.00         9.99        25.02 
TCGA-A8-A0A7 TCGA-AC-A62V TCGA-AC-A62Y TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0FK 
        0.99        11.44        17.42         1.78         9.96         7.00 
TCGA-AN-A0FY TCGA-AN-A0XU TCGA-AO-A12A TCGA-AO-A12B TCGA-AQ-A04L TCGA-AR-A0TW 
        0.33         0.33        90.58        98.27       130.09        98.93 
TCGA-AR-A24K TCGA-AR-A24V TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0X0 
       50.89       105.30        65.72       165.76       100.70       129.70 
TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0DG 
       73.51        68.12        61.51        21.70        45.57        23.44 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0GY TCGA-BH-A18M TCGA-BH-A18T TCGA-BH-A18U 
       17.26        15.65        30.35        72.56         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       51.16        91.99       114.15        26.14        38.60        57.83 
TCGA-BH-A209 TCGA-D8-A140 TCGA-D8-A1JF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XW 
      130.16        13.25        12.03        21.80        14.50        43.04 
TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15R TCGA-E2-A1AZ 
       16.54        14.14        69.96        23.34        56.94        76.57 
TCGA-E2-A1B0 TCGA-E2-A1II TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1R6 TCGA-E9-A1RB 
       53.62        33.70        38.76        34.16        11.15        32.09 
TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A1P8 
        0.69         7.13         0.79        28.77        23.11         7.86 
TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GM-A2DB TCGA-GM-A2DH 
       22.09        17.49        24.99        33.21        79.10        72.10 
TCGA-LL-A441 TCGA-OL-A66I TCGA-PL-A8LZ TCGA-UU-A93S 
       32.75        23.47         9.93         3.81 

$`11Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       14.27        47.24        13.68         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       89.36       118.45        79.76        74.40        72.00        35.05 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       48.46        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       35.93        50.37        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        26.96        21.14        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       35.47        30.61        37.45        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J1 
       23.80        21.73        20.61        22.32        11.34        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       21.17        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        43.00        19.99        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       32.05         9.99        10.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       45.07        15.06        36.95        13.02         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       30.97        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB 
       12.00        19.04        13.02        21.04        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95        22.95        73.91         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU 
       24.79        29.26        16.80        14.53        19.33        14.96 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       13.71        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.96         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        61.35        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       95.70        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       65.10        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12D 
      115.27        99.25       108.72       106.78       108.03        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      140.55        98.33         5.26        84.10       109.02        75.22 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       97.68        98.33        96.00        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        94.29        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28       112.77        97.84       105.27        77.69 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       32.58        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       281.29        12.13       275.87       129.57        50.70 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       113.79       206.86       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B 
       37.87         7.07        85.35        70.16        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        62.93        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       81.44        40.83        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.95        49.94        77.95        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI 
       89.06        90.97        45.83        77.98        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       13.91        78.28         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.58        24.49        31.00        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       32.91         4.90        35.93        20.12        90.84        26.66 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A1EN 
       37.74        30.28        55.63        37.55        66.05        67.50 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       83.31        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
       20.88        18.64        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56         3.16        13.51         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.92         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.28         0.16        12.03        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         9.53         0.03         9.50        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       19.46        56.81        20.88        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       55.50        15.78        18.15        18.90        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       18.97        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        15.22        14.73        19.92        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         9.93        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
        4.80         1.61        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       32.02        31.96        69.34        18.51        63.62        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C 
       19.43        21.04        23.87        14.79        25.05        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       14.07        51.39        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        60.36        73.64        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        50.07       106.75       102.61         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       26.99        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.20        36.56        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC 
        2.56         6.12         3.02        48.23        45.01        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 
       41.03        41.72        40.73        40.50        20.12        38.99 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        15.68        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       52.96        29.82        18.48        30.08        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       55.00        52.73        25.91        34.03        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       15.22        16.77        31.30         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK 
      216.76        83.34        75.02        70.85        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        7.10        13.28        10.62        24.95        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       17.06        15.32        14.70        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       86.96         0.16         0.26        18.81        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.33               0.03 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            165.76             282.90 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            25.005             28.075 
[1] "0.3 - 165.8 (25.0)" "0.0 - 282.9 (28.1)"
[1] "hr=" "1.4"
D22V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q GAIN MUTATED         9        6        0        2        34        23
  11Q GAIN WILD-TYPE      80       79        6        4       319       229
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           0          9          3          4        2
  11Q GAIN WILD-TYPE         2        145         26         61       18
                    vv
clus                 STAGE TIS STAGE X
  11Q GAIN MUTATED           1       1
  11Q GAIN WILD-TYPE         0      12
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  6                 79
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                34                319
  STAGE IIB                23                229
  STAGE III                 0                  2
  STAGE IIIA                9                145
  STAGE IIIB                3                 26
  STAGE IIIC                4                 61
  STAGE IV                  2                 18
  STAGE TIS                 1                  0
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED    22  59   8   4
  11Q GAIN WILD-TYPE 254 565 128  36
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               22                254
  T2               59                565
  T3                8                128
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q GAIN MUTATED    48  33   7   5
  11Q GAIN WILD-TYPE 459 325 112  72
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               48                459
  N1               33                325
  N2                7                112
  N3                5                 72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    83   2
  11Q GAIN WILD-TYPE 806  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     83    2
  11Q GAIN WILD-TYPE  806   20
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               83                806
  1                2                 20
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    93   1
  11Q GAIN WILD-TYPE 975  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     93    1
  11Q GAIN WILD-TYPE  975   11
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               93                975
  MALE                  1                 11
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    29  47
  11Q GAIN WILD-TYPE 400 471
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     29   47
  11Q GAIN WILD-TYPE  400  471
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                29                400
  YES               47                471
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q GAIN MUTATED                            0                            77
  11Q GAIN WILD-TYPE                          1                           693
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q GAIN MUTATED                                4                   2
  11Q GAIN WILD-TYPE                            196                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11Q GAIN MUTATED                       1                                2
  11Q GAIN WILD-TYPE                     8                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11Q GAIN MUTATED                    1              7
  11Q GAIN WILD-TYPE                 16             40
D22V9, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  77                693
  INFILTRATING LOBULAR CARCINOMA                  4                196
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  7                 40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     1
  11Q GAIN WILD-TYPE                                1    59
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                          18    66
  11Q GAIN WILD-TYPE                       163   679
D22V11, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           1                 59
  BLACK OR AFRICAN AMERICAN                      18                163
  WHITE                                          66                679
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V12, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     5  76
  11Q GAIN WILD-TYPE  34 799
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5   76
  11Q GAIN WILD-TYPE   34  799
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO               76                799
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   194  32
  12P GAIN WILD-TYPE 723 115
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               226                838 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                32                115 
$`12P GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P 
      129.14        48.10        39.32        28.01        19.20        18.02 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D0 
       73.84        87.25        77.19         5.19        56.81        67.33 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0YE TCGA-A2-A0YH 
       35.05        34.29        31.82        63.29        18.21        21.67 
TCGA-A2-A0YM TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XW TCGA-A7-A0CD 
       31.73        17.36        19.20        33.93        56.28        38.30 
TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD 
       35.31        29.79        20.19        25.15        20.61        22.32 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.70        13.74        14.50        21.17        14.73        12.10 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A07U 
        9.37        10.42        53.98         9.01         8.98        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S 
        9.99        45.07        19.96        37.05        31.00        33.01 
TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 
       30.97         9.99         1.02         1.02        14.01        12.00 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A5XU 
       27.02        22.95        26.04        33.04        16.57        14.96 
TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0FJ TCGA-AN-A0FT TCGA-AN-A0FW 
       13.71         0.33         1.78         7.96         7.04         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P 
        0.33         0.33         0.33        80.28        66.77        95.70 
TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A124 TCGA-AO-A12E 
       32.78        20.32        53.03        72.00       115.27        57.30 
TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TQ 
       48.36        61.87         0.53         5.65        32.91        98.33 
TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AQ TCGA-AR-A1AV TCGA-AR-A24H 
       83.87       107.21       103.86        99.32        61.28       160.90 
TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LM 
      104.28       105.30        32.58        98.66        89.00        63.62 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I2 TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0WV 
       57.27        73.35       143.38       165.76       162.05        79.63 
TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A400 TCGA-B6-A402 
      113.79       245.10        43.59        73.51         7.07        70.16 
TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B5 TCGA-BH-A0B9 TCGA-BH-A0BA 
       68.12        62.93        59.84        70.22        51.68        37.22 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0E0 
       61.51        74.89        45.57        44.02        45.83         4.41 
TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0HX TCGA-BH-A0WA TCGA-BH-A18K 
       44.81        24.49        30.35        27.25        23.05        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU 
       26.66        37.74        37.55        51.16        91.99        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A202 TCGA-BH-A203 
       12.00        55.69       114.15        45.63        26.14        38.60 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12O 
       18.64        23.51         9.63        18.87        11.93        12.66 
TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A278 
       12.66         3.16        12.03        12.33         8.28         9.50 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD 
       20.88        14.17        19.20        14.17        15.78        18.15 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XY 
       20.09        19.40        17.16        21.80        12.99        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 
       15.32        15.52        13.48        10.09        12.26        18.51 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14W 
       34.42        46.59        37.51        40.11        44.68        32.02 
TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A15S TCGA-E2-A1AZ 
       69.96        23.34        18.21        50.79        14.07        76.57 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 
       33.73        33.70        43.04        26.99         8.28        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB 
       34.16        36.20        35.24         9.86        11.15        32.09 
TCGA-E9-A1RC TCGA-E9-A1RG TCGA-E9-A22D TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A295 
       40.24        21.27        41.03        20.12        38.99        12.33 
TCGA-E9-A2JS TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 
       29.72        28.77        22.82        29.82        23.11         7.86 
TCGA-EW-A2FV TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A3XL 
       25.91        24.99       109.87        75.02        85.15        69.30 
TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A6FP 
        2.60        21.24         7.10        24.95        32.75        22.26 
TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A5RZ TCGA-OL-A66O TCGA-S3-A6ZF 
        2.63        19.53        34.92        22.32        17.36        18.81 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-Z7-A8R5 
       18.48        19.27        17.03       108.07 

$`12P GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        13.68        31.79         7.96        18.21       143.15 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       78.41       121.94        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D2 
      107.93        75.25        98.99       107.93        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72        89.36        80.28       118.45 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       79.76        74.40        72.00        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI 
       20.75        32.55        25.28        50.47        21.90        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX 
       18.61        19.33        48.46        23.77        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        91.07        29.98        32.75        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       26.96        21.14        21.90        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13G TCGA-A7-A13H 
       37.45        35.67        33.11        31.73        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY 
       31.36        24.26        23.74        23.80        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VY TCGA-A8-A06O 
       17.92        10.72        11.05        10.29         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        17.03        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
        7.99        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       28.96        33.01        12.00         9.99        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
      112.08        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
       12.00         9.99        12.00        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB 
        0.99        19.04        13.02        21.04         0.99        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        73.91         5.72         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       74.14        19.33        14.66        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 
       14.83        22.19        24.13        25.05        14.99        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       15.48        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       19.33        11.44        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        2.30         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         9.96         7.36         7.46         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         0.33         6.44         5.65         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        7.17         6.90         0.33         5.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        61.35        81.63        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       29.13        21.40        52.18        26.04        37.48        22.36 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G 
      106.78       108.03        90.58        98.27        64.04        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H 
       40.57        14.73        82.62        70.39        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
       26.93       130.09        15.62        32.52         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
      140.55         5.26        84.10       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       64.83        55.86       107.24        65.36       133.22       134.14 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      125.16       108.36       101.00        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       86.07        93.90        17.23        37.81        94.29        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.43        33.73        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       112.77        97.84       105.27        77.69 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.76        99.62        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        66.15        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       39.39        40.54        33.30        38.96        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        12.13       275.87       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       81.17        78.02       263.28       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
       89.46       282.90       157.41        97.48       188.68        18.35 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
       21.47       206.86       129.70        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A409 
      101.52       139.17       170.17        37.87        85.35        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
      103.63        71.15        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BC 
       40.83        39.55        39.16        81.63        84.13        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       18.21        43.53        21.70        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       74.14        76.60        53.95        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       41.75        89.06        90.97        77.98        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       29.98        13.91        78.28        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        67.86        70.88        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       14.30         9.63        46.19        32.58        31.00        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        51.32        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18S 
       35.93        20.12        72.56        30.28        55.63        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX 
        7.36        51.39        67.50       113.82        82.85        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 
       55.00        72.07       144.59        72.07        28.14        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 
      109.28        20.88         5.26         9.70        21.76         9.44 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53        12.56        13.51         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       11.28         0.16        10.42        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.53        12.36        12.95         9.67         9.53         0.03 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       24.56        14.43        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        56.81        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JE 
       13.48        21.14        17.49        16.50        55.50        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       12.03        53.00        14.01        18.97        20.09        20.12 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       12.39        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
       55.30        16.41        15.85        16.31        16.64        15.16 
TCGA-D8-A1XW TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       43.04         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43        48.03        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U 
        1.61        13.08        12.53        33.37        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10E 
       12.66        25.22        43.00        27.52        40.41        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       75.98        43.33        34.26        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       63.62        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H 
       25.05        22.82        17.29        20.71        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P 
       55.63        53.92         9.04        20.58        11.05        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       56.94        51.39        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        60.36        73.64        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       28.90        50.07       106.75       102.61         8.75        34.55 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       34.82        32.88        36.82        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        25.84        18.94        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD 
        2.56         6.12         3.02        48.23        45.01         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       46.65         6.58        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT 
       40.50         0.69         1.94         7.13        24.56         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       38.07        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       26.70         0.79        25.81        26.40        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       39.78        52.96        18.48        30.08        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       55.00        52.73        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       23.51        15.22        16.77        31.30        33.21         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.47        11.84        11.57        13.22        13.28        10.62 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       29.23        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 
       14.79        16.08        15.68         7.46        14.50        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        40.08        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        26.04        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
        8.91        47.01        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        9.93        21.07        20.68        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       17.26        13.94         3.81        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       29.03        15.35        16.04       107.05 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.33               0.03 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             245.1              282.9 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             27.63              27.88 
[1] "0.3 - 245.1 (27.6)" "0.0 - 282.9 (27.9)"
[1] "hr=" "1.1"
D23V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P GAIN MUTATED        18       16        0        3        77        45
  12P GAIN WILD-TYPE      71       69        6        3       276       207
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           0         37          6         18        4
  12P GAIN WILD-TYPE         2        117         23         47       16
                    vv
clus                 STAGE TIS STAGE X
  12P GAIN MUTATED           0       3
  12P GAIN WILD-TYPE         1      10
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  18                 71
  STAGE IA                 16                 69
  STAGE IB                  0                  6
  STAGE II                  3                  3
  STAGE IIA                77                276
  STAGE IIB                45                207
  STAGE III                 0                  2
  STAGE IIIA               37                117
  STAGE IIIB                6                 23
  STAGE IIIC               18                 47
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED    45 148  26   9
  12P GAIN WILD-TYPE 231 476 110  31
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1               45                231
  T2              148                476
  T3               26                110
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P GAIN MUTATED   110  64  29  21
  12P GAIN WILD-TYPE 397 294  90  56
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0              110                397
  N1               64                294
  N2               29                 90
  N3               21                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   192   5
  12P GAIN WILD-TYPE 697  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    192    5
  12P GAIN WILD-TYPE  697   17
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              192                697
  1                5                 17
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   224   5
  12P GAIN WILD-TYPE 844   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    224    5
  12P GAIN WILD-TYPE  844    7
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE              224                844
  MALE                  5                  7
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    86 116
  12P GAIN WILD-TYPE 343 402
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     86  116
  12P GAIN WILD-TYPE  343  402
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                86                343
  YES              116                402
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P GAIN MUTATED                            1                           181
  12P GAIN WILD-TYPE                          0                           589
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P GAIN MUTATED                               28                   2
  12P GAIN WILD-TYPE                            172                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12P GAIN MUTATED                       2                                8
  12P GAIN WILD-TYPE                     7                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12P GAIN MUTATED                    1              5
  12P GAIN WILD-TYPE                 16             42
D23V9, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 181                589
  INFILTRATING LOBULAR CARCINOMA                 28                172
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  5                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     9
  12P GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          43   155
  12P GAIN WILD-TYPE                       138   590
D23V11, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 51
  BLACK OR AFRICAN AMERICAN                      43                138
  WHITE                                         155                590
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V12, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     5 186
  12P GAIN WILD-TYPE  34 689
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      5  186
  12P GAIN WILD-TYPE   34  689
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              186                689
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED   162  27
  12Q GAIN WILD-TYPE 755 120
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               189                875 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                27                120 
$`12Q GAIN MUTATED`
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04U TCGA-A2-A0CS 
       39.32        28.01        19.20        18.02        87.25        77.19 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SW 
       56.81        67.33        35.05        34.29        31.82        44.88 
TCGA-A2-A0T7 TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E 
       20.75        21.67        17.36        19.20        42.44       105.34 
TCGA-A2-A3XW TCGA-A7-A0CD TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26J TCGA-A7-A2KD 
       56.28        38.30        29.79        25.15        20.61        22.32 
TCGA-A7-A425 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A8-A06R TCGA-A8-A06T 
       14.70        13.74        21.17        14.73        17.98        53.06 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A07Z 
       53.98         9.01        10.98         8.98         9.99        45.07 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09A 
       19.96        37.05        31.00        33.01        30.97         9.99 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0A1 TCGA-AC-A23E 
        1.02        45.07         1.02        14.01        12.00        22.95 
TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A3W5 TCGA-AC-A5XU TCGA-AC-A62X TCGA-AN-A03Y 
        5.72        26.04        16.57        14.96        13.71         0.33 
TCGA-AN-A0FF TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N 
        5.65         7.04         0.36         0.33        80.28        66.77 
TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A12E 
       95.70        32.78        20.32        53.03        72.00        57.30 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR 
       61.87         0.53         5.65        32.91        98.33         5.26 
TCGA-AR-A0U2 TCGA-AR-A1AK TCGA-AR-A1AV TCGA-AR-A24M TCGA-AR-A24Q TCGA-AR-A24V 
       83.87       103.86        61.28       120.33       104.28       105.30 
TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LM TCGA-AR-A5QM TCGA-B6-A0IO 
       32.58        98.66        89.00        63.62        73.35       165.76 
TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI 
      162.05        79.63       113.79       245.10        43.59        73.51 
TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BT 
       68.12        62.93        70.22        37.22        74.89        45.57 
TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0E7 TCGA-BH-A0EB TCGA-BH-A0GY 
       77.95        44.02        45.83        44.81        24.49        30.35 
TCGA-BH-A0H7 TCGA-BH-A0HX TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18N 
       23.08        27.25        23.05        90.84        26.66        37.74 
TCGA-BH-A18R TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1FC TCGA-BH-A1FM 
       37.55        42.28        12.00        55.69       114.15        45.63 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A130 
       23.51         9.63        18.87        11.93        12.66         3.16 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A278 TCGA-D8-A13Z 
        4.08        11.28        12.03         8.28         9.50        20.88 
TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1XD TCGA-D8-A1XJ 
       14.17        15.78        18.15        18.90        17.16        21.80 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W 
       12.99        16.54        15.32        13.48        10.09        12.26 
TCGA-D8-A3Z6 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O 
       18.51        34.42        46.59        37.51        40.11        44.68 
TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A15S 
       32.02        69.96        23.34        18.21        50.79        14.07 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L8 TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E9-A1N6 
       33.73        33.70        73.64        43.04         8.28        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RB 
       34.16        36.20        35.24         9.86        11.15        32.09 
TCGA-E9-A1RC TCGA-E9-A22D TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y 
       40.24        41.03        38.99        12.33        29.72        23.84 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A2FV TCGA-GM-A2DI 
       28.77        22.82        29.85        23.11        25.91        85.15 
TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A6FQ 
        2.60        21.24         7.10        15.32        22.26         2.63 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-OL-A5RV TCGA-OL-A66O TCGA-S3-A6ZF TCGA-S3-A6ZG 
       14.50        19.53        34.92        17.36        18.81        18.48 
TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-Z7-A8R5 
       19.27        17.03       108.07 

$`12Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V 
       18.21       143.15        78.41       121.94        73.84        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU 
      114.81        92.48        88.60       107.93        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       98.99       107.93        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       72.00        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       27.12        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        50.47        21.90        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       48.46        31.73        23.77        23.47        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       20.25        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15        10.59        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       29.98        32.75        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H 
       35.67        33.11        31.73        20.19        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A3IY 
       31.36        24.26        23.74        23.80        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        11.28        13.41        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        17.92        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B 
       29.03        31.00        26.01         1.02        17.03        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        9.99         7.99        24.99        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L 
        0.99        38.01        28.96        33.01        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99       112.08        43.00        40.01        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D 
       17.95        41.98        12.00         9.99        12.00        50.04 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       49.05        29.98        33.07        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       15.02         0.99        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A2B8 
       27.02        17.03        38.04         0.95        73.91         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       87.12        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV 
       16.80        14.53        19.33        11.44        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         2.30         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.62         2.96         1.78         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.46         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        7.96         7.00         7.59         7.17         6.90         0.33 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       61.35        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA 
       21.40        52.18        26.04        37.48        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F 
      106.78       108.03        90.58        98.27        64.04        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KT 
       41.62        40.57        14.73        82.62        70.39        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93       130.09        15.62        32.52         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       19.20       140.55        84.10       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       64.83        55.86       107.24        65.36       133.22       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM 
      107.21       125.16       108.36       101.00        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       96.00        86.07        93.90        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K 
       94.29        86.53        86.43        33.73       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S 
       94.22        99.78       118.59         2.76       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
      105.27        77.69        98.76        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       71.05        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       66.15        38.17        39.39        40.54        57.27        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      275.87       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      233.62        18.77       127.33        84.59       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      263.28       102.77       140.48       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ 
      157.41        97.48       188.68        18.35        21.47       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN 
      129.70        28.27        68.94        58.88       101.52       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 
      170.17        37.87         7.07        85.35        70.16        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
      103.63        71.15        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 
       81.44        40.83        39.55        39.16        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       51.68        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       49.94        49.05        41.75        89.06        90.97        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30         9.63        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        31.00        24.43        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P 
       32.91         4.90        35.93        20.12        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       55.63        66.05         7.36        51.39        51.16        67.50 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       91.99       113.82        82.85        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       31.53        89.16        97.48        24.62       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 
      109.28        20.88        18.64         5.26         9.70        21.76 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
        9.44        11.77        11.77        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 
       12.66        12.66        12.66        48.53        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.87        12.59        12.92         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.34         0.16        10.42        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
       20.25        12.53        12.36        12.95         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03        24.56        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        56.81        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 
       13.97        14.17        13.48        21.14        19.20        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       16.50        55.50        12.03        53.00        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       25.74        23.90        27.58        18.15        12.39        15.22 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        14.50        19.92        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       15.85        16.31        16.64        15.16        43.04        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        9.93        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43        48.03        16.41         4.80         1.61 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       13.08        12.53        33.37        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F 
       25.22        43.00        27.52        40.41        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       47.15        40.96        38.24        38.60        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        31.96        69.34        18.51        63.62 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        11.05        19.56        56.94 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        60.36        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 
       50.07       106.75       102.61         8.75        26.99        34.55 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       34.82        32.88        36.82        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.77        25.84        18.94        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RD 
        2.56         6.12         3.02        48.23        45.01         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E 
       32.05        42.25        37.74        39.09        38.37        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       40.73        40.50        20.12         0.69         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        26.70         0.79        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       16.57        15.68        25.94        29.95        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        29.82        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        52.73        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       17.49        10.16        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
       79.10        83.34        75.02        70.85        72.10        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.47        11.84        11.57        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
       24.95        32.75        29.23        25.05        17.06        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A7T0 
       14.47        14.79        16.08        15.68         7.46        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        58.62        40.08        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       24.72        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       41.92        42.77        26.04        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       40.11         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        0.26         9.93        21.07        20.68        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.39        17.26        13.94         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       107.05 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.33               0.03 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             245.1              282.9 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             27.25              27.91 
[1] "0.3 - 245.1 (27.2)" "0.0 - 282.9 (27.9)"
[1] "hr=" "1.2"
D24V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q GAIN MUTATED        14       12        0        1        58        39
  12Q GAIN WILD-TYPE      75       73        6        5       295       213
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           0         39          6         15        4
  12Q GAIN WILD-TYPE         2        115         23         50       16
                    vv
clus                 STAGE TIS STAGE X
  12Q GAIN MUTATED           0       2
  12Q GAIN WILD-TYPE         1      11
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  14                 75
  STAGE IA                 12                 73
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                58                295
  STAGE IIB                39                213
  STAGE III                 0                  2
  STAGE IIIA               39                115
  STAGE IIIB                6                 23
  STAGE IIIC               15                 50
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED    35 123  24   9
  12Q GAIN WILD-TYPE 241 501 112  31
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1               35                241
  T2              123                501
  T3               24                112
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q GAIN MUTATED    77  60  30  18
  12Q GAIN WILD-TYPE 430 298  89  59
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               77                430
  N1               60                298
  N2               30                 89
  N3               18                 59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   161   5
  12Q GAIN WILD-TYPE 728  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    161    5
  12Q GAIN WILD-TYPE  728   17
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0              161                728
  1                5                 17
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   186   5
  12Q GAIN WILD-TYPE 882   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    186    5
  12Q GAIN WILD-TYPE  882    7
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE              186                882
  MALE                  5                  7
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    79  91
  12Q GAIN WILD-TYPE 350 427
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     79   91
  12Q GAIN WILD-TYPE  350  427
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                79                350
  YES               91                427
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q GAIN MUTATED                            0                           150
  12Q GAIN WILD-TYPE                          1                           620
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q GAIN MUTATED                               26                   1
  12Q GAIN WILD-TYPE                            174                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12Q GAIN MUTATED                       0                                9
  12Q GAIN WILD-TYPE                     9                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12Q GAIN MUTATED                    1              3
  12Q GAIN WILD-TYPE                 16             44
D24V9, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 150                620
  INFILTRATING LOBULAR CARCINOMA                 26                174
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  3                 44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     9
  12Q GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          34   125
  12Q GAIN WILD-TYPE                       147   620
D24V11, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 51
  BLACK OR AFRICAN AMERICAN                      34                147
  WHITE                                         125                620
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V12, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     4 152
  12Q GAIN WILD-TYPE  35 723
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4  152
  12Q GAIN WILD-TYPE   35  723
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              152                723
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    79  13
  13Q GAIN WILD-TYPE 838 134
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                92                972 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                13                134 
$`13Q GAIN MUTATED`
TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0YJ TCGA-A2-A1FW 
       31.79        73.84        35.05        63.29        18.61        17.36 
TCGA-A2-A1G1 TCGA-A7-A0DA TCGA-A7-A26F TCGA-A7-A3J0 TCGA-A8-A07R TCGA-A8-A08G 
       19.20        35.67        24.26        10.29         8.98        19.96 
TCGA-A8-A08J TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09C TCGA-AC-A2FM 
       37.05        33.01        41.98        12.00         1.02        26.04 
TCGA-AC-A5XU TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FW 
       14.96         0.33         0.23         0.33         7.04         0.36 
TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AO-A03U TCGA-AO-A0J7 TCGA-AO-A0JB TCGA-AO-A12A 
        0.33        12.33        58.95        20.32        50.70        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AR-A0TT TCGA-AR-A0U3 TCGA-AR-A24U TCGA-AR-A250 
       98.27        64.04       109.02       134.14        77.69        89.00 
TCGA-AR-A2LR TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0WY 
       57.27       165.76       255.68       162.05       100.70       113.79 
TCGA-BH-A0B9 TCGA-BH-A0BT TCGA-BH-A0E2 TCGA-BH-A0EB TCGA-BH-A0HQ TCGA-BH-A18N 
       51.68        45.57        14.30        24.49        36.85        37.74 
TCGA-BH-A18V TCGA-BH-A1EX TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A5IZ TCGA-BH-A6R9 
       51.16        49.58        72.07        57.83        18.64         5.26 
TCGA-C8-A12L TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A275 TCGA-D8-A141 TCGA-D8-A1JF 
       11.93        13.51        12.59         0.03        20.58        12.03 
TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A14T TCGA-E2-A14X 
       15.22        21.80        10.09        12.26        75.98        31.96 
TCGA-E2-A14Y TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A1BD TCGA-E2-A1L9 TCGA-E2-A1LH 
       69.34        19.43        20.71        37.25        19.66       106.75 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1R3 TCGA-E9-A1RF 
       38.76        34.16        41.62        35.24         2.56         6.58 
TCGA-E9-A248 TCGA-E9-A5FL TCGA-EW-A1J6 TCGA-EW-A1P7 TCGA-EW-A2FV TCGA-EW-A423 
        1.94         0.79        28.77        30.08        25.91        10.16 
TCGA-EW-A6SA TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-MS-A51U 
       16.77        11.57         7.10         2.63        15.68        22.39 
TCGA-S3-A6ZG TCGA-UU-A93S 
       18.48         3.81 

$`13Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        13.68         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       56.81        67.33        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       72.00        34.29        31.82        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        49.48        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        36.23        39.65        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.90        38.30        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       23.61        29.56        31.36        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        22.32        11.34        10.59        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99         9.99        45.07        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I 
       13.02         0.99        38.01        28.96        33.01        12.00 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
        9.99        31.00        31.00         0.99        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A099 TCGA-A8-A09A 
       43.00        40.01        30.97        17.95         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        60.92        87.12        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       23.24        24.79        29.26        16.80        14.53        19.33 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       11.44        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        2.30         0.33         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.71         9.96         7.36         7.46         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        7.17         6.90         0.33         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        61.35        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       95.70        68.75        47.87        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       52.18        26.04        37.48        22.36        53.03        21.53 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
      106.78       108.03        57.30        48.36        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       84.10        75.22        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       133.22        83.87       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       93.90        99.32        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       86.53        86.43        33.73       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
       97.84       105.27       105.30        32.58        98.76        98.66 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       39.39        40.54        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH 
      127.33        84.59       129.07       140.88        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        81.17        78.02       263.28       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      170.17        37.87         7.07        85.35        70.16        68.12 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       18.84       103.63        71.15        62.93        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       25.55        63.09        81.44        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       70.22        81.63        84.13        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       43.53        61.51        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       75.48        74.14        76.60        53.95        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        89.06        90.97        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        23.44        38.01        29.98        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 
       70.88        16.27         4.41        15.68         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       46.19        32.58        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        53.26        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P 
       35.93        20.12        90.84        26.66        72.56        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       55.63        37.55        66.05         7.36        51.39        67.50 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        45.63       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        38.60        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       109.28        20.88        23.51         9.63 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A135 
       12.66        48.53        12.56         3.16         1.87        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        4.11         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
        0.16        12.03        10.42        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       20.25        12.53        12.36        12.95         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         9.50        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        55.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        53.00        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK 
       27.58        18.15        12.39        17.16        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         1.61        13.08        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 
       33.17        43.33        34.26        32.02        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       69.96        23.24        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        17.29        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        16.47        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI 
       73.64        24.59        75.81        28.90        50.07       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
        8.75        43.04        26.99        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE 
       36.82        22.29        36.20        36.56        39.55        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12        46.65        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       41.03        41.72        40.73        40.50        20.12         0.69 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       38.99         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       38.07        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P8 
       39.78        52.96        29.82        23.11        18.48         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       34.55        19.96        55.00        52.73        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       17.49        23.51        15.22        24.99        31.30        33.21 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.47        11.84        21.24        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        32.75        29.23        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z 
       14.70        14.47        14.79        22.26        16.08         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        19.53        12.36        19.59        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       18.81        21.07        20.68        19.27        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G 
       17.39        17.26        13.94        17.03        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.03               0.03 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            255.68             282.90 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            23.325             28.240 
[1] "0.0 - 255.7 (23.3)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q GAIN MUTATED         6        4        0        1        35        17
  13Q GAIN WILD-TYPE      83       81        6        5       318       235
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED           0         17          2          5        2
  13Q GAIN WILD-TYPE         2        137         27         60       18
                    vv
clus                 STAGE TIS STAGE X
  13Q GAIN MUTATED           0       2
  13Q GAIN WILD-TYPE         1      11
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                   6                 83
  STAGE IA                  4                 81
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                35                318
  STAGE IIB                17                235
  STAGE III                 0                  2
  STAGE IIIA               17                137
  STAGE IIIB                2                 27
  STAGE IIIC                5                 60
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED    18  61   8   4
  13Q GAIN WILD-TYPE 258 563 128  36
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               18                258
  T2               61                563
  T3                8                128
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q GAIN MUTATED    44  27  14   7
  13Q GAIN WILD-TYPE 463 331 105  70
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               44                463
  N1               27                331
  N2               14                105
  N3                7                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    81   2
  13Q GAIN WILD-TYPE 808  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     81    2
  13Q GAIN WILD-TYPE  808   20
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               81                808
  1                2                 20
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    91   1
  13Q GAIN WILD-TYPE 977  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     91    1
  13Q GAIN WILD-TYPE  977   11
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               91                977
  MALE                  1                 11
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    42  40
  13Q GAIN WILD-TYPE 387 478
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     42   40
  13Q GAIN WILD-TYPE  387  478
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                42                387
  YES               40                478
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q GAIN MUTATED                            0                            75
  13Q GAIN WILD-TYPE                          1                           695
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q GAIN MUTATED                                4                   0
  13Q GAIN WILD-TYPE                            196                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  13Q GAIN MUTATED                       3                                2
  13Q GAIN WILD-TYPE                     6                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  13Q GAIN MUTATED                    2              6
  13Q GAIN WILD-TYPE                 15             41
D25V9, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  75                695
  INFILTRATING LOBULAR CARCINOMA                  4                196
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  6                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     6
  13Q GAIN WILD-TYPE                                1    54
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                          13    66
  13Q GAIN WILD-TYPE                       168   679
D25V11, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 54
  BLACK OR AFRICAN AMERICAN                      13                168
  WHITE                                          66                679
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     6  73
  13Q GAIN WILD-TYPE  33 802
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      6   73
  13Q GAIN WILD-TYPE   33  802
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 33
  NOT HISPANIC OR LATINO               73                802
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED   125  18
  14Q GAIN WILD-TYPE 792 129
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
               143                921 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                18                129 
$`14Q GAIN MUTATED`
TCGA-A2-A0D2 TCGA-A2-A0T3 TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A25C TCGA-A2-A3KD 
       33.76        49.84        21.67        17.36        17.19        39.65 
TCGA-A2-A4RX TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A56D TCGA-A8-A075 TCGA-A8-A076 
       24.39        30.61        33.11        14.73        17.03        53.98 
TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 
       38.01        12.00        33.01        33.01        30.97        41.98 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 
        9.99         1.02        33.07         8.98        14.01        19.04 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2FM TCGA-AC-A5EI TCGA-AC-A62Y TCGA-AN-A04A 
       27.02        22.95        26.04        14.53        17.42         2.96 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.36         0.33        80.28        66.77        81.63        95.70 
TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AR-A24K TCGA-AR-A24M 
       20.32        72.00        76.77        71.80        50.89       120.33 
TCGA-AR-A24R TCGA-AR-A250 TCGA-AR-A2LK TCGA-AR-A5QM TCGA-B6-A0I5 TCGA-B6-A0IB 
      112.77        89.00        54.21        73.35       281.29       129.57 
TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ 
      162.05       100.70       282.90        79.63       113.79       206.86 
TCGA-B6-A1KN TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BP 
      139.17        85.35        68.12        37.22        74.89        75.48 
TCGA-BH-A0BT TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E9 TCGA-BH-A0EE 
       45.57        23.44        78.28         2.56        46.19        31.00 
TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0W7 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A1EN 
       20.38        27.25        44.81        90.84        26.66        67.50 
TCGA-BH-A1EV TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12O 
       12.00        45.63        72.07        23.51         5.26        12.66 
TCGA-C8-A12P TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A27A 
       11.77         3.16         1.87         4.08        11.28        24.56 
TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JD 
       20.88        20.58        14.17        21.14        14.17        18.15 
TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XZ 
       12.03        20.12        18.58        15.22        19.92        15.32 
TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14P TCGA-E2-A152 
       12.26        18.51        46.59        40.11        40.96        69.96 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15K 
       23.24        19.43        20.71        18.21        55.63         9.04 
TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A9RU TCGA-E9-A1NF 
       19.66        50.07        43.04        26.99        17.69        35.24 
TCGA-E9-A1NI TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A22D 
        9.86        40.24        46.65         6.58        46.59        41.03 
TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A5FL TCGA-E9-A5UP 
       41.72         0.69        38.99        12.33         0.79        26.40 
TCGA-EW-A1IY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A6SA 
        8.48        40.41        52.96        34.55        52.73        16.77 
TCGA-GM-A2DB TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A8F5 TCGA-MS-A51U 
       79.10        15.32        14.47         2.63        19.59        22.39 
TCGA-OL-A5RW TCGA-OL-A6VR TCGA-S3-A6ZG TCGA-WT-AB44 TCGA-Z7-A8R6 
       36.36        40.11        18.48        29.03       107.05 

$`14Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       39.32        28.01        19.20        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
       78.41       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
       98.99       107.93        56.81        67.33        34.55        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 
       50.43        44.28        17.52        17.13         8.38        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       50.47        21.90        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       31.73        23.77        23.47        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15       105.34        10.59        36.23        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ 
       29.98        32.75        56.28        47.31        35.93        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       50.83         7.30        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.90        38.30        35.31        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        29.79        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        17.92        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
        9.01        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
        0.99        28.96        33.01        19.96        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E 
       17.95        12.00         9.99        12.00        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V 
       45.07        29.98         1.02        25.02        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB 
        0.99        12.00        13.02        21.04         0.99        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        73.91         5.72         1.48        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       74.14        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       16.57        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       16.80        19.33        14.96        11.44        13.71        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         1.78         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.46         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        7.04         0.33         0.33         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.33         5.59        61.35        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF 
       22.36        53.03        21.53        50.70        50.86        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        62.04        55.33       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
      130.09         5.65        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       19.20       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      133.22        83.87       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       93.90        99.32        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24N 
       86.53        86.43        33.73       160.90        94.22        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
      118.59         2.76       104.28        97.84       105.27        77.69 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
      105.30        32.58        98.76        98.66        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 
       33.30        38.96        10.59        77.62       143.38        12.13 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      275.87        50.70        65.72       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      263.28       102.77       140.48        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68        18.35        21.47       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52        73.51       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
       37.87         7.07        70.16        18.84       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        70.22        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       51.68        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       61.68        72.23        74.14        76.60        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        49.05        41.75        44.02        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO 
       45.83        77.98        38.01        29.98        13.91        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         3.22        38.47        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
        4.41        15.68        14.30         9.63        44.81        32.58 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA 
       50.79         5.59        23.93        24.95        42.35        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N 
       32.91         4.90        35.93        20.12        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       30.28        55.63        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.16        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.62       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       36.92        63.35        55.00        72.07       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28        20.88        18.64 
TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        9.63         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       11.77        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       12.66        48.53        12.56        13.51        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.11        12.33        10.92        11.34         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       10.42        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.50        14.43        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A145 
       13.41        19.46        56.81        13.25        13.97        13.48 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE 
       19.20        17.49        16.50        55.50        15.78        18.90 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       53.00        14.01        18.97        20.09        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       20.38        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        14.73        21.80        14.50        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       16.41        15.85        16.31        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       43.04        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         1.61        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       12.53        33.37        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       43.00        34.42        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        44.68        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       18.51        63.62        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J 
       23.34        22.82        17.29        21.63        12.92        53.92 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA 
       60.99        11.08        54.18        60.36        73.64        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 
       75.81        28.90       106.75       102.61         8.75        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       43.56         8.28        30.61        34.92        38.76        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH 
       36.56        39.55        41.62        35.77        25.84        18.94 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG 
       11.15        48.23        45.01        32.09         1.12        21.27 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 
       38.37        40.73        40.50        20.12         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A6HE 
       30.44        23.90        23.84        26.70        25.81        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
        7.86        18.90        19.99         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       14.43        19.96        55.00        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        10.16        23.51        15.22        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       33.21         7.40       109.87        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y 
       17.06        14.70        14.79        22.26        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        19.53        12.36        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        28.21        19.73         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       86.96         0.16         0.26         9.93        18.81        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       13.94        17.03         3.81        66.84        11.41        52.96 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       15.35        16.04       108.07 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              0.33               0.03 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            282.90             275.87 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             27.25              27.91 
[1] "0.3 - 282.9 (27.2)" "0.0 - 275.9 (27.9)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q GAIN MUTATED         9        8        2        2        46        29
  14Q GAIN WILD-TYPE      80       77        4        4       307       223
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           1         27          4         10        1
  14Q GAIN WILD-TYPE         1        127         25         55       19
                    vv
clus                 STAGE TIS STAGE X
  14Q GAIN MUTATED           0       2
  14Q GAIN WILD-TYPE         1      11
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  8                 77
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA                46                307
  STAGE IIB                29                223
  STAGE III                 1                  1
  STAGE IIIA               27                127
  STAGE IIIB                4                 25
  STAGE IIIC               10                 55
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED    29  94  15   5
  14Q GAIN WILD-TYPE 247 530 121  35
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               29                247
  T2               94                530
  T3               15                121
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q GAIN MUTATED    61  44  24  11
  14Q GAIN WILD-TYPE 446 314  95  66
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               61                446
  N1               44                314
  N2               24                 95
  N3               11                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED   121   1
  14Q GAIN WILD-TYPE 768  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    121    1
  14Q GAIN WILD-TYPE  768   21
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0              121                768
  1                1                 21
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED   142   1
  14Q GAIN WILD-TYPE 926  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED    142    1
  14Q GAIN WILD-TYPE  926   11
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE              142                926
  MALE                  1                 11
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    53  75
  14Q GAIN WILD-TYPE 376 443
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     53   75
  14Q GAIN WILD-TYPE  376  443
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                53                376
  YES               75                443
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q GAIN MUTATED                            0                           110
  14Q GAIN WILD-TYPE                          1                           660
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q GAIN MUTATED                               15                   0
  14Q GAIN WILD-TYPE                            185                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  14Q GAIN MUTATED                       3                                8
  14Q GAIN WILD-TYPE                     6                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  14Q GAIN MUTATED                    2              5
  14Q GAIN WILD-TYPE                 15             42
D26V9, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 110                660
  INFILTRATING LOBULAR CARCINOMA                 15                185
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 21
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  5                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     9
  14Q GAIN WILD-TYPE                                1    51
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                          24    94
  14Q GAIN WILD-TYPE                       157   651
D26V11, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           9                 51
  BLACK OR AFRICAN AMERICAN                      24                157
  WHITE                                          94                651
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V12, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2 117
  14Q GAIN WILD-TYPE  37 758
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2  117
  14Q GAIN WILD-TYPE   37  758
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 37
  NOT HISPANIC OR LATINO              117                758
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    75  11
  15Q GAIN WILD-TYPE 842 136
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                86                978 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                136 
$`15Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SF TCGA-A1-A0SN TCGA-A2-A0CV TCGA-A2-A0D2 TCGA-A2-A0EV 
      129.14        48.10        39.32        98.99        33.76        31.82 
TCGA-A2-A0T2 TCGA-A2-A1FW TCGA-A2-A1G4 TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XY 
        8.38        17.36        19.56        17.19        91.07        35.93 
TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A3IY TCGA-A7-A4SE 
       35.31        37.45        25.15        23.74        11.34        21.17 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A07P TCGA-A8-A07U TCGA-A8-A08B TCGA-A8-A08P 
       13.02         1.02        10.98        24.99        38.01        31.00 
TCGA-A8-A097 TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-AC-A2QH TCGA-AN-A0XU 
       12.00        49.05        29.98        33.07        33.04         0.33 
TCGA-AO-A0J2 TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A12D TCGA-AQ-A04L TCGA-AR-A0TP 
       32.78        71.80       115.27        64.04       130.09       140.55 
TCGA-AR-A0U2 TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A254 TCGA-AR-A2LH 
       83.87        61.28        86.43        50.89        85.64        20.25 
TCGA-B6-A0I5 TCGA-B6-A0IM TCGA-B6-A400 TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0DL 
      281.29       127.33         7.07        61.51        75.48        78.28 
TCGA-BH-A0DS TCGA-BH-A0EE TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18V TCGA-BH-A1FH 
        2.56        31.00        23.05        37.74        51.16        36.92 
TCGA-BH-A5J0 TCGA-C8-A12O TCGA-C8-A132 TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A26X 
       23.51        12.66         1.87        11.28        12.33        12.36 
TCGA-C8-A26Z TCGA-D8-A1JP TCGA-D8-A27R TCGA-E2-A10A TCGA-E2-A15D TCGA-E2-A15E 
        8.28        21.01        10.09        40.41        17.29        20.71 
TCGA-E2-A1IL TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E9-A1N8 
        3.88        28.90       106.75        43.04         8.28        34.16 
TCGA-E9-A1NF TCGA-E9-A1R3 TCGA-E9-A1RA TCGA-E9-A54X TCGA-EW-A1IY TCGA-EW-A1J6 
       35.24         2.56        45.01        23.90         8.48        28.77 
TCGA-EW-A1OW TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GM-A2DF TCGA-GM-A2DK TCGA-LL-A5YM 
       22.82        23.11        19.99        70.85        86.96        15.32 
TCGA-OL-A5RV TCGA-PL-A8LX 
       34.92         0.16 

$`15Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       77.19        75.25         5.19       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       34.55        61.58        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      118.45        79.76        74.40        72.00        35.05        34.29 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       44.88        50.43        44.28        17.52        17.13        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.21        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX 
       19.33        48.46        31.73        23.77        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.20        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       42.44        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ 
       33.93        29.98        32.75        56.28        47.31        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       21.14        21.90        38.30        34.29        35.47        30.61 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       35.67        33.11        29.79        31.73        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        24.26        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       22.32        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        14.50        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
        8.75        13.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       26.01         1.02        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 
        9.99         8.98         7.99         9.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       36.95        13.02         0.99        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S 
       12.00        37.05         9.99        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
      112.08        43.00        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       45.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95        22.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       73.91         5.72         1.48        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       86.66        90.71        60.92        87.12        26.04        74.14 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       15.48        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       19.33        14.96        11.44        13.71        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.58        12.26         1.68         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         5.36         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       66.77        81.63        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       29.13        21.40        52.18        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       76.77        65.10        26.24        50.24        62.04        55.33 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       61.87        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       98.33         5.26        84.10       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 
       64.83        55.86       107.24        65.36       133.22       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
      107.21       125.16       108.36       101.00       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       98.33        96.00        86.07        93.90        99.32        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       37.81        94.29        86.53        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 
       98.66        89.00        99.62        93.30        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       143.38        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       233.62        18.77 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       165.76       129.07       140.88       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
       85.35        70.16        68.12        18.84       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        70.22        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        43.53        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       74.89        61.68        72.23        74.14        76.60        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       45.57        49.94        77.95        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       89.06        90.97        45.83        77.98        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT 
       29.98        13.91        17.26        15.65         3.22        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI 
        9.63        44.81        46.19        32.58        24.49        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       32.91         4.90        35.93        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        67.50        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
       74.73       122.89        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28        20.88        18.64         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 
       48.53        12.56         3.16        13.51        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
        4.11         4.08        12.33        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42        12.95        12.33        20.25        12.53 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
       12.95         9.67         9.53         0.03         9.50        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       19.46        56.81        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        55.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       53.00        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        20.38        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.80        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         1.61        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       69.34        18.51        63.62        69.96        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO 
       33.73        33.70        28.44        59.18        22.19        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        60.36        73.64        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 
       75.81        50.07       102.61         8.75        26.99        34.55 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        22.29        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       39.55        41.62        35.77        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       24.82        28.27        34.95         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       48.23        32.09        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.18        30.44        23.84        26.70         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 
       26.40        27.85        12.20        39.72        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08         7.86        18.90         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        10.16        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        75.02        72.10 
TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       85.15       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       29.23        25.05        17.06        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       22.26         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       64.21        86.96         0.26         9.93        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       21.07        20.68        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.26        13.94        17.03         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.16               0.03 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            281.29             282.90 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            31.000             27.185 
[1] "0.2 - 281.3 (31.0)" "0.0 - 282.9 (27.2)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q GAIN MUTATED        10        6        0        0        29        17
  15Q GAIN WILD-TYPE      79       79        6        6       324       235
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           1         13          2          5        3
  15Q GAIN WILD-TYPE         1        141         27         60       17
                    vv
clus                 STAGE TIS STAGE X
  15Q GAIN MUTATED           0       1
  15Q GAIN WILD-TYPE         1      12
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                  6                 79
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                29                324
  STAGE IIB                17                235
  STAGE III                 1                  1
  STAGE IIIA               13                141
  STAGE IIIB                2                 27
  STAGE IIIC                5                 60
  STAGE IV                  3                 17
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED    23  48  12   3
  15Q GAIN WILD-TYPE 253 576 124  37
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               23                253
  T2               48                576
  T3               12                124
  T4                3                 37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q GAIN MUTATED    41  27  10   7
  15Q GAIN WILD-TYPE 466 331 109  70
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               41                466
  N1               27                331
  N2               10                109
  N3                7                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    75   3
  15Q GAIN WILD-TYPE 814  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     75    3
  15Q GAIN WILD-TYPE  814   19
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               75                814
  1                3                 19
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    86   1
  15Q GAIN WILD-TYPE 982  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     86    1
  15Q GAIN WILD-TYPE  982   11
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               86                982
  MALE                  1                 11
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    34  46
  15Q GAIN WILD-TYPE 395 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     34   46
  15Q GAIN WILD-TYPE  395  472
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                34                395
  YES               46                472
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q GAIN MUTATED                            0                            75
  15Q GAIN WILD-TYPE                          1                           695
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q GAIN MUTATED                                3                   0
  15Q GAIN WILD-TYPE                            197                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  15Q GAIN MUTATED                       1                                1
  15Q GAIN WILD-TYPE                     8                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  15Q GAIN MUTATED                    2              4
  15Q GAIN WILD-TYPE                 15             43
D27V9, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  75                695
  INFILTRATING LOBULAR CARCINOMA                  3                197
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                  4                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     8
  15Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                          15    52
  15Q GAIN WILD-TYPE                       166   693
D27V11, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      15                166
  WHITE                                          52                693
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V12, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     3  69
  15Q GAIN WILD-TYPE  36 806
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3   69
  15Q GAIN WILD-TYPE   36  806
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO               69                806
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   392  66
  16P GAIN WILD-TYPE 525  81
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               458                606 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                66                 81 
$`16P GAIN MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04N 
       48.10        14.27        20.88        13.68        28.01       143.15 
TCGA-A2-A04P TCGA-A2-A04V TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       18.02        63.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO 
       77.19        56.81        33.76        61.58       101.72        80.28 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        34.29        31.82        54.64        27.12        44.88 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0YD TCGA-A2-A0YE 
       17.13         8.38        49.84        17.46        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW 
       50.47        21.90        21.67        18.61        23.77        17.36 
TCGA-A2-A1G0 TCGA-A2-A259 TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A2-A4S2 
       20.25        52.47        47.31        35.93        26.96        21.14 
TCGA-A7-A0CE TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26H 
       35.31        33.11        29.79        29.56        31.36        23.80 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       14.70        11.97        13.74        21.17        17.92        12.10 
TCGA-A7-A6VX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X 
       10.42        13.02         1.02        17.98        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R 
       26.01         1.02        18.97        12.00        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I 
        0.99        38.01        28.96        33.01        19.96        12.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       31.00        33.01       112.08        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09E 
       17.95        41.98        12.00         9.99        12.00        49.05 
TCGA-A8-A09K TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A7 
       29.98        19.04        15.02        14.01        12.00         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       27.02        17.03        38.04        22.95        73.91         1.48 
TCGA-AC-A2FG TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3QP TCGA-AC-A3QQ 
       60.92        74.14        19.33        32.45        22.19        24.13 
TCGA-AC-A3W5 TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       16.57        19.33        14.96        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6NO TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 
       18.67         1.68         0.33         0.33         0.23         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FV 
        2.96         1.78         9.96         0.16         7.00         0.33 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XS 
        0.36         0.33         0.33         5.36        12.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V 
        0.33         0.33        80.28        66.77        81.63        29.13 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A0JM 
       20.32        22.36        53.03        76.77        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ 
      115.27        99.25        90.58        57.30        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TR 
        0.53        24.79         5.65        15.62        32.91         5.26 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AK 
       84.10        75.22        98.93        83.87       108.36       103.86 
TCGA-AR-A1AL TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24L 
       97.68        93.90        37.81        61.28        86.43        94.22 
TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 
       99.78         2.76       104.28        98.76        89.00        85.64 
TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LO TCGA-AR-A5QM 
       71.05        54.21        66.15        63.62        39.39        73.35 
TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       38.96       143.38       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RI TCGA-B6-A0RM 
      112.37       165.76       129.07       140.88       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0WS 
      263.28       162.05       102.77       140.48       100.70        97.48 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-B6-A1KI 
      188.68       113.79       206.86       245.10       101.52        73.51 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        68.12       103.63        71.15        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BG 
       20.45        25.55        39.55        70.22        37.22        61.51 
TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BT TCGA-BH-A0C1 TCGA-BH-A0C3 
       74.89        75.48        74.14        45.57        44.02        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       90.97        38.01        78.28        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E6 TCGA-BH-A0E7 
       38.47        67.86        70.88        16.27         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H3 
       46.19        32.58        24.49        31.00        30.35        37.78 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX 
       24.56        41.00        20.38        36.85        12.89        27.25 
TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I 
       23.93        42.35        44.81        23.05        32.91        35.93 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V 
       26.66        72.56        37.74        55.63         7.36        51.16 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB 
       91.99        12.00        49.58        31.53        89.16       120.62 
TCGA-BH-A1FG TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 
      122.89        45.63        72.07        26.14        83.31        57.83 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O 
       20.88        23.51         9.63        11.93        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        48.53        12.56        13.51         1.87 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26W 
        4.08        11.28        12.03        12.33        12.95        12.53 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A141 
       12.95         8.28         9.53        13.02        20.88        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 
       13.97        14.17        13.48        21.14        14.17        17.49 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.15        18.90        12.03        53.00        20.09        20.12 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       18.58        17.79        16.73        27.58        18.15        12.39 
TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       15.22        21.80        19.92        15.85        16.31        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27I 
       43.04        16.54        15.32         9.93        14.24        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A73X TCGA-E2-A107 
       48.03        16.41        12.26        33.37        25.22        34.42 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q 
       40.41        37.51        40.11        28.87        44.68        38.24 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 
       43.33        34.26        31.96        18.51        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G 
       19.43        23.87        22.82        17.29        20.71        18.21 
TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A1B0 TCGA-E2-A1B5 
       55.63         9.04        11.05        50.79        53.62        32.35 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IJ TCGA-E2-A1IO TCGA-E2-A1IU 
       16.47        37.25        37.41        28.44        60.99        11.08 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       73.64        19.66        50.07        43.04        26.99        34.55 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NG 
        8.28        30.61        36.82        34.16        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
        9.86        24.82        28.27         2.56         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
       11.15        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A22B 
       46.65        21.27        46.59        47.64        34.45        38.37 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       41.72        40.50        38.99         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FL TCGA-E9-A5UP 
       29.72        32.91        30.44        23.84         0.79        26.40 
TCGA-E9-A6HE TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OZ 
       27.85         8.48        16.57        25.94        22.82        40.41 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PG TCGA-EW-A2FS 
       52.96        29.82        23.11        18.48        34.55        52.73 
TCGA-EW-A3E8 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       34.03        16.77        31.30        33.21         7.40       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A3XN 
      216.76        79.10        75.02        85.15       101.62        66.38 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YX TCGA-LD-A66U TCGA-LL-A5YL TCGA-LL-A5YM 
       13.55        18.12        11.57        21.24        17.06        15.32 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A9Q3 
       14.79        22.26         2.63        15.68        19.53        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D8 TCGA-OL-A5RV TCGA-OL-A5RX 
       27.91        22.39         2.10        31.99        34.92        28.87 
TCGA-OL-A5RZ TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DE TCGA-PL-A8LZ 
       22.32        41.92        26.04        19.73        86.96         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB44 
       18.48        21.07        17.03        66.84        11.41        29.03 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

$`16P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SH 
       48.36         9.96         8.52        14.37        43.43        47.24 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04Q 
       31.79         7.96        39.32        19.20        18.21        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        73.84        87.25       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
      136.73        99.12       107.93        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EP 
      107.93        67.33        34.55        25.22        89.36       118.45 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       79.76        74.40        72.00        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T6 
       99.19        50.43        44.28        17.52        20.52        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       20.75        32.55        49.48        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        19.20        19.56        16.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        50.37        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       23.21        21.90        38.30        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       37.45        35.67        31.73        20.19        25.15        23.61 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SD 
       10.59        10.29        11.28        13.41        14.93        14.50 
TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       14.73        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       13.02        53.06        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07U 
       19.99        18.97        14.01        32.05         9.99        24.99 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A099 
       37.05         9.99        31.00         0.99        43.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        50.04        45.07        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-AC-A23C 
        8.98         0.99        19.04        13.02        21.04         0.95 
TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN 
       87.12        26.04        33.04        14.66         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       14.83        25.05        14.99        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A6IW TCGA-AC-A6IX 
       24.79        29.26        16.80        14.53        13.58        12.26 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS 
        0.33         1.71         7.36         7.46         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR 
        6.90         7.04         0.33         0.33         0.30         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
        5.33         5.59        61.35        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        72.00        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B 
       50.24        62.04       108.72       106.78       108.03        98.27 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR 
       64.04        48.36        41.62        40.57        14.73        70.39 
TCGA-AO-A1KT TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 
       17.79        26.93       130.09        32.52         2.56        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      140.55        98.33       109.02        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       133.22       134.14       107.21       125.16       101.00 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU 
       98.33        96.00        86.07        99.32        17.23        94.29 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24O 
       86.53        33.73       160.90        50.89       120.33       118.59 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      112.77        97.84       105.27        77.69       105.30        32.58 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       98.66        99.62        93.30        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QQ 
       86.53        38.17        40.54        57.27        33.30        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0IK 
       77.62       281.29        12.13       275.87       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL 
      127.33        84.59       255.68        68.45       212.25        81.17 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       282.90       157.41        79.63        18.35        21.47 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN 
      129.70        28.27        68.94        58.88        43.59       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AZ 
      170.17        37.87         7.07        70.16        18.84        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       81.44        40.83        39.16        81.63        84.13        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        43.53        21.70        61.68        72.23 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       76.60        53.95        49.94        77.95        49.05        41.75 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ 
       45.83        77.98        23.44        29.98        13.91         3.22 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
        4.41        15.68        14.30        24.43        10.78        15.16 
TCGA-BH-A0H5 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       53.26        23.08        52.96        26.50         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G 
       13.61        51.32        50.79         5.59        24.95         4.90 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U 
       20.12        90.84        30.28        37.55        66.05        51.39 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EY 
       67.50       113.82        82.85        42.28        55.69        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       25.81        97.48        24.62       114.15        33.17        74.73 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       36.92        63.35        55.00       144.59        72.07        28.14 
TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       38.60       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
      109.28        18.64         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12X 
        9.44        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        3.16        12.59        12.92         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X 
       11.34         0.16        10.42        12.33        20.25        12.36 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         0.03         9.50        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       12.95        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JH TCGA-D8-A1JI 
       19.20        16.50        55.50        15.78        14.01        18.97 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK 
       14.70        25.74        23.90        17.16        14.73        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y0 
       17.69        55.30        16.41        16.64        15.16        15.52 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M 
       14.14        17.42        16.04        13.45        13.05        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z6 
        4.80         1.61        10.09        13.08        12.53        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       21.67        16.18        12.66        43.00        27.52        46.59 
TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T 
       28.44        47.15        40.96        38.60        33.17        75.98 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 
       32.02        69.34        63.62        21.04        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15P 
       23.34        21.63        12.92        53.92        20.58        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        14.07        51.39        76.57        87.22        33.01 
TCGA-E2-A1B6 TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK 
       28.50        77.65        70.36        33.73        33.70        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LB 
        3.88        22.19        54.18        60.36        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX TCGA-E2-A573 
       28.90       106.75       102.61         8.75        43.56        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N6 
       38.76        34.29        17.69        34.82        32.88        22.29 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NH 
       36.20        36.56        39.55        41.62        35.77        18.94 
TCGA-E9-A1R2 TCGA-E9-A1RF TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       34.95         6.58        32.05        42.25        37.74        39.09 
TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A2JT 
       41.03        40.73        20.12         0.69         1.94         9.47 
TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-EW-A1IW 
       38.07        30.18        23.90        26.70        25.81        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1J6 
       39.72        18.21        18.90        13.25        15.68        28.77 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P7 TCGA-EW-A1P8 
       29.95        29.85        41.13        39.78        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-EW-A423 
       19.96        55.00        25.91        22.09        17.49        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF 
       23.51        15.22        24.99        59.57        83.34        70.85 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DO TCGA-GM-A3NW 
       72.10        86.96       115.69       106.06        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-HN-A2OB 
       38.20        43.73        69.30        72.03         2.60        62.47 
TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.84        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FR 
       32.75        29.23        25.05        14.70        14.47        16.08 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D6 TCGA-OL-A5D7 
        7.46        14.50        12.36        19.59        36.30        58.52 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RW TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       58.62        40.08        36.36        24.72        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       23.47        65.62        42.77        17.36        14.07        28.21 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21         0.16         0.26 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       18.81        20.68        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       17.26        13.94         3.81        52.96        15.35        16.04 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.16               0.03 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            263.28             282.90 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            28.355             26.700 
[1] "0.2 - 263.3 (28.4)" "0.0 - 282.9 (26.7)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P GAIN MUTATED        41       35        3        5       143       112
  16P GAIN WILD-TYPE      48       50        3        1       210       140
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           1         68         17         23        8
  16P GAIN WILD-TYPE         1         86         12         42       12
                    vv
clus                 STAGE TIS STAGE X
  16P GAIN MUTATED           1       5
  16P GAIN WILD-TYPE         0       8
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  41                 48
  STAGE IA                 35                 50
  STAGE IB                  3                  3
  STAGE II                  5                  1
  STAGE IIA               143                210
  STAGE IIB               112                140
  STAGE III                 1                  1
  STAGE IIIA               68                 86
  STAGE IIIB               17                 12
  STAGE IIIC               23                 42
  STAGE IV                  8                 12
  STAGE TIS                 1                  0
  STAGE X                   5                  8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED   114 270  60  18
  16P GAIN WILD-TYPE 162 354  76  22
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1              114                162
  T2              270                354
  T3               60                 76
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P GAIN MUTATED   218 152  57  27
  16P GAIN WILD-TYPE 289 206  62  50
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0              218                289
  N1              152                206
  N2               57                 62
  N3               27                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   385   9
  16P GAIN WILD-TYPE 504  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    385    9
  16P GAIN WILD-TYPE  504   13
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0              385                504
  1                9                 13
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   457   7
  16P GAIN WILD-TYPE 611   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    457    7
  16P GAIN WILD-TYPE  611    5
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE              457                611
  MALE                  7                  5
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   183 226
  16P GAIN WILD-TYPE 246 292
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    183  226
  16P GAIN WILD-TYPE  246  292
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               183                246
  YES              226                292
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P GAIN MUTATED                            1                           338
  16P GAIN WILD-TYPE                          0                           432
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P GAIN MUTATED                               88                   2
  16P GAIN WILD-TYPE                            112                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16P GAIN MUTATED                       3                               16
  16P GAIN WILD-TYPE                     6                               13
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16P GAIN MUTATED                    2             13
  16P GAIN WILD-TYPE                 15             34
D28V9, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 338                432
  INFILTRATING LOBULAR CARCINOMA                 88                112
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)               16                 13
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 13                 34
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  1    23
  16P GAIN WILD-TYPE                                0    37
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          61   325
  16P GAIN WILD-TYPE                       120   420
D28V11, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          23                 37
  BLACK OR AFRICAN AMERICAN                      61                120
  WHITE                                         325                420
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    11 366
  16P GAIN WILD-TYPE  28 509
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     11  366
  16P GAIN WILD-TYPE   28  509
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                   11                 28
  NOT HISPANIC OR LATINO              366                509
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   113  27
  16Q GAIN WILD-TYPE 804 120
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               140                924 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                27                120 
$`16Q GAIN MUTATED`
TCGA-A1-A0SG TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A04P TCGA-A2-A0CM TCGA-A2-A0CX 
       14.27        20.88        13.68        18.02        24.79        56.81 
TCGA-A2-A0D2 TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0YG 
       33.76        35.05        31.82        27.12        44.88        21.90 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0DC 
       23.77        17.36        47.31        35.93        26.96        29.79 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A5ZV TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07W 
       14.70        11.97        12.10        26.01         1.02         9.99 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A0A7 TCGA-AC-A3BB TCGA-AC-A62V TCGA-AC-A62Y 
       33.01        12.00         0.99        32.45        11.44        17.42 
TCGA-AC-A6IV TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0FY 
       18.67         0.23         0.62         2.96         9.96         0.33 
TCGA-AN-A0XO TCGA-AO-A03V TCGA-AO-A0JE TCGA-AO-A0JL TCGA-AO-A1KQ TCGA-AQ-A54O 
       12.33        29.13        76.77        55.33        61.87        32.91 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A250 
        5.26        84.10        98.93        61.28        86.43        89.00 
TCGA-AR-A255 TCGA-B6-A0IE TCGA-B6-A0IO TCGA-B6-A0RM TCGA-B6-A0RO TCGA-B6-A0RQ 
       71.05        65.72       165.76        78.02       162.05       140.48 
TCGA-B6-A0RS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A401 
      100.70       188.68       113.79       101.52        73.51        85.35 
TCGA-B6-A409 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0DL TCGA-BH-A0H6 
       18.84        61.51        74.89        45.57        78.28        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0W5 TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18M 
       23.08        41.00        42.35        35.93        26.66        72.56 
TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EX TCGA-BH-A1FB TCGA-BH-A1FN TCGA-BH-A204 
       55.63        51.16        49.58       120.62        72.07        83.31 
TCGA-BH-A208 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12W TCGA-C8-A131 TCGA-C8-A132 
       57.83         9.63        11.93        12.66        13.51         1.87 
TCGA-C8-A1HK TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A8HP TCGA-D8-A142 TCGA-D8-A143 
       12.03        12.95         8.28        13.02        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1X7 TCGA-D8-A1XB 
       13.48        21.14        12.03        20.12        16.73        18.15 
TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 
       15.22        21.80        12.99        43.04        15.32        14.24 
TCGA-D8-A27I TCGA-D8-A27W TCGA-E2-A10F TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 
       14.43        12.26        28.87        31.96        69.96        19.43 
TCGA-E2-A15M TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1IJ TCGA-E2-A1LL TCGA-E9-A1NI 
       11.05        53.62        32.35        28.44        43.04         9.86 
TCGA-E9-A1RC TCGA-E9-A22B TCGA-E9-A247 TCGA-E9-A2JS TCGA-E9-A5FL TCGA-EW-A1OW 
       40.24        38.37        38.99        29.72         0.79        22.82 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD 
       29.82        23.11       109.87       216.76        79.10        75.02 
TCGA-GM-A3XN TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ 
       66.38        15.32        14.79         2.63        15.68        19.53 
TCGA-OK-A5Q2 TCGA-OL-A5RZ TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-UL-AAZ6 
        2.10        22.32        86.96         9.93        21.07        17.03 
TCGA-V7-A7HQ TCGA-Z7-A8R5 
       66.84       108.07 

$`16Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        78.41       121.94        73.84        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 
        5.19        98.99       107.93        67.33        34.55        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       74.40        72.00        34.29        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       99.19        54.64        50.43        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
        8.38        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        18.21        50.47        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX 
       18.61        19.33        48.46        31.73        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        50.37        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       35.47        30.61        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       20.19        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A4SA TCGA-A7-A4SB 
       10.59        10.29        11.28        13.41        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        21.17        17.92        14.73        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 
        1.02        17.98        53.06        29.03        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99        24.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
        0.99        38.01        28.96        19.96        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       31.00        31.00         0.99        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        33.01        30.97        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       45.07        29.98        33.07         1.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       13.02        21.04        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       22.95        73.91         5.72         1.48        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN 
       74.14        33.04        19.33        14.66         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       14.83        22.19        24.13        25.05        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       19.79        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6IX 
       14.53        19.33        14.96        13.71        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A04D 
        2.30         0.33         0.33         0.33         1.78         1.71 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        5.36         0.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 
       81.63        95.70        68.75        47.87        58.95        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        72.00        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        62.04        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       70.39         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        32.52         2.56        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       98.33       109.02        75.22        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
       65.36       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       86.07        93.90        99.32        17.23        37.81        94.29 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.53        33.73       160.90        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      105.27        77.69       105.30        32.58        98.76        98.66 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       99.62        93.30        85.64        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       86.53        54.21        66.15        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70       146.50       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
       84.59       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RT TCGA-B6-A0RU 
      234.28        81.17       263.28       102.77        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ 
      157.41        97.48        79.63        18.35        21.47       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.88        43.59 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 
      139.17       170.17        37.87         7.07        70.16        68.12 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        62.93        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       63.09        81.44        40.83        39.55        39.16        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.63        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       43.53        21.70        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       76.60        53.95        49.94        77.95        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        29.98        13.91        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       37.78        53.26        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W7 TCGA-BH-A0WA 
       50.79         5.59        23.93        24.95        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P 
       32.91         4.90        20.12        90.84        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        67.50        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY 
      113.82        82.85        42.28        12.00        55.69        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FC 
       25.81        31.53        89.16        97.48        24.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       45.63       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        18.64        23.51         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        3.16        12.59        12.92         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34        11.28         0.16        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 
       12.95        12.33        20.25        12.53        12.36         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.53         0.03         9.50        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       12.95        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.25        20.58        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH 
       55.50        15.78        18.15        18.90        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.97        20.09        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X8 
       12.20        13.32        14.70        18.58        17.79        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XK 
       23.90        27.58        12.39        17.16        14.73        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       16.64        15.16        16.54        15.52         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L 
       17.42        16.04        13.45        13.05        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       69.34        18.51        63.62        23.24        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        50.79        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       76.57        87.22        33.01        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IK 
       77.65        37.41        70.36        33.73        33.70        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       73.64        19.66        24.59        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       18.94        24.82        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
        3.02        11.15        48.23        45.01        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E 
       32.05        42.25        37.74        39.09        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 
       40.73        40.50        20.12         0.69         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56        12.33         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       30.44        23.90        23.84        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX 
       13.25        16.57        15.68        28.77        25.94        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 
       29.85        40.41        41.13        39.78        52.96        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD 
       30.08         7.86        18.90        19.99         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       15.22        16.77        24.99        31.30        33.21         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       59.57        83.34        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       43.73        69.30        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z 
       17.06        14.70        14.47        22.26        16.08         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        12.36        19.59        17.49        27.91        22.39 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        0.16         0.26        18.81        18.48        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S 
       13.84        18.87        17.39        17.26        13.94         3.81 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       11.41        52.96        29.03        15.35        16.04       107.05 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.23               0.03 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            216.76             282.90 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            26.810             28.075 
[1] "0.2 - 216.8 (26.8)" "0.0 - 282.9 (28.1)"
[1] "hr=" "1.5"
D29V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q GAIN MUTATED        11        8        0        1        42        33
  16Q GAIN WILD-TYPE      78       77        6        5       311       219
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           0         27          7          7        4
  16Q GAIN WILD-TYPE         2        127         22         58       16
                    vv
clus                 STAGE TIS STAGE X
  16Q GAIN MUTATED           1       1
  16Q GAIN WILD-TYPE         0      12
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                  8                 77
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                42                311
  STAGE IIB                33                219
  STAGE III                 0                  2
  STAGE IIIA               27                127
  STAGE IIIB                7                 22
  STAGE IIIC                7                 58
  STAGE IV                  4                 16
  STAGE TIS                 1                  0
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED    31  81  20   8
  16Q GAIN WILD-TYPE 245 543 116  32
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1               31                245
  T2               81                543
  T3               20                116
  T4                8                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q GAIN MUTATED    63  44  24   7
  16Q GAIN WILD-TYPE 444 314  95  70
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               63                444
  N1               44                314
  N2               24                 95
  N3                7                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   115   4
  16Q GAIN WILD-TYPE 774  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    115    4
  16Q GAIN WILD-TYPE  774   18
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0              115                774
  1                4                 18
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   138   4
  16Q GAIN WILD-TYPE 930   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    138    4
  16Q GAIN WILD-TYPE  930    8
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE              138                930
  MALE                  4                  8
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    57  63
  16Q GAIN WILD-TYPE 372 455
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     57   63
  16Q GAIN WILD-TYPE  372  455
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                57                372
  YES               63                455
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q GAIN MUTATED                            1                           111
  16Q GAIN WILD-TYPE                          0                           659
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q GAIN MUTATED                               17                   1
  16Q GAIN WILD-TYPE                            183                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16Q GAIN MUTATED                       3                                4
  16Q GAIN WILD-TYPE                     6                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16Q GAIN MUTATED                    1              4
  16Q GAIN WILD-TYPE                 16             43
D29V9, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 111                659
  INFILTRATING LOBULAR CARCINOMA                 17                183
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  4                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  0     8
  16Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          29    96
  16Q GAIN WILD-TYPE                       152   649
D29V11, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      29                152
  WHITE                                          96                649
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V12, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     2 125
  16Q GAIN WILD-TYPE  37 750
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      2  125
  16Q GAIN WILD-TYPE   37  750
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 37
  NOT HISPANIC OR LATINO              125                750
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    90  17
  17P GAIN WILD-TYPE 827 130
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               107                957 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                17                130 
$`17P GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A2-A0CX TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
        9.96        13.68        56.81        35.05        34.29        31.82 
TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A259 TCGA-A2-A3XU TCGA-A2-A3XX 
       18.61        23.77        60.72        52.47        29.98        47.31 
TCGA-A2-A3XZ TCGA-A7-A0CD TCGA-A7-A0DC TCGA-A7-A26J TCGA-A7-A3J0 TCGA-A8-A07P 
       50.37        38.30        29.79        20.61        10.29        10.98 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A097 TCGA-A8-A09B 
       19.96        37.05        31.00        33.01        12.00        12.00 
TCGA-A8-A09E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A5XU 
       49.05        73.91         5.72        26.04        33.04        14.96 
TCGA-AC-A8OP TCGA-AN-A04A TCGA-AO-A03L TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JL 
       20.19         2.96        80.28        26.04        20.32        55.33 
TCGA-AO-A124 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A1KQ TCGA-AR-A0TQ TCGA-AR-A1AV 
      115.27        98.27        57.30        61.87        98.33        61.28 
TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A252 TCGA-AR-A2LK 
       86.53        50.89       104.28       112.77        93.30        54.21 
TCGA-AR-A2LL TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A401 
       66.15        21.47        43.59        73.51        37.87        85.35 
TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B4 TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0C0 
       62.93        20.45        39.16        61.51        45.57        41.75 
TCGA-BH-A0C7 TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A18N TCGA-BH-A1EX TCGA-BH-A1F0 
       90.97        36.85        51.32        37.74        49.58        25.81 
TCGA-BH-A1FC TCGA-BH-A204 TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A1HI 
      114.15        83.31        12.66         3.16         1.87        11.28 
TCGA-C8-A1HN TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1XB 
       12.95        14.17        55.50        12.03        20.09        18.15 
TCGA-D8-A1XS TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14T 
       16.31        12.26        34.42        46.59        44.68        75.98 
TCGA-E2-A14W TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1LK TCGA-E2-A574 TCGA-E9-A1QZ 
       32.02        87.22        32.35         8.75        38.76        24.82 
TCGA-E9-A1R6 TCGA-E9-A1RH TCGA-E9-A22E TCGA-E9-A54Y TCGA-EW-A1OX TCGA-EW-A1OY 
       11.15        46.59        41.72        23.84        29.95        29.85 
TCGA-EW-A1PC TCGA-EW-A2FS TCGA-EW-A6SA TCGA-GM-A2DK TCGA-HN-A2NL TCGA-LL-A5YP 
        6.15        52.73        16.77        86.96         2.60        14.79 
TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OL-A66K TCGA-OL-A6VO TCGA-S3-A6ZG 
       19.53        22.39        41.92        28.21        18.48 

$`17P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        75.25         5.19        98.99       107.93 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        50.47        21.90        21.67        49.48 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ 
       19.33        48.46        31.73        23.47        17.36        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.20        19.56        16.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 
       33.93        91.07        32.75        56.28        35.93        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
        7.30        24.39        21.30        23.21        26.96        21.14 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       21.90        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       22.32        11.34        10.59        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       11.97        14.93        13.74        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.42         8.75        13.02        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S 
       14.01        12.00        32.05         9.99         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L 
        0.99        38.01        28.96        33.01        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       30.97        17.95        41.98         9.99         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q 
       50.04        45.07        29.98        33.07         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04         0.95        22.95         1.48        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       40.57        86.66        90.71        60.92        87.12        74.14 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       15.48        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       19.33        11.44        13.71        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OR 
       12.26         1.68         8.22         0.03         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.90         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.36         0.33         0.33         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.33         5.59        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       52.18        37.48        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       62.04        71.80        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        64.04        48.36        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        70.39         0.53        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
      130.09         5.65        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       140.55         5.26        84.10       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       83.87       134.14       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      103.86        97.68        98.33        96.00        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY 
       99.32        17.23        37.81        94.29        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      160.90        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.66        89.00        99.62        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        20.25        86.53        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY 
      157.41        97.48       188.68        79.63        18.35       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 
      101.52       139.17       170.17         7.07        70.16        68.12 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ 
       18.84       103.63        71.15        59.84        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       81.44        40.83        39.55        70.22        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       51.68        37.22        32.02        18.21        43.53        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        49.94        77.95        49.05        44.02        89.06 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       78.28        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        12.89        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       32.91         4.90        35.93        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        67.50        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        12.00        55.69        17.69        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.62       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        26.14        38.60        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       18.64        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       12.56        13.51        12.59        12.92         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.33        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A 
        8.28         9.67         9.53         0.03         9.50        24.56 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       19.46        56.81        20.88        13.25        20.58        13.97 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       15.78        18.15        18.90        53.00        14.01        18.97 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.12        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       23.90        27.58        12.39        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       21.80        14.50        19.92        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       15.85        16.64        12.99        15.16        43.04        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       43.00        27.52        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.33        34.26        31.96        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       69.96        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       25.05        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        50.79        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       76.57        53.62        33.01        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       60.36        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       50.07       106.75       102.61        43.04        26.99        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU 
       43.56         8.28        30.61        34.92        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
       18.94         9.86        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       46.65         6.58        21.27        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.03        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.18        30.44        23.90        26.70         0.79        25.81 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       22.82        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       15.22        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        85.15       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       29.23        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       22.26         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 
       12.36        19.59        17.49        27.91         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I 
       28.87        24.72        22.32        20.38        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       65.62        42.77        26.04        17.36        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       40.11         8.91        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         9.93        18.81        21.07        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        18.87        17.39        17.26        13.94        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
        3.81        66.84        11.41        52.96        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.87               0.03 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            115.27             282.90 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             34.29              26.66 
[1] "1.9 - 115.3 (34.3)" "0.0 - 282.9 (26.7)"
[1] "hr=" "1.3"
D30V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P GAIN MUTATED         7        6        0        1        38        24
  17P GAIN WILD-TYPE      82       79        6        5       315       228
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1         19          6          2        3
  17P GAIN WILD-TYPE         1        135         23         63       17
                    vv
clus                 STAGE TIS STAGE X
  17P GAIN MUTATED           0       0
  17P GAIN WILD-TYPE         1      13
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   7                 82
  STAGE IA                  6                 79
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                38                315
  STAGE IIB                24                228
  STAGE III                 1                  1
  STAGE IIIA               19                135
  STAGE IIIB                6                 23
  STAGE IIIC                2                 63
  STAGE IV                  3                 17
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED    23  58  17   9
  17P GAIN WILD-TYPE 253 566 119  31
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1               23                253
  T2               58                566
  T3               17                119
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P GAIN MUTATED    47  38  17   3
  17P GAIN WILD-TYPE 460 320 102  74
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               47                460
  N1               38                320
  N2               17                102
  N3                3                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    91   3
  17P GAIN WILD-TYPE 798  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     91    3
  17P GAIN WILD-TYPE  798   19
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               91                798
  1                3                 19
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED   101   6
  17P GAIN WILD-TYPE 967   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED    101    6
  17P GAIN WILD-TYPE  967    6
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE              101                967
  MALE                  6                  6
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    34  62
  17P GAIN WILD-TYPE 395 456
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     34   62
  17P GAIN WILD-TYPE  395  456
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                34                395
  YES               62                456
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P GAIN MUTATED                            0                            83
  17P GAIN WILD-TYPE                          1                           687
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P GAIN MUTATED                               11                   1
  17P GAIN WILD-TYPE                            189                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17P GAIN MUTATED                       1                                2
  17P GAIN WILD-TYPE                     8                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17P GAIN MUTATED                    3              6
  17P GAIN WILD-TYPE                 14             41
D30V9, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  83                687
  INFILTRATING LOBULAR CARCINOMA                 11                189
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              3                 14
  OTHER  SPECIFY                                  6                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  0     7
  17P GAIN WILD-TYPE                                1    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          21    70
  17P GAIN WILD-TYPE                       160   675
D30V11, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      21                160
  WHITE                                          70                675
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V12, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4  86
  17P GAIN WILD-TYPE  35 789
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4   86
  17P GAIN WILD-TYPE   35  789
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO               86                789
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   179  35
  17Q GAIN WILD-TYPE 738 112
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               214                850 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                35                112 
$`17Q GAIN MUTATED`
TCGA-4H-AAAK TCGA-5T-A9QA TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A2-A04R TCGA-A2-A0CU 
       11.44         9.96        47.24        13.68       121.94         5.19 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       56.81        33.76        25.22        35.05        34.29        31.82 
TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A259 
       49.84        20.75        23.77        60.72        20.25        52.47 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A7-A0CD 
       18.15       105.34        29.98        47.31        50.37        38.30 
TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD 
       35.67        29.79        25.15        23.80        20.61        22.32 
TCGA-A7-A3J0 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A06Z 
       10.29        14.93        17.92        13.02        29.03         1.02 
TCGA-A8-A07G TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J 
       18.97        10.98         9.99        33.01        19.96        37.05 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       31.00        33.01        30.97        12.00         9.99        12.00 
TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09X TCGA-AC-A23G TCGA-AC-A23H 
       49.05        33.07         8.98        14.01        73.91         5.72 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3QQ TCGA-AC-A5XU TCGA-AC-A7VB TCGA-AC-A8OP 
       26.04        33.04        24.13        14.96         8.22        20.19 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AO-A03L 
        0.23         2.96         6.44         0.33         5.36        80.28 
TCGA-AO-A03P TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A124 TCGA-AO-A12B TCGA-AO-A12E 
       95.70        26.04        20.32       115.27        98.27        57.30 
TCGA-AO-A1KQ TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A1AK 
       61.87        32.52        32.91        98.33        83.87       103.86 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24P 
       61.28        86.53       160.90        50.89        94.22         2.76 
TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LK 
      112.77       105.30        98.66        93.30        71.05        54.21 
TCGA-AR-A2LL TCGA-B6-A0WV TCGA-B6-A0X1 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A3ZX 
       66.15        79.63       245.10        43.59        73.51        37.87 
TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B4 
       85.35        70.16        62.93        20.45        63.09        39.16 
TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DP 
       45.57        49.05        41.75        90.97        77.98        15.65 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A18U 
       36.85        51.32        26.66        37.74        66.05        51.39 
TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A1FG TCGA-BH-A1FJ 
       55.69        49.58        25.81       114.15       122.89        63.35 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12W 
       26.14        38.60        83.31       130.16        18.64        12.66 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM 
        3.16         1.87         4.08        11.34        11.28        12.33 
TCGA-C8-A1HN TCGA-C8-A27A TCGA-C8-A3M8 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB 
       12.95        24.56        12.95        13.97        14.17        55.50 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JT TCGA-D8-A1X7 TCGA-D8-A1XB 
       12.03        53.00        20.09        13.32        16.73        18.15 
TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y2 
       15.22        19.92        17.69        16.31        16.54        14.24 
TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O 
       10.09        12.26        34.42        46.59        40.11        44.68 
TCGA-E2-A14T TCGA-E2-A14W TCGA-E2-A15A TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B5 
       75.98        32.02        23.34        51.39        87.22        32.35 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1LA TCGA-E2-A1LK 
       77.65        70.36        33.73        28.44        24.59         8.75 
TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1QZ TCGA-E9-A1R2 
        8.28        38.76        34.16        35.24        24.82        34.95 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RH 
        6.12         3.02        11.15        48.23        46.65        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A247 TCGA-E9-A2JS 
       47.64        34.45        38.37        41.72        38.99        29.72 
TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J2 TCGA-EW-A1J5 TCGA-EW-A1OX 
       23.84        25.81        26.40        13.25        15.68        29.95 
TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A2FS 
       29.85        52.96        23.11         6.15        13.94        52.73 
TCGA-EW-A423 TCGA-EW-A6SA TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A3XL TCGA-HN-A2NL 
       10.16        16.77        83.34        86.96        69.30         2.60 
TCGA-LL-A5YM TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-MS-A51U TCGA-OL-A5RZ TCGA-OL-A66K 
       15.32        19.53        12.36        22.39        22.32        41.92 
TCGA-OL-A6VO TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 
       28.21        18.48        21.07        19.27 

$`17Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
        8.52        14.37        43.43        48.10        14.27        20.88 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       31.79         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      143.15        18.02        78.41        73.84        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        77.19        75.25 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM 
       98.99       107.93        67.33        34.55        61.58       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        18.90        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       50.47        21.90        21.67        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 
       48.46        31.73        23.47        17.36        22.45        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25F 
       19.56        16.47       107.70        42.44        17.19        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       36.23        39.65        33.93        91.07        32.75        56.28 
TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       35.93        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G 
       30.61        37.45        33.11        31.73        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A3IY 
       29.56        31.36        24.26        23.74        21.73        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB 
       10.59        11.28        13.41        14.70        11.97        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        21.17        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       17.98        53.06        31.00        26.01        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
        9.01        43.00        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
       32.05         9.99         8.98         7.99        24.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       12.00         9.99        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09C 
       40.01        33.01        17.95        41.98         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T 
       50.04        45.07        29.98         1.02        25.02        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02         0.99        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95        22.95 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        1.48        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       60.92        87.12        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN 
        6.48        16.31        14.83        22.19        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       16.57        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       16.80        14.53        19.33        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OQ 
       18.67        13.58        12.26         1.68         0.03         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.33         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         0.33         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.90         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.33         0.33         5.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        21.40        52.18        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 
       26.24        50.24        62.04        55.33        71.80        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F 
      108.72       106.78       108.03        90.58        64.04        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS 
       41.62        40.57        14.73        82.62        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
        2.56        19.20       140.55         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
      133.22       134.14       107.21       125.16       108.36       101.00 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       97.68        98.33        96.00        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24M 
       17.23        37.81        94.29        86.43        33.73       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       99.78       118.59       104.28        97.84       105.27        77.69 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 
       32.58        98.76        89.00        99.62        85.64        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
      166.42        20.25        86.53        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
      157.41        97.48       188.68        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      206.86       129.70        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
      139.17       170.17         7.07        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       71.15        59.84        25.55        81.44        40.83        39.55 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       70.22        81.63        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV 
       72.23        75.48        74.14        76.60        53.95        49.94 
TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH 
       77.95        44.02        89.06        45.83        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        78.28        17.26         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX 
       20.38         5.85         2.50        13.61        12.89        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18V 
       72.56        30.28        55.63        37.55         7.36        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV 
       67.50        91.99       113.82        82.85        42.28        12.00 
TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        31.53        89.16        97.48        24.62       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
       33.17        74.73        36.92        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q 
      144.59        72.07        28.14        57.83        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       109.28        20.88        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 
       12.66        12.66        48.53        12.56        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.92         4.11        12.33        10.92         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       10.42        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        8.28         9.67         9.53         0.03         9.50        14.43 
TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       33.99        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.88        13.25        20.58        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       14.17        17.49        16.50        15.78        18.15        18.90 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X8 
       21.01        12.20        14.70        18.58        17.79        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       23.90        27.58        12.39        17.16        14.73        21.80 
TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU 
       14.50        55.30        16.41        15.85        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       15.16        43.04        15.32        15.52         9.93        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       16.41        13.48         4.80         1.61        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       43.00        27.52        40.41        37.51        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U 
       47.15        40.96        38.24        38.60        33.17        43.33 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       34.26        31.96        69.34        18.51        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B4 
       19.56        56.94        14.07        76.57        53.62        33.01 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IK 
       28.50        16.47        37.25        37.41        33.70        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       73.64        19.66        75.81        28.90        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 
      102.61        43.04        26.99        34.55        43.56        30.61 
TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       22.29        36.20        36.56        39.55        41.62        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1RA 
       25.84        18.94         9.86        28.27         2.56        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A227 
       32.09        40.24         1.12         6.58        21.27        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       42.25        37.74        39.09        41.03        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.12         0.69         1.94         7.13        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       26.70         0.79        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J3 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       18.21        18.90        16.57        28.77        25.94        22.82 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       40.41        41.13        39.78        29.82        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
        7.86        18.90        19.99        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        25.91        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       23.51        15.22        24.99        31.30        33.21         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
      109.87        59.57       216.76        79.10        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        85.15       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       18.12        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       25.05        17.06        14.70        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
        2.63        16.08        15.68         7.46        14.50        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       17.49        27.91         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        23.47        65.62        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       17.36        14.07        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       20.68        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       17.03         3.81        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.23               0.03 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             245.1              282.9 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            30.475             26.945 
[1] "0.2 - 245.1 (30.5)" "0.0 - 282.9 (26.9)"
[1] "hr=" "1.4"
D31V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q GAIN MUTATED        16       15        1        2        77        49
  17Q GAIN WILD-TYPE      73       70        5        4       276       203
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           1         32          8         11        4
  17Q GAIN WILD-TYPE         1        122         21         54       16
                    vv
clus                 STAGE TIS STAGE X
  17Q GAIN MUTATED           0       1
  17Q GAIN WILD-TYPE         1      12
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  16                 73
  STAGE IA                 15                 70
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA                77                276
  STAGE IIB                49                203
  STAGE III                 1                  1
  STAGE IIIA               32                122
  STAGE IIIB                8                 21
  STAGE IIIC               11                 54
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED    50 132  24  11
  17Q GAIN WILD-TYPE 226 492 112  29
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1               50                226
  T2              132                492
  T3               24                112
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q GAIN MUTATED   101  72  26  12
  17Q GAIN WILD-TYPE 406 286  93  65
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0              101                406
  N1               72                286
  N2               26                 93
  N3               12                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   183   5
  17Q GAIN WILD-TYPE 706  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    183    5
  17Q GAIN WILD-TYPE  706   17
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0              183                706
  1                5                 17
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   209   8
  17Q GAIN WILD-TYPE 859   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    209    8
  17Q GAIN WILD-TYPE  859    4
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE              209                859
  MALE                  8                  4
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    78 112
  17Q GAIN WILD-TYPE 351 406
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     78  112
  17Q GAIN WILD-TYPE  351  406
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                78                351
  YES              112                406
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q GAIN MUTATED                            0                           169
  17Q GAIN WILD-TYPE                          1                           601
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q GAIN MUTATED                               26                   2
  17Q GAIN WILD-TYPE                            174                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17Q GAIN MUTATED                       1                                5
  17Q GAIN WILD-TYPE                     8                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17Q GAIN MUTATED                    5              9
  17Q GAIN WILD-TYPE                 12             38
D31V9, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 169                601
  INFILTRATING LOBULAR CARCINOMA                 26                174
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 24
  MUCINOUS CARCINOMA                              5                 12
  OTHER  SPECIFY                                  9                 38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  0    12
  17Q GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          38   143
  17Q GAIN WILD-TYPE                       143   602
D31V11, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 48
  BLACK OR AFRICAN AMERICAN                      38                143
  WHITE                                         143                602
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V12, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 178
  17Q GAIN WILD-TYPE  33 697
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  178
  17Q GAIN WILD-TYPE   33  697
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 33
  NOT HISPANIC OR LATINO              178                697
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED   153  22
  18P GAIN WILD-TYPE 764 125
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               175                889 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                22                125 
$`18P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U 
      129.14        42.81        31.79        19.20        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EM TCGA-A2-A0EQ TCGA-A2-A0T2 TCGA-A2-A0YJ 
       24.79        33.76       101.72        79.76         8.38        18.61 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A7-A0CD TCGA-A7-A0CJ 
       31.73        23.47        33.93        47.31        38.30        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV 
       35.67        31.73        20.19        14.50        21.17        10.29 
TCGA-A7-A6VW TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07R TCGA-A8-A086 
        9.37         1.02        17.03         9.01         8.98        13.02 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 
       28.96        12.00        31.00       112.08        43.00        33.01 
TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09W TCGA-A8-A0A9 TCGA-A8-A0AB 
       12.00        29.98         8.98         0.99        27.02        17.03 
TCGA-AC-A2BK TCGA-AC-A2QH TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AN-A03Y 
       73.05        33.04        17.42        13.58         1.68         0.33 
TCGA-AN-A04C TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FY TCGA-AO-A03P TCGA-AO-A0J2 
        1.78         0.33         7.96         0.33        95.70        32.78 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS 
       55.33       115.27        90.58        48.36        61.87         0.53 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AR-A0TS TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AQ 
       17.79         2.56        84.10        65.36       101.00        99.32 
TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24U TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LH 
       50.89       104.28        77.69        98.66        89.00        20.25 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IQ 
       77.62       143.38       129.57       112.37       127.33       140.88 
TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A400 
      255.68       162.05       282.90        97.48        43.59         7.07 
TCGA-B6-A401 TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0C1 TCGA-BH-A0DD 
       85.35        68.12        61.51        74.89        44.02        45.83 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E9 TCGA-BH-A0EB 
       15.65         2.56        38.47         4.41        46.19        24.49 
TCGA-BH-A0EE TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18T TCGA-BH-A1FC TCGA-BH-A1FU 
       31.00        23.05        37.74         7.36       114.15        72.07 
TCGA-BH-A208 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U 
       57.83         9.63         5.26        11.93        11.77        12.66 
TCGA-C8-A1HG TCGA-C8-A27A TCGA-D8-A13Z TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JL 
       11.34        24.56        20.88        15.78        12.03        20.09 
TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1XW TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-D8-A27N 
       21.01        13.32        43.04        14.24        13.05         4.80 
TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A15C 
       37.51        40.96        75.98        31.96        63.62        22.82 
TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15O TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L7 
       17.29        18.21        50.79        22.19        11.08        60.36 
TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E9-A1N6 TCGA-E9-A1N8 
       73.64       106.75        26.99         8.28        22.29        34.16 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD 
       35.24         9.86         2.56         6.12        45.01         1.12 
TCGA-E9-A1RH TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 TCGA-E9-A5UP TCGA-E9-A6HE 
       46.59        40.73         0.69         7.13        26.40        27.85 
TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A3U0 
       28.77        22.82        29.82        23.11        19.99        17.49 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DC TCGA-GM-A3XL TCGA-HN-A2NL 
       16.77        24.99       109.87        83.34        69.30         2.60 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A8F5 
       14.47        14.79        16.08        15.68        19.53        19.59 
TCGA-OL-A5D7 TCGA-OL-A66I TCGA-OL-A6VO TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG 
       58.52        23.47        28.21         8.91         9.93        18.48 
TCGA-S3-AA12 
       18.87 

$`18P GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
      143.15        18.02        78.41       121.94        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        67.33        34.55        61.58        25.22 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       89.36        80.28       118.45        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       49.48        19.33        48.46        23.77        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       36.23        39.65        91.07        29.98        32.75        56.28 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       35.93        50.37        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        26.96        21.14        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G 
       35.47        37.45        33.11        29.79        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       13.41        14.70        11.97        14.93        13.74        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY 
       14.73        12.10        10.72        11.05        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99         9.99        45.07        15.06        36.95 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L 
        0.99        38.01        33.01        19.96        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 
       31.00         0.99        33.01        40.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T 
       49.05        45.07        33.07         1.02        25.02        19.04 
TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
       15.02        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
        0.99        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       87.12        26.04        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       29.26        16.80        14.53        19.33        14.96        11.44 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       13.71        18.67        12.26         8.22         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         2.30         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         9.96         7.36         7.46 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK 
        0.16         0.33         0.33         6.44         5.65         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.59         7.17         6.90         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T 
       80.28        61.35        66.77        81.63        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        21.40        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        65.10        26.24        50.24        62.04 
TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B 
       71.80        99.25       108.72       106.78       108.03        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        40.57        14.73        82.62 
TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       70.39        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        98.93        64.83        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      133.22        83.87       134.14       107.21       125.16       108.36 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      103.86        97.68        98.33        96.00        86.07        93.90 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        94.29        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W 
        2.76       112.77        97.84       105.27       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.76        99.62        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
       10.59       281.29        12.13       275.87        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50       233.62        18.77        84.59       165.76       129.07 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WT 
      102.77       140.48       100.70        89.46       157.41       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        18.35        21.47       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      245.10        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B 
      139.17       170.17        37.87        70.16        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        62.93        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       81.44        40.83        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       53.95        45.57        49.94        77.95        49.05        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       89.06        90.97        77.98        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV TCGA-BH-A0DX 
       13.91        78.28        17.26         3.22        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA 
       16.27        15.68        14.30         9.63        44.81        32.58 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       44.81        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        30.28        55.63        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        67.50        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       31.53        89.16        97.48        24.62       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       72.07       144.59        28.14        26.14        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       20.88        18.64        23.51         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V 
        9.44        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        48.53        12.56         3.16        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87        12.59        12.92         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.28         0.16        12.03        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
        8.28         9.67         9.53         0.03         9.50        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       56.81        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        55.50 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.15        18.90        53.00        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       20.12        19.40        20.38        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.80        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.64        12.99        15.16        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I 
        9.93        14.14        17.42        16.04        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       48.03        16.41        13.48         1.61        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       12.66        25.22        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       40.41        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        38.60        33.17        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        18.51        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F 
       23.87        14.79        25.05        23.34        20.71        21.63 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA 
       59.18         3.88        60.99        54.18        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       75.81        28.90        50.07       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56        30.61        34.92        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA 
       17.69        34.82        32.88        36.82        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ 
       39.55        41.62        35.77        25.84        18.94        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB 
       28.27        34.95         3.02        11.15        48.23        32.09 
TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
       40.24        46.65         6.58        21.27        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A 
       41.72        40.50        20.12        38.99         1.94        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.33        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.44        23.90        23.84        26.70         0.79        25.81 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       16.57        15.68        25.94        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       41.13        39.78        52.96        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       10.16        23.51        15.22        31.30        33.21         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       18.12        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
       25.05        17.06        15.32        14.70        22.26         2.63 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        14.50        12.36        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX 
       19.73        40.11        47.01        64.21        86.96         0.16 
TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26        18.81        21.07        20.68        19.27        13.84 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.39        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.33               0.03 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            282.90             281.29 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             26.99              28.14 
[1] "0.3 - 282.9 (27.0)" "0.0 - 281.3 (28.1)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P GAIN MUTATED        10       14        0        2        76        34
  18P GAIN WILD-TYPE      79       71        6        4       277       218
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           1         18          6          8        4
  18P GAIN WILD-TYPE         1        136         23         57       16
                    vv
clus                 STAGE TIS STAGE X
  18P GAIN MUTATED           0       3
  18P GAIN WILD-TYPE         1      10
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 14                 71
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                76                277
  STAGE IIB                34                218
  STAGE III                 1                  1
  STAGE IIIA               18                136
  STAGE IIIB                6                 23
  STAGE IIIC                8                 57
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    36 112  21   6
  18P GAIN WILD-TYPE 240 512 115  34
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               36                240
  T2              112                512
  T3               21                115
  T4                6                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P GAIN MUTATED   101  44  16  13
  18P GAIN WILD-TYPE 406 314 103  64
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0              101                406
  N1               44                314
  N2               16                103
  N3               13                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   150   4
  18P GAIN WILD-TYPE 739  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    150    4
  18P GAIN WILD-TYPE  739   18
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0              150                739
  1                4                 18
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED   174   3
  18P GAIN WILD-TYPE 894   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED    174    3
  18P GAIN WILD-TYPE  894    9
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE              174                894
  MALE                  3                  9
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    65  92
  18P GAIN WILD-TYPE 364 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     65   92
  18P GAIN WILD-TYPE  364  426
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                65                364
  YES               92                426
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P GAIN MUTATED                            0                           145
  18P GAIN WILD-TYPE                          1                           625
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P GAIN MUTATED                               15                   2
  18P GAIN WILD-TYPE                            185                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18P GAIN MUTATED                       2                                5
  18P GAIN WILD-TYPE                     7                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18P GAIN MUTATED                    0              7
  18P GAIN WILD-TYPE                 17             40
D32V9, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 145                625
  INFILTRATING LOBULAR CARCINOMA                 15                185
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 24
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  7                 40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     7
  18P GAIN WILD-TYPE                                1    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                          49   101
  18P GAIN WILD-TYPE                       132   644
D32V11, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      49                132
  WHITE                                         101                644
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V12, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     3 141
  18P GAIN WILD-TYPE  36 734
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3  141
  18P GAIN WILD-TYPE   36  734
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO              141                734
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED   129  22
  18Q GAIN WILD-TYPE 788 125
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               151                913 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                22                125 
$`18Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A04U 
      129.14        42.81        31.79        19.20        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D2 TCGA-A2-A0EM TCGA-A2-A0EQ TCGA-A2-A0T2 TCGA-A2-A0YJ 
       24.79        33.76       101.72        79.76         8.38        18.61 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        23.47       105.34        33.93        47.31        35.93 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A13E TCGA-A7-A4SD TCGA-A7-A6VW TCGA-A8-A079 
       38.30        30.61        20.19        14.50         9.37         9.01 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A086 TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08T 
       10.98         8.98        13.02        28.96        12.00       112.08 
TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A0A9 
       43.00        33.01        12.00        29.98         8.98        27.02 
TCGA-A8-A0AB TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AN-A03Y TCGA-AN-A04C 
       17.03        14.96        13.58         1.68         0.33         1.78 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FY TCGA-AN-A0XO 
        0.33         0.33         0.33         7.96         0.33        12.33 
TCGA-AO-A03P TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A12A TCGA-AO-A12F TCGA-AO-A1KQ 
       95.70        55.33       115.27        90.58        48.36        61.87 
TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A24K TCGA-AR-A24Q 
        0.53         2.56        65.36       101.00        50.89       104.28 
TCGA-AR-A24Z TCGA-AR-A2LH TCGA-B6-A0I2 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IM 
       98.66        20.25       143.38       129.57       112.37       127.33 
TCGA-B6-A0IQ TCGA-B6-A0RO TCGA-B6-A0WS TCGA-B6-A1KC TCGA-B6-A400 TCGA-B6-A401 
      140.88       162.05        97.48        43.59         7.07        85.35 
TCGA-B6-A408 TCGA-BH-A0BL TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DP 
       68.12        74.89        41.75        44.02        45.83        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EB 
        2.56        38.47         4.41         9.63        46.19        24.49 
TCGA-BH-A0HB TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q 
       26.50        50.79        23.05        26.66        37.74        55.63 
TCGA-BH-A18T TCGA-BH-A208 TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L 
        7.36        57.83        18.64         9.63         5.26        11.93 
TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A1HG TCGA-C8-A1HN TCGA-C8-A27A TCGA-D8-A1JF 
       11.77        12.66        11.34        12.95        24.56        12.03 
TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1Y2 TCGA-D8-A27H TCGA-E2-A10B 
       20.09        21.01        13.32        14.24        13.05        37.51 
TCGA-E2-A14T TCGA-E2-A14X TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A1IN 
       75.98        31.96        22.82        17.29        18.21        22.19 
TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A56Z 
       11.08        60.36        73.64       106.75        26.99         8.28 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 
       22.29        34.16        35.24         9.86        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A249 
        6.12        45.01         1.12        40.73         0.69         7.13 
TCGA-E9-A3HO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1P4 
       38.07        26.40        27.85        28.77        22.82        29.82 
TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-EW-A6SA TCGA-EW-A6SB TCGA-GM-A2DC TCGA-GM-A3XL 
       23.11        19.99        16.77        24.99        83.34        69.30 
TCGA-LD-A7W5 TCGA-LL-A5YP TCGA-LL-A7SZ TCGA-OL-A66I TCGA-OL-A97C TCGA-S3-A6ZG 
        7.10        14.79        19.53        23.47         8.91        18.48 
TCGA-S3-AA10 
       19.27 

$`18Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
      143.15        18.02        78.41       121.94        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        67.33        34.55        61.58        25.22 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
       89.36        80.28       118.45        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13        49.84        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       32.55        25.28        18.21        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       49.48        19.33        48.46        23.77        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        42.44        17.19        18.15        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       39.65        91.07        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.14        21.90        35.31        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        29.79        31.73        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.42         8.75        13.02        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       12.00        32.05         9.99         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08F 
       45.07        15.06        36.95         0.99        38.01        33.01 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       19.96        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       33.01        40.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        50.04        49.05        45.07 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02        25.02        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95        22.95        73.91         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V 
       24.79        29.26        16.80        14.53        19.33        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC 
       13.71        17.42        18.67        12.26         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 
       20.19         1.12         1.32         2.30         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.33         0.62         2.96         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL 
        7.46         0.16         6.44         5.65         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         7.04         0.33         0.36         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.36         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       32.78        21.40        52.18        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       76.77        65.10        26.24        50.24        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D 
       99.25       108.72       106.78       108.03        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       57.30        41.62        40.57        14.73        82.62        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       93.90        99.32        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 
       77.69       105.30        32.58        98.76        89.00        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ 
       93.30        85.64        71.05        93.83       166.42        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      281.29        12.13       275.87        50.70        65.72       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE 
      233.62        18.77        84.59       165.76       129.07       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
      188.68        79.63        18.35        21.47       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       245.10        28.27        68.94        58.88       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A402 TCGA-B6-A409 
       73.51       139.17       170.17        37.87        70.16        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        62.93        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       63.09        81.44        40.83        39.55        39.16        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.63        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        61.51        21.70        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        53.95        45.57        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       49.05        89.06        90.97        77.98        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DV 
       29.98        13.91        78.28        17.26         3.22        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA 
       70.88        16.27        15.68        14.30        44.81        32.58 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI 
       53.26        24.56        23.08        41.00        52.96        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M 
       32.91         4.90        35.93        20.12        90.84        72.56 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       30.28        37.55        66.05        51.39        51.16        67.50 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       91.99       113.82        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.62       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
       72.07        28.14        26.14        38.60        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5J0 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N 
       23.51         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56         3.16        13.51         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI 
       12.92         4.11         4.08        12.33        10.92        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        10.42        12.33        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.53        12.36        12.95         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.50        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       14.17        17.49        16.50        55.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        53.00        14.01        18.97        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       19.40        20.38        12.20        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT 
       17.69        55.30        16.41        15.85        16.31        16.64 
TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       12.99        15.16        43.04        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I 
        9.93        14.14        17.42        16.04        13.45        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       48.03        16.41        13.48         4.80         1.61        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18        12.66        25.22        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       46.59        40.41        40.11        28.44        28.87        47.15 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U 
       44.68        40.96        38.24        38.60        33.17        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       34.26        32.02        69.34        18.51        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       23.34        20.71        21.63        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        51.39        76.57        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       60.99        54.18        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
       50.07       102.61         8.75        43.04        34.55        43.56 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        38.76        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       32.88        36.82        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R5 
       35.77        25.84        18.94        24.82        28.27         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
       11.15        48.23        32.09        40.24        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H 
       37.74        39.09        38.37        41.03        41.72        40.50 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       20.12        38.99         1.94        24.56        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
        9.47        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       26.70         0.79        25.81        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
       18.21        18.90        13.25        16.57        15.68        25.94 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90         6.15        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       15.22        31.30        33.21         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
      216.76        79.10        75.02        70.85        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        15.32        14.70        14.47        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 
       16.08        15.68         7.46        14.50        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        20.38        26.70        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       42.77        26.04        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
       40.11        47.01        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
        9.93        18.81        21.07        20.68        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.39        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.33               0.03 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            162.05             282.90 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             24.56              28.50 
[1] "0.3 - 162.1 (24.6)" "0.0 - 282.9 (28.5)"
[1] "hr=" "1.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q GAIN MUTATED         9       10        0        2        64        32
  18Q GAIN WILD-TYPE      80       75        6        4       289       220
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           1         16          4          9        4
  18Q GAIN WILD-TYPE         1        138         25         56       16
                    vv
clus                 STAGE TIS STAGE X
  18Q GAIN MUTATED           0       2
  18Q GAIN WILD-TYPE         1      11
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                 10                 75
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                64                289
  STAGE IIB                32                220
  STAGE III                 1                  1
  STAGE IIIA               16                138
  STAGE IIIB                4                 25
  STAGE IIIC                9                 56
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    29 101  17   5
  18Q GAIN WILD-TYPE 247 523 119  35
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               29                247
  T2              101                523
  T3               17                119
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q GAIN MUTATED    83  42  13  13
  18Q GAIN WILD-TYPE 424 316 106  64
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               83                424
  N1               42                316
  N2               13                106
  N3               13                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED   134   4
  18Q GAIN WILD-TYPE 755  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    134    4
  18Q GAIN WILD-TYPE  755   18
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0              134                755
  1                4                 18
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED   150   3
  18Q GAIN WILD-TYPE 918   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED    150    3
  18Q GAIN WILD-TYPE  918    9
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE              150                918
  MALE                  3                  9
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    62  72
  18Q GAIN WILD-TYPE 367 446
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     62   72
  18Q GAIN WILD-TYPE  367  446
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                62                367
  YES               72                446
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q GAIN MUTATED                            0                           126
  18Q GAIN WILD-TYPE                          1                           644
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q GAIN MUTATED                               13                   1
  18Q GAIN WILD-TYPE                            187                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18Q GAIN MUTATED                       1                                5
  18Q GAIN WILD-TYPE                     8                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18Q GAIN MUTATED                    0              6
  18Q GAIN WILD-TYPE                 17             41
D33V9, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 126                644
  INFILTRATING LOBULAR CARCINOMA                 13                187
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 24
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  6                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     8
  18Q GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                          37    92
  18Q GAIN WILD-TYPE                       144   653
D33V11, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      37                144
  WHITE                                          92                653
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V12, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     3 120
  18Q GAIN WILD-TYPE  36 755
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3  120
  18Q GAIN WILD-TYPE   36  755
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO              120                755
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED   168  20
  19P GAIN WILD-TYPE 749 127
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               188                876 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                127 
$`19P GAIN MUTATED`
TCGA-4H-AAAK TCGA-A1-A0SF TCGA-A1-A0SK TCGA-A2-A04Q TCGA-A2-A0CT TCGA-A2-A0D0 
       11.44        48.10        31.79        78.41        75.25        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EY 
       34.55        33.76        79.76        35.05        34.29        63.29 
TCGA-A2-A0SX TCGA-A2-A0T6 TCGA-A2-A0YJ TCGA-A2-A1G1 TCGA-A2-A3XU TCGA-A2-A3Y0 
       50.43        18.90        18.61        19.20        29.98        50.83 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC 
       21.14        38.30        35.31        30.61        33.11        29.79 
TCGA-A7-A26E TCGA-A7-A3J0 TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A8-A06X TCGA-A8-A07R 
       31.36        10.29        21.17        12.10        31.00         8.98 
TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E 
       38.01        43.00        17.95        12.00        12.00        49.05 
TCGA-A8-A09M TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FO 
       33.07         0.99        27.02        22.95        73.91        74.14 
TCGA-AC-A3OD TCGA-AC-A5EI TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A03Y 
       14.83        14.53        17.42        13.58        20.19         0.33 
TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN 
        1.78         7.36         7.00         0.36         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A0JL 
        5.59        80.28        81.63        32.78        20.32        55.33 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A1KS 
      115.27       106.78        90.58        98.27        64.04         0.53 
TCGA-AQ-A54O TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K 
       32.91        65.36        61.28        86.53        86.43        50.89 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LQ TCGA-AR-A2LR 
      105.30        32.58        71.05        93.83        40.54        57.27 
TCGA-AR-A5QM TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A0WY 
       73.35       112.37       233.62       282.90        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0B6 
      206.86        43.59        73.51        85.35        62.93        81.63 
TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD 
       37.22        21.70        41.75        44.02        90.97        45.83 
TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K TCGA-BH-A18N 
       17.26        46.19        30.35        36.85        90.84        37.74 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A208 TCGA-BH-A5IZ 
       55.63         7.36        51.16        91.99        57.83        18.64 
TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12V TCGA-C8-A130 TCGA-C8-A1HM TCGA-C8-A275 
        5.26        11.93        12.66         3.16        12.33         0.03 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JF 
       20.88        14.17        13.48        19.20        14.17        12.03 
TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XU 
       14.01        20.09        20.38        17.79        21.80        12.99 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B TCGA-E2-A14N 
        4.80        10.09        12.53        12.26        37.51        47.15 
TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       38.60        31.96        69.34        18.51        63.62        23.24 
TCGA-E2-A15M TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A576 
       11.05        33.70        22.19        28.90        50.07        34.29 
TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF TCGA-E9-A1R6 
       17.69        34.16        36.20        36.56        35.24        11.15 
TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A22E TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       45.01         1.12        41.72        20.12         0.69         1.94 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP 
        7.13        12.33        30.18        26.70         0.79        26.40 
TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A423 TCGA-EW-A6SB 
       28.77        29.82        19.99        13.94        10.16        24.99 
TCGA-GI-A2C9 TCGA-GM-A2DD TCGA-HN-A2NL TCGA-LD-A7W6 TCGA-LL-A5YN TCGA-LL-A5YP 
      109.87        75.02         2.60        13.28        14.70        14.79 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RW TCGA-OL-A97C 
        2.63        15.68        19.59        17.49        36.36         8.91 
TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 
        9.93        18.48        21.07        20.68        19.27        18.87 
TCGA-UU-A93S TCGA-W8-A86G 
        3.81        11.41 

$`19P GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        18.02       121.94        73.84        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       114.81        92.48        88.60       107.93        77.19 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D3 TCGA-A2-A0D4 
        5.19        98.99       107.93        56.81        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       118.45        74.40        72.00 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       50.47        21.90        21.67        49.48        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        91.07        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D 
       21.90        34.29        35.47        37.45        35.67        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G 
       20.19        25.15        23.61        29.56        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        17.92        14.73        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       17.98        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       53.98         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       14.01        12.00        32.05         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
        9.99        31.00        31.00         0.99        33.01       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A 
       40.01        33.01        30.97        41.98         9.99         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q 
        1.02        50.04        45.07        29.98         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       19.04        13.02        21.04        17.03        38.04         0.95 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI 
       90.71        60.92        87.12        26.04        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ 
       14.66        32.45         6.48        16.31        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       24.79        29.26        16.80        19.33        14.96        11.44 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       13.71        18.67        12.26         1.68         8.22         0.03 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 
        1.12         1.32         2.30         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM 
        0.62         2.96         1.71         9.96         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY 
        7.59         7.17         6.90         7.04         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.36        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        0.33         0.33         5.33        61.35        66.77        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 
       68.75        47.87        58.95        29.13        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        37.48        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E 
       62.04        71.80        99.25       108.72       108.03        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        32.52         2.56        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24       133.22        83.87       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      125.16       108.36       101.00       103.86        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       96.00        86.07        93.90        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       94.29        33.73       160.90        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       77.69        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL 
       85.64       166.42        20.25        86.53        54.21        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       63.62        38.17        39.39        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48       100.70        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       79.63        18.35       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
       58.88       101.52       139.17       170.17        37.87         7.07 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
       70.16        68.12        18.84       103.63        71.15        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       20.45        25.55        63.09        81.44        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        70.22        84.13        51.68        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        61.51        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        53.95        45.57        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       49.05        89.06        77.98        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        32.58        24.49        31.00        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P 
        4.90        35.93        20.12        26.66        72.56        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET 
       37.55        66.05        51.39        67.50       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.62       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A8FY 
       10.52       109.28        20.88        23.51         9.63         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       12.56        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.08        12.33        10.92        11.34        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 
       12.36        12.95         8.28         9.67         9.53         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       24.56        14.43        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       13.41        19.46        56.81        13.25        20.58        13.97 
TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        17.49        16.50        55.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM 
       18.90        53.00        18.97        20.09        20.12        19.40 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        18.58        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        14.50        19.92        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31        16.64        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       16.41        13.48         1.61        13.08        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        40.11        28.44        28.87 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       44.68        40.96        38.24        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       34.26        32.02        69.96        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        50.79        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18         3.88        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       60.36        73.64        19.66        24.59        75.81       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        34.92        38.76        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        22.29        39.55        41.62        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE 
        6.12         3.02        48.23        32.09        40.24        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
        6.58        21.27        46.59        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G 
       42.25        37.74        39.09        38.37        41.03        40.73 
TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
       40.50        38.99        24.56        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE 
       32.91        30.44        23.90        23.84        25.81        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        18.90         6.15        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC 
       34.03        17.49        23.51        15.22        16.77        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
       33.21         7.40        59.57       216.76        79.10        83.34 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 
       11.57        21.24        13.22         7.10        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO 
       32.75        29.23        25.05        17.06        15.32        14.47 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       22.26        16.08         7.46        14.50        19.53        12.36 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF 
       47.01        64.21        86.96         0.16         0.26        18.81 
TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ 
       13.84        17.39        17.26        13.94        17.03        66.84 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.03               0.03 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            282.90             281.29 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            28.835             27.715 
[1] "0.0 - 282.9 (28.8)" "0.0 - 281.3 (27.7)"
[1] "hr=" "1.1"
D34V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P GAIN MUTATED        13       13        1        2        79        39
  19P GAIN WILD-TYPE      76       72        5        4       274       213
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           0         24          5         11        1
  19P GAIN WILD-TYPE         2        130         24         54       19
                    vv
clus                 STAGE TIS STAGE X
  19P GAIN MUTATED           0       0
  19P GAIN WILD-TYPE         1      13
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  13                 76
  STAGE IA                 13                 72
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA                79                274
  STAGE IIB                39                213
  STAGE III                 0                  2
  STAGE IIIA               24                130
  STAGE IIIB                5                 24
  STAGE IIIC               11                 54
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED    37 122  24   7
  19P GAIN WILD-TYPE 239 502 112  33
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               37                239
  T2              122                502
  T3               24                112
  T4                7                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P GAIN MUTATED   104  55  19  12
  19P GAIN WILD-TYPE 403 303 100  65
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0              104                403
  N1               55                303
  N2               19                100
  N3               12                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   163   1
  19P GAIN WILD-TYPE 726  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    163    1
  19P GAIN WILD-TYPE  726   21
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0              163                726
  1                1                 21
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED   186   4
  19P GAIN WILD-TYPE 882   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED    186    4
  19P GAIN WILD-TYPE  882    8
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE              186                882
  MALE                  4                  8
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    71  96
  19P GAIN WILD-TYPE 358 422
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     71   96
  19P GAIN WILD-TYPE  358  422
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                71                358
  YES               96                422
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P GAIN MUTATED                            1                           140
  19P GAIN WILD-TYPE                          0                           630
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P GAIN MUTATED                               26                   2
  19P GAIN WILD-TYPE                            174                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19P GAIN MUTATED                       3                                5
  19P GAIN WILD-TYPE                     6                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19P GAIN MUTATED                    2             11
  19P GAIN WILD-TYPE                 15             36
D34V9, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 140                630
  INFILTRATING LOBULAR CARCINOMA                 26                174
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 24
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 11                 36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     8
  19P GAIN WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                          36   134
  19P GAIN WILD-TYPE                       145   611
D34V11, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      36                145
  WHITE                                         134                611
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V12, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     6 157
  19P GAIN WILD-TYPE  33 718
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      6  157
  19P GAIN WILD-TYPE   33  718
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 33
  NOT HISPANIC OR LATINO              157                718
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED   196  24
  19Q GAIN WILD-TYPE 721 123
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               220                844 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                24                123 
$`19Q GAIN MUTATED`
TCGA-4H-AAAK TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A2-A04P TCGA-A2-A04Q 
       11.44        48.10        13.68        31.79        18.02        78.41 
TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET 
       75.25        67.33        33.76        25.22        79.76        35.05 
TCGA-A2-A0EU TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T2 TCGA-A2-A0T3 
       34.29        24.72        63.29        50.43         8.38        49.84 
TCGA-A2-A0T6 TCGA-A2-A0YH TCGA-A2-A1G0 TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3Y0 
       18.90        21.67        20.25        33.93        29.98        50.83 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D 
       21.14        38.30        30.61        33.11        29.79        31.73 
TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A3J0 TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VX 
       31.36        21.73        10.29        14.50        21.17        10.42 
TCGA-A8-A06O TCGA-A8-A07B TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08X TCGA-A8-A092 
       13.02        43.00         8.98        38.01        43.00        30.97 
TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09Q TCGA-A8-A0A7 
       17.95        12.00        12.00        49.05        25.02         0.99 
TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A5EI 
       27.02        22.95        73.91        74.14        14.83        14.53 
TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A8OS TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK 
       17.42        13.58         2.30         0.33         1.78         7.36 
TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XW 
        0.16         7.00         0.36         0.33         0.33         5.59 
TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J7 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
       81.63        32.78        20.32       106.78        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AQ-A54O 
       64.04        48.36        70.39         0.53         2.56        32.91 
TCGA-AR-A0TQ TCGA-AR-A0TW TCGA-AR-A0U0 TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       98.33        98.93        65.36        61.28        86.53        86.43 
TCGA-AR-A24K TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 
       50.89       105.30        32.58        98.66        89.00        71.05 
TCGA-AR-A256 TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0IH TCGA-B6-A0IJ 
       93.83        40.54        57.27        73.35       112.37       233.62 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A0WZ 
      165.76       140.88       100.70       282.90       113.79       206.86 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B3 
       43.59        73.51        85.35        62.93        20.45        39.55 
TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0C1 
       81.63        37.22        61.51        21.70        74.89        44.02 
TCGA-BH-A0DD TCGA-BH-A0DO TCGA-BH-A0E9 TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18K 
       45.83        17.26        46.19        30.35        36.85        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN 
       26.66        37.74        55.63         7.36        51.16        67.50 
TCGA-BH-A1EO TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A208 TCGA-BH-A6R9 TCGA-C8-A12L 
       91.99        12.00        55.69        57.83         5.26        11.93 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A130 TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       12.66        12.66         3.16        12.03        12.33        12.95 
TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 
        8.28         9.53         0.03        20.88        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       13.48        19.20        14.17        12.03        53.00        14.01 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XU 
       20.09        20.38        14.70        17.79        21.80        12.99 
TCGA-D8-A1XW TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A10B 
       43.04         4.80        10.09        12.53        12.26        37.51 
TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       40.11        47.15        38.60        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15F TCGA-E2-A15M TCGA-E2-A1II 
       63.62        69.96        23.24        21.63        11.05        33.70 
TCGA-E2-A1IN TCGA-E2-A1LG TCGA-E2-A576 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1R6 
       22.19        50.07        34.29        34.16        36.20        11.15 
TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A248 
       45.01         1.12        47.64        38.37        41.72         1.94 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FK TCGA-E9-A5FL 
        7.13        12.33        30.18        30.44        26.70         0.79 
TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PD TCGA-EW-A1PH 
       26.40        28.77        29.82         7.86        13.94        19.96 
TCGA-EW-A423 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GM-A2DD TCGA-HN-A2NL TCGA-LD-A7W6 
       10.16        24.99        33.21        75.02         2.60        13.28 
TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
       14.79         2.63        15.68        19.59        17.49        22.39 
TCGA-OL-A5RW TCGA-OL-A66I TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       36.36        23.47         8.91         9.93        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 TCGA-W8-A86G 
       20.68        19.27        18.87        11.41 

$`19Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        42.81        40.14        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        14.37        43.43        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
      143.15       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48        88.60       107.93        77.19         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93        56.81        34.55        61.58       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
       80.28       118.45        74.40        72.00        31.82        61.94 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       17.13        20.52        17.46        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       18.21        50.47        21.90        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       48.46        31.73        23.77        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       39.65        91.07        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA 
       21.90        35.31        34.29        35.47        37.45        35.67 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G 
       20.19        25.15        23.61        29.56        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 
       23.80        20.61        22.32        11.34        10.59        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF 
       13.41        14.70        11.97        14.93        13.74        17.92 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       14.73        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99        24.99         9.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
       15.06        36.95        13.02         0.99        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       19.96        12.00        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 
        0.99        33.01       112.08        40.01        33.01        41.98 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99         1.02        50.04        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02         8.98        19.04        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB 
       14.01        12.00        19.04        13.02        21.04        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       38.04         0.95         5.72         1.48        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       33.04        19.33        14.66        32.45         6.48        16.31 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XS 
       15.48        23.24        24.79        29.26        16.80        19.33 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO 
       14.96        11.44        13.71        18.67        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X 
        8.22         0.03        20.19         1.12         1.32         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         2.96         1.71         9.96 
TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         0.33         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.96         7.59         7.17         6.90         7.04         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         5.36         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         0.33         5.33        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       21.40        52.18        26.04        37.48        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       99.25       108.72       108.03        57.30        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        82.62        61.87        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP 
      130.09         5.65        15.62        32.52        19.20       140.55 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
        5.26        84.10       109.02        75.22        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       86.07        93.90        99.32        17.23        37.81        94.29 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28       112.77        97.84       105.27        77.69 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       98.76        99.62        93.30        85.64       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       86.53        54.21        66.15        63.62        38.17        39.39 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       33.30        38.96        10.59        77.62       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       275.87       129.57        50.70        65.72       146.50 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RG 
       18.77       127.33        84.59       129.07       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      102.77       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       79.63        18.35        21.47       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.88       101.52       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        70.16        68.12        18.84       103.63        71.15 
TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       59.84        25.55        63.09        81.44        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        84.13        51.68        32.02        18.21        43.53 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 
       45.57        49.94        77.95        49.05        41.75        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ 
       44.81        32.58        24.49        31.00        24.43        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        53.26        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       35.93        20.12        72.56        30.28        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX TCGA-BH-A1EY 
       51.39       113.82        82.85        42.28        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.62       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        38.60        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       109.28        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
        9.63         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12X 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       48.53        12.56        13.51         1.87        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
        4.11         4.08        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
        0.16        10.42        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
       12.95         9.67         9.50        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A146 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.25        20.58        21.14        17.49        16.50        55.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       15.78        18.15        18.90        18.97        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 
       19.40        21.01        12.20        13.32        18.58        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        14.50        19.92        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY 
       16.41        15.85        16.31        16.64        15.16        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.32        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.48         1.61        13.08        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       16.18        12.66        25.22        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P 
       46.59        40.41        28.44        28.87        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        17.29        20.71        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
       53.92         9.04        20.58        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       14.07        51.39        76.57        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO 
       70.36        33.73        28.44        59.18         3.88        60.99 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        60.36        73.64        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       75.81        28.90       106.75       102.61         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       26.99        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       38.76        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE 
        6.12         3.02        48.23        32.09        40.24        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        6.58        21.27        46.59        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        41.03        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        0.69        38.99        24.56        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       32.91        23.90        23.84        25.81        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       15.68        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99         6.15        10.52        14.43        34.55 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 
       23.51        15.22        16.77        31.30         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DF TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       13.55        18.12        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
       13.22         7.10        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       25.05        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 
       16.08         7.46        14.50        19.53        12.36        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       28.21        19.73        40.11        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZF TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 
        0.16         0.26        18.81        13.84        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        66.84        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.03               0.03 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            282.90             281.29 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             26.86              27.96 
[1] "0.0 - 282.9 (26.9)" "0.0 - 281.3 (28.0)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q GAIN MUTATED        18       15        2        2        93        44
  19Q GAIN WILD-TYPE      71       70        4        4       260       208
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           0         28          8         10        1
  19Q GAIN WILD-TYPE         2        126         21         55       19
                    vv
clus                 STAGE TIS STAGE X
  19Q GAIN MUTATED           0       0
  19Q GAIN WILD-TYPE         1      13
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  18                 71
  STAGE IA                 15                 70
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA                93                260
  STAGE IIB                44                208
  STAGE III                 0                  2
  STAGE IIIA               28                126
  STAGE IIIB                8                 21
  STAGE IIIC               10                 55
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    49 138  27   9
  19Q GAIN WILD-TYPE 227 486 109  31
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               49                227
  T2              138                486
  T3               27                109
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q GAIN MUTATED   122  69  20  11
  19Q GAIN WILD-TYPE 385 289  99  66
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0              122                385
  N1               69                289
  N2               20                 99
  N3               11                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   199   1
  19Q GAIN WILD-TYPE 690  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    199    1
  19Q GAIN WILD-TYPE  690   21
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0              199                690
  1                1                 21
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED   219   4
  19Q GAIN WILD-TYPE 849   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED    219    4
  19Q GAIN WILD-TYPE  849    8
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE              219                849
  MALE                  4                  8
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    90 105
  19Q GAIN WILD-TYPE 339 413
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     90  105
  19Q GAIN WILD-TYPE  339  413
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                90                339
  YES              105                413
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q GAIN MUTATED                            0                           170
  19Q GAIN WILD-TYPE                          1                           600
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q GAIN MUTATED                               30                   3
  19Q GAIN WILD-TYPE                            170                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19Q GAIN MUTATED                       3                                5
  19Q GAIN WILD-TYPE                     6                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19Q GAIN MUTATED                    2             10
  19Q GAIN WILD-TYPE                 15             37
D35V9, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 170                600
  INFILTRATING LOBULAR CARCINOMA                 30                170
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 24
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 10                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0    12
  19Q GAIN WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                          38   159
  19Q GAIN WILD-TYPE                       143   586
D35V11, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 48
  BLACK OR AFRICAN AMERICAN                      38                143
  WHITE                                         159                586
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V12, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     9 182
  19Q GAIN WILD-TYPE  30 693
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      9  182
  19Q GAIN WILD-TYPE   30  693
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              182                693
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   353  59
  20P GAIN WILD-TYPE 564  88
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               412                652 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                59                 88 
$`20P GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
      129.14       131.67        14.37        48.10        14.27        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04X 
       13.68         7.96        39.32        19.20        18.02        55.43 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       99.12        24.79        77.19        75.25         5.19        98.99 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET 
       56.81        67.33        33.76        25.22        79.76        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       34.29        31.82        63.29        27.12        44.88        50.43 
TCGA-A2-A0T2 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ 
        8.38        20.75        25.28        21.90        21.67        18.61 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A3KC 
       23.77        17.36        60.72        20.25        19.20        36.23 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A4RX TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ 
       33.93        91.07        24.39        21.14        38.30        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E 
       37.45        35.67        33.11        29.79        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SD 
       25.15        23.74        20.61        14.70        14.93        14.50 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U 
       14.73        10.29         9.37        13.02        17.98        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U 
       26.01        17.03        53.98        10.98         8.98        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08J 
        9.99        45.07        13.02        38.01        12.00        37.05 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       31.00         0.99        33.01        30.97        17.95        41.98 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N 
        1.02        50.04        49.05        45.07        29.98         1.02 
TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23G TCGA-AC-A23H 
        8.98        12.00         0.99        27.02        73.91         5.72 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3QQ TCGA-AC-A5EH 
       99.35        26.04        33.04        14.66        24.13        16.80 
TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A8OP 
       19.33        11.44        17.42        13.58         1.68        20.19 
TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AJ 
        1.12         0.33         0.33         2.96         1.78         9.96 
TCGA-AN-A0AS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO 
        0.33         0.33         0.36         0.33         5.36        12.33 
TCGA-AN-A0XP TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.30        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JE 
       29.13        52.18        20.32        53.03        72.00        76.77 
TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
       50.24        55.33        71.80       106.78        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A04L 
       57.30        48.36        82.62        61.87         0.53       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT TCGA-AR-A0TV 
       15.62        32.91        19.20        98.33       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AP 
       98.93        64.83        65.36        83.87       108.36        93.90 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       61.28        86.53       160.90       104.28       112.77        97.84 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
      105.30        32.58        98.66        89.00        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-B6-A0I1 
       71.05        93.83        54.21        66.15        73.35        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IO 
      143.38       281.29       129.57        65.72       112.37       165.76 
TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY 
      255.68       212.25       162.05       282.90        79.63       113.79 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 
       43.59        73.51        85.35        70.16        68.12        18.84 
TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0BA 
      103.63        62.93        20.45        40.83        81.63        37.22 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV 
       43.53        61.51        74.89        75.48        45.57        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DL 
       49.05        41.75        44.02        45.83        23.44        78.28 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI 
        4.41        14.30         9.63        46.19        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HQ 
       30.35        23.08        41.00        26.50        20.38        36.85 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       27.25        50.79         5.59        42.35        44.81        23.05 
TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       90.84        37.74        55.63         7.36        51.39        67.50 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 
       91.99        42.28        12.00        55.69        49.58        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A203 
       97.48        24.62        36.92        72.07        26.14        38.60 
TCGA-BH-A28Q TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L 
        6.44        18.64        23.51         9.63         5.26        11.93 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A138 TCGA-C8-A1HI 
       48.53         3.16        13.51         1.87         4.08        11.28 
TCGA-C8-A1HM TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M8 TCGA-C8-A8HR 
       12.33         8.28         9.53         9.50        12.95        13.41 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.88        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       14.17        55.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 
       53.00        14.01        18.97        21.01        13.32        18.58 
TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XW 
       18.15        15.22        19.92        16.31        12.99        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27I TCGA-D8-A27L 
       16.54        15.32        15.52         9.93        14.43        16.41 
TCGA-D8-A27M TCGA-D8-A27W TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A10B TCGA-E2-A10C 
       13.48        12.26        16.18        25.22        37.51        40.11 
TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Z 
       44.68        40.96        75.98        34.26        31.96        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15C 
       63.62        69.96        23.24        19.43        25.05        22.82 
TCGA-E2-A15H TCGA-E2-A15K TCGA-E2-A15O TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD 
       12.92         9.04        50.79        76.57        53.62        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L9 
       33.73        33.70        22.19        60.99        60.36        19.66 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
      106.75       102.61         8.75         8.28        30.61        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND 
       34.29        17.69        22.29        34.16        36.20        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R4 
       35.77        35.24         9.86        24.82         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG 
        3.02        45.01        32.09        40.24         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       46.59        34.45        37.74        38.37        41.03        41.72 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y 
       38.99         1.94         7.13        12.33        29.72        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J5 
       26.70         0.79        26.40         8.48        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB 
       28.77        29.85        41.13        23.11        18.48        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A6SA TCGA-EW-A6SD 
        6.15        13.94        19.96        52.73        16.77        33.21 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U 
       83.34        75.02        72.10        69.30         2.60        21.24 
TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ 
        7.10        32.75        15.32        14.70        22.26         2.63 
TCGA-LL-A73Z TCGA-LL-A7SZ TCGA-LQ-A4E4 TCGA-OL-A5RZ TCGA-OL-A66I TCGA-OL-A66N 
        7.46        19.53        27.91        22.32        23.47        26.04 
TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 
        8.91        86.96         9.93        18.81        18.48        19.27 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-Z7-A8R6 
       13.94        17.03        11.41       107.05 

$`20P GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SQ 
        8.52        43.43        47.24        31.79        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      143.15        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      101.98        36.13       136.73       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
      107.93       107.93        34.55        61.58       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX 
       80.28       118.45        74.40        72.00        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 
       99.19        54.64        44.28        17.52        17.13        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YF 
       20.52        17.46        18.90        32.55        18.21        50.47 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       49.48        19.33        48.46        31.73        23.47        22.45 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV 
       18.15       105.34        10.59        39.65        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        26.96        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       35.47        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZV 
       13.41        11.97        13.74        21.17        17.92        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.72        11.05        10.42         8.75        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       53.06        31.00         1.02         9.01        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
        7.99        15.06        36.95         0.99        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       19.96         9.99        31.00       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09M 
       33.01        12.00         9.99         9.99        12.00        33.07 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 
       25.02        19.04        15.02         0.99        14.01        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04        17.03        38.04         0.95        22.95 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        73.05        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       87.12        74.14        19.33        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       14.83        22.19        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XU 
       15.48        23.24        24.79        29.26        14.53        14.96 
TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OR 
       13.71        18.67        12.26         8.22         0.03         1.32 
TCGA-AC-A8OS TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04D TCGA-AN-A0AK 
        2.30         0.23         0.33         0.62         1.71         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.90         7.04 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33         0.33         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        0.33         5.33         5.59        68.75        47.87        58.95 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA 
       32.78        21.40        26.04        37.48        22.36        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 
       50.70        50.86        65.10        26.24        62.04       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H 
       99.25       108.72       108.03        64.04        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A0Y5 
       14.73        70.39        17.79        24.79        26.93         5.65 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY 
       32.52         2.56       140.55         5.26        84.10        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
      107.24       133.22       134.14       107.21       125.16       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
      103.86        97.68        98.33        96.00        86.07        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       17.23        37.81        94.29        86.43        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T 
       94.22       120.33        99.78       118.59         2.76       105.27 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       77.69        98.76        99.62       166.42        20.25        86.53 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN 
       63.62        38.17        39.39        40.54        57.27        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IG 
       38.96        10.59        12.13       275.87        50.70       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      233.62        18.77       127.33        84.59       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
       68.45       234.28        81.17        78.02       263.28       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48       100.70        89.46       157.41        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.88       101.52       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
        7.07        71.15        59.84        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.55        39.16        70.22        84.13        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       18.21        21.70        61.68        72.23        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DH 
       53.95        77.95        89.06        90.97        77.98        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       29.98        13.91        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 
       38.47        67.86        70.88        16.27        15.68        44.81 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.58        24.49        10.78        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU 
       24.56        52.96         5.85         2.50        13.61        12.89 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       51.32        23.93        24.95        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       20.12        26.66        72.56        30.28        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       51.16       113.82        82.85        17.69        25.81        89.16 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
      120.62       114.15        33.17        74.73       122.89        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 
       55.00        45.63       144.59        72.07        28.14        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
       57.83       130.16        10.65        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
       20.88         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
       11.77        12.66        12.56        12.59        12.92         4.11 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34         0.16        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP 
        9.67         0.03        24.56        14.43        33.99        13.02 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A1J9 
       12.49        19.46        56.81        13.25        20.58        17.49 
TCGA-D8-A1JA TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       16.50        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        14.70        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       27.58        12.39        17.16        14.73        21.80        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV 
       17.69        55.30        16.41        15.85        16.64        15.16 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27K TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       48.03         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A107 
       33.37        18.51        21.67        12.66        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       27.52        46.59        40.41        28.44        28.87        47.15 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y 
       38.24        38.60        33.17        43.33        32.02        69.34 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        14.79        23.34        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M 
       21.63        18.21        55.63        53.92        20.58        11.05 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        56.94        14.07        51.39        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       28.44        59.18         3.88        11.08        54.18        73.64 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 
       24.59        75.81        28.90        50.07        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.55        43.56        34.92        34.82        32.88        36.82 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R2 
       36.56        39.55        25.84        18.94        28.27        34.95 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RI TCGA-E9-A227 
       11.15        48.23         1.12        46.65        47.64        32.05 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       42.25        39.09        40.73        40.50        20.12         0.69 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ 
       23.90        25.81        27.85        12.20        39.72        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ 
       18.90        13.25        25.94        22.82        29.95        40.41 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        29.82        30.08         7.86        18.90 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW 
       10.52        14.43        34.55        55.00        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB 
       34.03        17.49        10.16        23.51        15.22        24.99 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U 
       13.55        18.12        62.47        11.84        11.57        13.22 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        10.62        24.95        29.23        25.05        17.06 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7T0 
       14.47        14.79        16.08        15.68        14.50        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       19.59        17.49        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       24.72        20.38        26.70        65.62        41.92        42.77 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC 
       17.36        14.07        28.21        19.73        40.11        47.01 
TCGA-PE-A5DD TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 
       64.21         0.16         0.26        21.07        20.68        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB41 
       18.87        17.39        17.26         3.81        66.84        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       29.03        15.35        16.04       108.07 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.30               0.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            282.90             275.87 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            27.185             28.075 
[1] "0.3 - 282.9 (27.2)" "0.0 - 275.9 (28.1)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P GAIN MUTATED        37       28        1        2       142        90
  20P GAIN WILD-TYPE      52       57        5        4       211       162
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED           1         66         13         19       10
  20P GAIN WILD-TYPE         1         88         16         46       10
                    vv
clus                 STAGE TIS STAGE X
  20P GAIN MUTATED           1       3
  20P GAIN WILD-TYPE         0      10
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  37                 52
  STAGE IA                 28                 57
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA               142                211
  STAGE IIB                90                162
  STAGE III                 1                  1
  STAGE IIIA               66                 88
  STAGE IIIB               13                 16
  STAGE IIIC               19                 46
  STAGE IV                 10                 10
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED   102 251  42  18
  20P GAIN WILD-TYPE 174 373  94  22
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1              102                174
  T2              251                373
  T3               42                 94
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P GAIN MUTATED   197 127  61  23
  20P GAIN WILD-TYPE 310 231  58  54
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              197                310
  N1              127                231
  N2               61                 58
  N3               23                 54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   357  10
  20P GAIN WILD-TYPE 532  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    357   10
  20P GAIN WILD-TYPE  532   12
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              357                532
  1               10                 12
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   407   9
  20P GAIN WILD-TYPE 661   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    407    9
  20P GAIN WILD-TYPE  661    3
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              407                661
  MALE                  9                  3
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   164 198
  20P GAIN WILD-TYPE 265 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    164  198
  20P GAIN WILD-TYPE  265  320
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               164                265
  YES              198                320
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P GAIN MUTATED                            0                           339
  20P GAIN WILD-TYPE                          1                           431
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P GAIN MUTATED                               46                   2
  20P GAIN WILD-TYPE                            154                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20P GAIN MUTATED                       5                                9
  20P GAIN WILD-TYPE                     4                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20P GAIN MUTATED                    1             13
  20P GAIN WILD-TYPE                 16             34
D36V9, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 339                431
  INFILTRATING LOBULAR CARCINOMA                 46                154
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 13                 34
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0    22
  20P GAIN WILD-TYPE                                1    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          75   280
  20P GAIN WILD-TYPE                       106   465
D36V11, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                 38
  BLACK OR AFRICAN AMERICAN                      75                106
  WHITE                                         280                465
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V12, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    12 337
  20P GAIN WILD-TYPE  27 538
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     12  337
  20P GAIN WILD-TYPE   27  538
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              337                538
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   385  62
  20Q GAIN WILD-TYPE 532  85
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               447                617 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                62                 85 
$`20Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG 
      129.14       131.67         9.96        14.37        48.10        14.27 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04W 
       20.88        13.68         7.96        19.20        18.02       101.98 
TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       55.43        99.12        24.79        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D4 TCGA-A2-A0EQ 
       98.99        56.81        67.33        33.76        25.22        79.76 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SW TCGA-A2-A0SX 
       35.05        34.29        31.82        63.29        44.88        50.43 
TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ 
       20.75        25.28        18.21        21.90        21.67        18.61 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A25B 
       23.77        17.36        60.72        20.25        19.20        42.44 
TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A4RX 
      105.34        36.23        33.93        91.07        47.31        24.39 
TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       21.14        38.30        30.61        37.45        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A425 
       31.73        20.19        25.15        23.74        20.61        14.70 
TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV 
       14.93        14.50        21.17        17.92        14.73        10.29 
TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 
       13.02        17.98        29.03        26.01        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.01        10.98         8.98        24.99         9.99        45.07 
TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P 
       13.02        38.01        19.96        12.00        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
        0.99        33.01        43.00        30.97        17.95        41.98 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A0A1 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23G 
        1.02         8.98        12.00         0.99        27.02        73.91 
TCGA-AC-A23H TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3QQ 
        5.72        99.35        26.04        33.04        14.66        24.13 
TCGA-AC-A3W5 TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62Y 
       16.57        16.80        14.53        19.33        11.44        17.42 
TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A03X TCGA-AN-A03Y 
       13.58         1.68        20.19         1.12         0.33         0.33 
TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL 
        1.78         9.96         0.16         0.36         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33        12.33         0.30        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD 
       81.63        47.87        29.13        20.32        53.03        72.00 
TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12A 
       76.77        50.24        55.33        71.80       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT 
       98.27        57.30        48.36        82.62        61.87        17.79 
TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TT 
       24.79       130.09        15.62        19.20        98.33       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AI 
       75.22        98.93        64.83       107.24        83.87       108.36 
TCGA-AR-A1AK TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L 
      103.86        93.90        61.28        86.53       160.90        94.22 
TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z 
      104.28       112.77        97.84       105.30        32.58        98.66 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL 
       89.00        93.30        71.05        93.83        54.21        66.15 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       57.27        73.35        77.62       143.38       281.29        12.13 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE 
      129.57        65.72       112.37       233.62       165.76       255.68 
TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC 
       81.17       162.05       282.90        79.63       113.79        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 
      101.52        73.51       139.17        85.35        70.16        68.12 
TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B6 
       18.84       103.63        62.93        20.45        25.55        81.63 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BV 
       37.22        43.53        74.89        75.48        45.57        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DL 
       49.05        41.75        44.02        45.83        23.44        78.28 
TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI 
        3.22         4.41        14.30        46.19        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HQ 
       30.35        23.08        41.00        26.50        20.38        36.85 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18K 
       27.25        50.79         5.59        42.35        44.81        90.84 
TCGA-BH-A18L TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       26.66        37.74        55.63         7.36        51.39        67.50 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 
       91.99        42.28        12.00        55.69        49.58        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 
       97.48        24.62        36.92        45.63        72.07        26.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28Q TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       38.60        57.83         6.44        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
        5.26        11.93        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        48.53         3.16        13.51         1.87 
TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Z 
        4.08        11.34        11.28        12.33        12.95         8.28 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A13Z 
        9.53         9.50        24.56        12.95        13.41        20.88 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       14.17        55.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 
       53.00        14.01        18.97        21.01        13.32        18.58 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS 
       27.58        18.15        15.22        19.92        16.41        16.31 
TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       12.99        43.04        16.54        15.32        15.52         9.93 
TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A73X 
       14.43        16.41        13.48        10.09        12.26        25.22 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S 
       37.51        40.11        44.68        40.96        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       75.98        34.26        31.96        63.62        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15K 
       19.43        25.05        23.34        22.82        12.92         9.04 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD 
       11.05        50.79        56.94        76.57        53.62        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1L9 
       33.73        33.70        22.19        60.99        60.36        19.66 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
      106.75       102.61         8.75         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       38.76        34.29        17.69        36.82        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 
       36.20        35.77         9.86        24.82        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        6.12         3.02        11.15        45.01        32.09        40.24 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A229 
       46.65         6.58        21.27        46.59        34.45        37.74 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       38.37        41.03        41.72         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
        7.13        12.33        29.72        23.84        26.70         0.79 
TCGA-E9-A5UP TCGA-EW-A1IY TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OY 
       26.40         8.48        16.57        15.68        28.77        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1PB TCGA-EW-A1PC 
       40.41        41.13        23.11        18.48        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A6SA TCGA-EW-A6SD TCGA-GI-A2C8 
       13.94        52.73        10.16        16.77        33.21         7.40 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A3XL TCGA-HN-A2NL 
       83.34        75.02        70.85        85.15        69.30         2.60 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN 
       11.84        21.24         7.10        32.75        15.32        14.70 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LQ-A4E4 
       22.26         2.63        15.68        19.53        12.36        27.91 
TCGA-OL-A5RZ TCGA-OL-A66I TCGA-OL-A66N TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE 
       22.32        23.47        26.04         8.91        47.01        86.96 
TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA17 
        0.16         9.93        18.81        18.48        19.27        13.94 
TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-Z7-A8R6 
       17.03        11.41       107.05 

$`20Q GAIN WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SE TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       43.43        47.24        31.79        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      143.15        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       36.13       136.73       114.81        92.48        88.60       107.93 
TCGA-A2-A0CW TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
      107.93        34.55        61.58       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
      118.45        74.40        72.00        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       54.64        27.12        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YF 
       49.84        20.52        17.46        18.90        32.55        50.47 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       49.48        19.33        48.46        31.73        23.47        22.45 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25F TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       10.59        39.65        29.98        32.75        56.28        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         7.30        21.30        23.21        26.96 
TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0DA TCGA-A7-A13G 
       21.90        35.31        34.29        35.47        35.67        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD 
       29.56        31.36        24.26        23.80        21.73        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A426 
       11.34        10.59        10.29        11.28        13.41        11.97 
TCGA-A7-A4SB TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX 
       13.74        12.10        10.72        11.05         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z 
        8.75        13.02         1.02        53.06        31.00         1.02 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A 
       32.05         9.99         7.99        15.06        36.95         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z 
       28.96        33.01         9.99        31.00       112.08        40.01 
TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09Q 
       33.01        12.00         9.99         9.99        12.00        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02         0.99        14.01        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2B8 
       21.04        17.03        38.04         0.95        22.95         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       73.05        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       74.14        19.33        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        25.05        14.99        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IX 
       24.79        29.26        14.96        13.71        18.67        12.26 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A041 TCGA-AN-A046 
        8.22         0.03         1.32         2.30         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        0.62         2.96         1.71         7.36         7.46         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX 
        7.59         7.17         6.90         7.04         0.33         0.33 
TCGA-AN-A0FY TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.33         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 
        5.59        95.70        68.75        58.95        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB 
       52.18        26.04        37.48        22.36        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 
       50.86        65.10        26.24        62.04       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      108.72       108.03        64.04        41.62        40.57        14.73 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       70.39         0.53        26.93         5.65        32.52         2.56 
TCGA-AQ-A54O TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0U0 
       32.91       140.55         5.26        84.10        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL 
      133.22       134.14       107.21       125.16       101.00        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       98.33        96.00        86.07        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A24N 
       94.29        86.43        33.73        50.89       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 
      118.59         2.76       105.27        77.69        98.76        99.62 
TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       85.64       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0IA 
       39.39        40.54        33.30        38.96        10.59       275.87 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
       50.70       146.50        18.77       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      140.88        68.45       212.25       234.28        78.02       263.28 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS 
      102.77       140.48       100.70        89.46       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        18.35        21.47       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
       28.27        68.94        58.88       170.17        37.87         7.07 
TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 
       71.15        59.84        63.09        81.44        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        70.22        84.13        51.68        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       61.51        21.70        61.68        72.23        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE TCGA-BH-A0DH 
       53.95        77.95        89.06        90.97        77.98        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       29.98        13.91        17.26        15.65         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 
       67.86        70.88        16.27        15.68         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.58        24.49        10.78        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0HA TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU 
       24.56        52.96         5.85         2.50        13.61        12.89 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       51.32        23.93        24.95        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       35.93        20.12        72.56        30.28        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 
       51.16       113.82        82.85        17.69        25.81        89.16 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ 
      120.62       114.15        33.17        74.73       122.89        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 
       55.00       144.59        72.07        28.14        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A8FY 
       10.65        20.12        10.52       109.28        20.88         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12X 
       18.87        21.76         9.44        11.77        11.77        12.66 
TCGA-C8-A12Z TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.56        12.59        12.92         4.11        12.33        10.92 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
        0.16        12.03        10.42        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 
       12.36        12.95         9.67         0.03        14.43        33.99 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A141 TCGA-D8-A1J9 
       13.02        12.49        19.46        56.81        20.58        17.49 
TCGA-D8-A1JA TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       16.50        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        14.70        17.79        16.73        25.74        23.90 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM 
       12.39        17.16        14.73        21.80        14.50        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       55.30        15.85        16.64        15.16        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27N 
       17.42        16.04        13.45        13.05        48.03         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        1.61        13.08        12.53        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       16.18        12.66        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14U 
       40.41        28.44        28.87        47.15        38.24        43.33 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       32.02        69.34        18.51        21.04        23.87        14.79 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        21.63        18.21        55.63        53.92 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 
       20.58        19.56        14.07        51.39        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       28.44        59.18         3.88        11.08        54.18        73.64 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 
       24.59        75.81        28.90        50.07        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1NC 
       34.55        43.56        34.82        32.88        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R7 
       41.62        35.24        25.84        18.94        28.27        48.23 
TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22G 
        1.12        47.64        32.05        42.25        39.09        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       40.50        20.12        24.56         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       30.18        30.44        23.90        25.81        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1OV TCGA-EW-A1OW 
       39.72        18.21        18.90        13.25        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1P8 
       29.95        39.78        52.96        29.82        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       18.90        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 
       25.91        22.09        34.03        17.49        23.51        15.22 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       24.99        31.30       109.87        59.57       216.76        79.10 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       18.12        62.47        11.57        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP 
       24.95        29.23        25.05        17.06        14.47        14.79 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U 
       16.08         7.46        14.50        19.59        17.49        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        36.36        28.87        24.72        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        41.92        42.77        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DD TCGA-PL-A8LY TCGA-S3-A6ZH TCGA-S3-AA0Z 
       19.73        40.11        64.21         0.26        21.07        20.68 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UU-A93S TCGA-V7-A7HQ 
       13.84        18.87        17.39        17.26         3.81        66.84 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       52.96        29.03        15.35        16.04       108.07 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.16               0.03 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            282.90             275.87 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             26.70              28.27 
[1] "0.2 - 282.9 (26.7)" "0.0 - 275.9 (28.3)"
[1] "hr=" "1.1"
D37V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q GAIN MUTATED        36       30        2        2       153       101
  20Q GAIN WILD-TYPE      53       55        4        4       200       151
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED           1         71         15         24        9
  20Q GAIN WILD-TYPE         1         83         14         41       11
                    vv
clus                 STAGE TIS STAGE X
  20Q GAIN MUTATED           1       3
  20Q GAIN WILD-TYPE         0      10
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  36                 53
  STAGE IA                 30                 55
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA               153                200
  STAGE IIB               101                151
  STAGE III                 1                  1
  STAGE IIIA               71                 83
  STAGE IIIB               15                 14
  STAGE IIIC               24                 41
  STAGE IV                  9                 11
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED   104 278  44  22
  20Q GAIN WILD-TYPE 172 346  92  18
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1              104                172
  T2              278                346
  T3               44                 92
  T4               22                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q GAIN MUTATED   208 142  64  28
  20Q GAIN WILD-TYPE 299 216  55  49
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              208                299
  N1              142                216
  N2               64                 55
  N3               28                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   385  10
  20Q GAIN WILD-TYPE 504  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    385   10
  20Q GAIN WILD-TYPE  504   12
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              385                504
  1               10                 12
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   443   8
  20Q GAIN WILD-TYPE 625   4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    443    8
  20Q GAIN WILD-TYPE  625    4
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              443                625
  MALE                  8                  4
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   177 219
  20Q GAIN WILD-TYPE 252 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    177  219
  20Q GAIN WILD-TYPE  252  299
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               177                252
  YES              219                299
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q GAIN MUTATED                            0                           368
  20Q GAIN WILD-TYPE                          1                           402
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q GAIN MUTATED                               50                   1
  20Q GAIN WILD-TYPE                            150                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20Q GAIN MUTATED                       6                                9
  20Q GAIN WILD-TYPE                     3                               20
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20Q GAIN MUTATED                    1             16
  20Q GAIN WILD-TYPE                 16             31
D37V9, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 368                402
  INFILTRATING LOBULAR CARCINOMA                 50                150
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           6                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                9                 20
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 16                 31
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0    26
  20Q GAIN WILD-TYPE                                1    34
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          83   299
  20Q GAIN WILD-TYPE                        98   446
D37V11, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          26                 34
  BLACK OR AFRICAN AMERICAN                      83                 98
  WHITE                                         299                446
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V12, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    12 368
  20Q GAIN WILD-TYPE  27 507
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     12  368
  20Q GAIN WILD-TYPE   27  507
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              368                507
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED   159  36
  21Q GAIN WILD-TYPE 758 111
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
               195                869 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                36                111 
$`21Q GAIN MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04U 
      129.14        20.88        13.68        28.01        18.02        87.25 
TCGA-A2-A0CM TCGA-A2-A0CU TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV 
       24.79         5.19        79.76        63.29        99.19        27.12 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YM 
       17.13         8.38        49.84        18.21        21.90        31.73 
TCGA-A2-A1G1 TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A4S1 
       19.20        39.65        29.98        56.28        47.31        26.96 
TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26H 
       35.67        29.79        31.73        20.19        25.15        23.80 
TCGA-A7-A26I TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q 
       21.73        13.74        21.17        10.29        13.02         1.02 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W 
       26.01        17.03        53.98         8.98        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A08B TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08X TCGA-A8-A091 
       45.07        38.01         9.99        31.00        43.00        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09X TCGA-A8-A0AB 
       30.97        17.95        29.98         1.02        14.01        17.03 
TCGA-AC-A23G TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A62Y TCGA-AC-A6IW 
       73.91        26.04        33.04        14.66        17.42        13.58 
TCGA-AN-A03Y TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         7.04         0.33        66.77        81.63 
TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A1KT TCGA-AQ-A54O 
       71.80       106.78        98.27        64.04        17.79        32.91 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AR TCGA-AR-A1AV 
       98.93        55.86        65.36       101.00        17.23        61.28 
TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A2LR 
       86.43        50.89       112.77        98.66        99.62        57.27 
TCGA-AR-A5QM TCGA-B6-A0I1 TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
       73.35        77.62       112.37        18.77        84.59       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KF 
      140.88       255.68       162.05       282.90       113.79       101.52 
TCGA-B6-A1KI TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AY TCGA-BH-A0B7 TCGA-BH-A0BL 
       73.51        70.16        18.84        25.55        84.13        74.89 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DS TCGA-BH-A0E6 
       76.60        45.57        49.05        44.02         2.56         9.63 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A18Q TCGA-BH-A1EN 
       24.49        31.00        30.35        36.85        55.63        67.50 
TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1FC TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 
       12.00        49.58       114.15        72.07        26.14        38.60 
TCGA-BH-A5IZ TCGA-C8-A12P TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       18.64        11.77        12.56         3.16        13.51         1.87 
TCGA-C8-A135 TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A275 TCGA-C8-A278 TCGA-D8-A13Y 
       12.92        12.33        12.95         0.03         9.50        56.81 
TCGA-D8-A13Z TCGA-D8-A147 TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1XD 
       20.88        19.20        53.00        14.01        20.12        17.16 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XU TCGA-D8-A1XW TCGA-E2-A10B TCGA-E2-A14O 
       21.80        14.50        12.99        43.04        37.51        44.68 
TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A154 TCGA-E2-A159 
       40.96        38.60        31.96        18.51        19.43        25.05 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1IN TCGA-E2-A1L9 
       11.05        50.79        76.57        53.62        22.19        19.66 
TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1R7 
       28.90         8.75        26.99        34.92        17.69        48.23 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A2JS 
        1.12        46.65        46.59        41.03         0.69        29.72 
TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 
       30.44        26.40        40.41        29.82        23.11         7.86 
TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-GM-A2DC 
        6.15        19.96        55.00        25.91        10.16        83.34 
TCGA-GM-A2DF TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A73Y 
       70.85         7.10        32.75        14.47        14.79        15.68 
TCGA-LL-A73Z TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-S3-AA0Z 
        7.46        12.36        19.59        36.36        20.38        20.68 
TCGA-S3-AA10 TCGA-UL-AAZ6 TCGA-W8-A86G 
       19.27        17.03        11.41 

$`21Q GAIN WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
      143.15        78.41       121.94        73.84        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        77.19        75.25        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       56.81        67.33        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       118.45        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SU 
       35.05        34.29        31.82        61.94        24.72        54.64 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.88        50.43        44.28        17.52        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH 
       18.90        20.75        32.55        25.28        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       49.48        18.61        19.33        48.46        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY 
       10.59        36.23        33.93        91.07        32.75        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       30.61        37.45        33.11        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.74        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T 
        9.37        10.42         8.75        13.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       29.03        31.00         1.02         9.01        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       10.98         7.99        15.06        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
       28.96        33.01        19.96        12.00        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A095 TCGA-A8-A097 
        0.99        33.01       112.08        40.01        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       45.07        33.07        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 
       27.02        38.04         0.95        22.95         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       87.12        74.14        19.33        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       14.83        22.19        24.13        25.05        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       19.79        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       14.53        19.33        14.96        11.44        13.71        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         7.46 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW 
        7.00         7.59         7.17         6.90         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         0.33         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       80.28        61.35        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        65.10        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       55.33       115.27        99.25       108.72       108.03        90.58 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87        70.39         0.53        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
        5.65        15.62        32.52         2.56        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX 
       98.33         5.26        84.10       109.02        75.22        64.83 
TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24       133.22        83.87       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      108.36       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AY 
       93.90        99.32        37.81        94.29        86.53        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      160.90        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
      104.28        97.84       105.27        77.69       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.76        89.00        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       38.17        39.39        40.54        33.30        38.96        10.59 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       281.29        12.13       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG 
       65.72       146.50       233.62       127.33       129.07        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RP 
      212.25       234.28        81.17        78.02       263.28       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48       100.70        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        18.35        21.47       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
       37.87         7.07        85.35        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       62.93        59.84        20.45        63.09        81.44        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        70.22        81.63        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       32.02        18.21        43.53        61.51        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW 
       72.23        75.48        74.14        53.95        49.94        77.95 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       41.75        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        29.98        13.91        78.28        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        3.22        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI 
       15.68        14.30        44.81        46.19        32.58        24.43 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.16        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       17.69        25.81        31.53        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A204 
       55.00        45.63        72.07       144.59        28.14        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28        20.88        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       48.53        12.59         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN 
       11.34        11.28         0.16        12.03        10.42        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.53        12.36         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.53        24.56        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       12.49        13.41        19.46        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        21.14        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JI 
       55.50        15.78        18.15        18.90        12.03        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       20.09        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG 
       23.90        27.58        18.15        12.39        15.22        14.73 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        15.16        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43        48.03        16.41        13.48         4.80         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       47.15        38.24        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 
       32.02        69.34        63.62        69.96        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 
       20.58        19.56        56.94        14.07        51.39        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
        3.88        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL 
       24.59        75.81        50.07       106.75       102.61        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56         8.28        30.61        38.76        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        6.12         3.02        11.15        45.01        32.09        40.24 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
        6.58        21.27        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       37.74        39.09        38.37        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.12        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y 
        9.47        38.07        32.91        30.18        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70         0.79        25.81        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       28.77        25.94        22.82        29.95        29.85        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       39.78        52.96        18.48        30.08        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FW 
       13.94        10.52        14.43        34.55        52.73        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       34.03        17.49        23.51        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        75.02        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       62.47        11.84        11.57        21.24        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       10.62        24.95        29.23        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A740 TCGA-LL-A7SZ 
       14.70        22.26         2.63        16.08        14.50        19.53 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        40.08        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       22.32        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
        8.91        47.01        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 
        9.93        18.81        18.48        21.07        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB41 
       17.39        17.26        13.94         3.81        66.84        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.03               0.03 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            282.90             281.29 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             27.12              27.91 
[1] "0.0 - 282.9 (27.1)" "0.0 - 281.3 (27.9)"
[1] "hr=" "1.5"
D38V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q GAIN MUTATED        12       12        1        1        71        39
  21Q GAIN WILD-TYPE      77       73        5        5       282       213
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           0         32          3         16        4
  21Q GAIN WILD-TYPE         2        122         26         49       16
                    vv
clus                 STAGE TIS STAGE X
  21Q GAIN MUTATED           0       3
  21Q GAIN WILD-TYPE         1      10
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  12                 77
  STAGE IA                 12                 73
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                71                282
  STAGE IIB                39                213
  STAGE III                 0                  2
  STAGE IIIA               32                122
  STAGE IIIB                3                 26
  STAGE IIIC               16                 49
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED    46 121  22   5
  21Q GAIN WILD-TYPE 230 503 114  35
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               46                230
  T2              121                503
  T3               22                114
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q GAIN MUTATED    85  66  22  17
  21Q GAIN WILD-TYPE 422 292  97  60
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               85                422
  N1               66                292
  N2               22                 97
  N3               17                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   169   4
  21Q GAIN WILD-TYPE 720  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    169    4
  21Q GAIN WILD-TYPE  720   18
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0              169                720
  1                4                 18
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED   194   2
  21Q GAIN WILD-TYPE 874  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED    194    2
  21Q GAIN WILD-TYPE  874   10
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE              194                874
  MALE                  2                 10
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    69 106
  21Q GAIN WILD-TYPE 360 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     69  106
  21Q GAIN WILD-TYPE  360  412
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                69                360
  YES              106                412
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q GAIN MUTATED                            0                           168
  21Q GAIN WILD-TYPE                          1                           602
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q GAIN MUTATED                               16                   2
  21Q GAIN WILD-TYPE                            184                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  21Q GAIN MUTATED                       4                                0
  21Q GAIN WILD-TYPE                     5                               29
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  21Q GAIN MUTATED                    1              5
  21Q GAIN WILD-TYPE                 16             42
D38V9, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 168                602
  INFILTRATING LOBULAR CARCINOMA                 16                184
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           4                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                0                 29
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  5                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1    10
  21Q GAIN WILD-TYPE                                0    50
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                          42   121
  21Q GAIN WILD-TYPE                       139   624
D38V11, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          10                 50
  BLACK OR AFRICAN AMERICAN                      42                139
  WHITE                                         121                624
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V12, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     9 152
  21Q GAIN WILD-TYPE  30 723
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      9  152
  21Q GAIN WILD-TYPE   30  723
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              152                723
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    82  15
  22Q GAIN WILD-TYPE 835 132
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                97                967 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                132 
$`22Q GAIN MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL 
        9.96        31.79        19.20        87.25       101.98        99.12 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0T1 TCGA-A2-A1FV TCGA-A2-A1G1 TCGA-A7-A0CD 
       56.81        33.76        17.13        23.47        19.20        38.30 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A079 
       29.79        25.15        10.29        10.42        13.02         9.01 
TCGA-A8-A08B TCGA-A8-A08R TCGA-A8-A091 TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09X 
       38.01         0.99        33.01        29.98        33.07        14.01 
TCGA-AC-A23H TCGA-AC-A2QJ TCGA-AC-A3W5 TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A0AL 
        5.72        14.66        16.57        11.44         1.12         7.46 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FL TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A12B 
        0.16         0.33         7.59         0.33         0.33        98.27 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TV 
       48.36        41.62       130.09         5.65       140.55        75.22 
TCGA-AR-A0U1 TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A2LR TCGA-B6-A0RS TCGA-B6-A0RU 
      133.22        77.69       105.30        57.27       100.70       282.90 
TCGA-B6-A0WV TCGA-B6-A1KC TCGA-B6-A400 TCGA-B6-A402 TCGA-BH-A0BG TCGA-BH-A0C0 
       79.63        43.59         7.07        70.16        61.51        41.75 
TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0HY TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1EN 
       78.28        14.30        50.79        55.63        51.39        67.50 
TCGA-BH-A1EV TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-C8-A12L 
       12.00        72.07        26.14        38.60        57.83        11.93 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A1HG TCGA-D8-A142 
       12.66        11.77        12.66        12.56        11.34        13.97 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JK TCGA-D8-A1XJ TCGA-D8-A1XW TCGA-D8-A1XZ 
       15.78        18.90        20.12        21.80        43.04        15.32 
TCGA-D8-A27M TCGA-D8-A27W TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A1B0 TCGA-E9-A1NC 
       13.48        12.26        31.96        69.96        53.62        39.55 
TCGA-E9-A22B TCGA-E9-A243 TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A424 TCGA-GI-A2C9 
       38.37        20.12        26.40        40.41        23.51       109.87 
TCGA-GM-A2DF TCGA-GM-A3XL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A7SZ 
       70.85        69.30        15.32        14.79        16.08        19.53 
TCGA-LL-A8F5 
       19.59 

$`22Q GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO 
       63.12        55.43        36.13       136.73        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 
       98.99       107.93        67.33        34.55        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       63.29        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.52         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       31.73        23.77        17.36        60.72        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        21.90        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       30.61        37.45        35.67        33.11        31.73        20.19 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       21.73        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       11.05         9.37         8.75        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        28.96        33.01        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
        9.99        31.00        31.00        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        30.97        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        50.04        49.05        45.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       17.03        38.04         0.95        22.95        73.91         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB 
       87.12        26.04        74.14        33.04        19.33        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y 
       16.80        14.53        19.33        14.96        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
       20.19         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        7.36         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.00         7.17         6.90         7.04         0.33         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         5.36        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12H 
      106.78       108.03        90.58        64.04        57.30        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       24.79        26.93        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
       19.20        98.33         5.26        84.10       109.02        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 
       64.83        55.86       107.24        65.36        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL 
      107.21       125.16       108.36       101.00       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR 
       98.33        96.00        86.07        93.90        99.32        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        94.29        61.28        86.53        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24W 
        2.76       104.28       112.77        97.84       105.27        32.58 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
       98.76        98.66        89.00        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       71.05        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM 
       66.15        63.62        38.17        39.39        40.54        73.35 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       33.30        38.96        10.59        77.62       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       275.87       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       233.62        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX 
       89.46       157.41        97.48       188.68        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.88       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        63.09        81.44        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        70.22        81.63        84.13        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       37.22        32.02        18.21        43.53        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       45.57        49.94        77.95        49.05        44.02        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        45.83        77.98        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 
       67.86        70.88        16.27         4.41        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.58        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       32.91         4.90        35.93        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        37.74        30.28        37.55        66.05         7.36 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW 
       51.16        91.99       113.82        82.85        42.28        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       24.62       120.62       114.15        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       28.14        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M 
        5.26         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.16        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.08        12.33        10.92        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       10.42        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.50        24.56        14.43        33.99        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       12.49        13.41        19.46        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       20.58        14.17        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG 
       17.49        16.50        55.50        18.15        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.09        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       55.30        16.41        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       32.02        69.34        18.51        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C 
       21.04        23.87        14.79        25.05        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       17.29        20.71        21.63        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        14.07        51.39        76.57        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        75.81        28.90        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       36.56        41.62        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        24.82        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
        1.12        46.65         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D 
       34.45        32.05        42.25        37.74        39.09        41.03 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       41.72        40.73        40.50         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        22.82        29.95        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       52.96        29.82        23.11        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB 
       34.03        17.49        10.16        15.22        16.77        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30        33.21         7.40        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       83.34        75.02        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       14.70        14.47        22.26         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       14.50        12.36        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       18.48        21.07        20.68        19.27        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.39        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       11.41        52.96        29.03        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.16               0.03 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            282.90             281.29 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             26.14              28.01 
[1] "0.2 - 282.9 (26.1)" "0.0 - 281.3 (28.0)"
[1] "hr=" "1.1"
D39V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q GAIN MUTATED         7        5        0        1        42        18
  22Q GAIN WILD-TYPE      82       80        6        5       311       234
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           0         15          7          3        1
  22Q GAIN WILD-TYPE         2        139         22         62       19
                    vv
clus                 STAGE TIS STAGE X
  22Q GAIN MUTATED           0       0
  22Q GAIN WILD-TYPE         1      13
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   7                 82
  STAGE IA                  5                 80
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                42                311
  STAGE IIB                18                234
  STAGE III                 0                  2
  STAGE IIIA               15                139
  STAGE IIIB                7                 22
  STAGE IIIC                3                 62
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    18  65   9   7
  22Q GAIN WILD-TYPE 258 559 127  33
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               18                258
  T2               65                559
  T3                9                127
  T4                7                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q GAIN MUTATED    53  27  11   4
  22Q GAIN WILD-TYPE 454 331 108  73
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               53                454
  N1               27                331
  N2               11                108
  N3                4                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    86   1
  22Q GAIN WILD-TYPE 803  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     86    1
  22Q GAIN WILD-TYPE  803   21
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               86                803
  1                1                 21
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    98   1
  22Q GAIN WILD-TYPE 970  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     98    1
  22Q GAIN WILD-TYPE  970   11
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               98                970
  MALE                  1                 11
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    40  46
  22Q GAIN WILD-TYPE 389 472
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     40   46
  22Q GAIN WILD-TYPE  389  472
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                40                389
  YES               46                472
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q GAIN MUTATED                            0                            81
  22Q GAIN WILD-TYPE                          1                           689
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q GAIN MUTATED                                4                   1
  22Q GAIN WILD-TYPE                            196                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  22Q GAIN MUTATED                       2                                2
  22Q GAIN WILD-TYPE                     7                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  22Q GAIN MUTATED                    1              8
  22Q GAIN WILD-TYPE                 16             39
D39V9, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  81                689
  INFILTRATING LOBULAR CARCINOMA                  4                196
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  8                 39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  1     7
  22Q GAIN WILD-TYPE                                0    53
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                          21    59
  22Q GAIN WILD-TYPE                       160   686
D39V11, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           7                 53
  BLACK OR AFRICAN AMERICAN                      21                160
  WHITE                                          59                686
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V12, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     3  84
  22Q GAIN WILD-TYPE  36 791
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3   84
  22Q GAIN WILD-TYPE   36  791
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 36
  NOT HISPANIC OR LATINO               84                791
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED   127  21
  XP GAIN WILD-TYPE 790 126
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              148               916 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               21               126 
$`XP GAIN MUTATED`
TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A0CL TCGA-A2-A0CX TCGA-A2-A0D2 
      131.67        13.68        28.01        99.12        56.81        33.76 
TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T7 
       79.76        44.88        17.13         8.38        49.84        20.75 
TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25B TCGA-A2-A25E 
       21.90        18.61        31.73        20.25        42.44       105.34 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0DA TCGA-A7-A0DB 
       47.31        35.93        21.14        38.30        35.67        33.11 
TCGA-A7-A3J0 TCGA-A7-A5ZV TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07L TCGA-A8-A07P 
       10.29        12.10        17.03        53.98        32.05        10.98 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B 
        8.98        24.99         9.99        45.07        13.02        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08P TCGA-A8-A08T TCGA-A8-A091 
       28.96        33.01        12.00        31.00       112.08        33.01 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A09Q TCGA-AC-A23H TCGA-AC-A2BK TCGA-AC-A3OD 
       17.95        41.98        25.02         5.72        73.05        14.83 
TCGA-AC-A5EI TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0FT TCGA-AN-A0FX 
       14.53        13.71         0.33         9.96         7.04         0.33 
TCGA-AN-A0FY TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A128 
        0.33        66.77        81.63        62.04        71.80       106.78 
TCGA-AO-A12B TCGA-AR-A0TR TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AV TCGA-AR-A1AX 
       98.27         5.26        98.93        83.87        61.28        86.43 
TCGA-AR-A24H TCGA-AR-A24Z TCGA-AR-A255 TCGA-AR-A2LR TCGA-AR-A5QM TCGA-B6-A0I2 
      160.90        98.66        71.05        57.27        73.35       143.38 
TCGA-B6-A0I5 TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-BH-A0AW TCGA-BH-A0AY 
      281.29       206.86       245.10       101.52        20.45        25.55 
TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0DS TCGA-BH-A0GY TCGA-BH-A0HQ TCGA-BH-A0HU 
       76.60        49.94         2.56        30.35        36.85        12.89 
TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1F0 
       37.74        55.63        91.99        82.85        12.00        25.81 
TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A209 TCGA-BH-A6R8 TCGA-C8-A12L TCGA-C8-A12M 
      114.15        26.14       130.16         9.63        11.93        11.77 
TCGA-C8-A130 TCGA-C8-A1HO TCGA-C8-A275 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JD 
        3.16        12.33         0.03        13.97        14.17        18.15 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XJ 
       20.09        20.12        20.09        13.32        18.58        21.80 
TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27V TCGA-D8-A27W 
       16.41        43.04        15.32        14.14        12.53        12.26 
TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X 
       18.51        37.51        40.96        33.17        34.26        31.96 
TCGA-E2-A154 TCGA-E2-A15D TCGA-E2-A15K TCGA-E2-A1B0 TCGA-E2-A56Z TCGA-E2-A573 
       19.43        17.29         9.04        53.62         8.28        34.92 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NF TCGA-E9-A1RC TCGA-E9-A2JS 
       17.69        22.29        36.20        35.24        40.24        29.72 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-EW-A1IY TCGA-EW-A1PB TCGA-GI-A2C9 TCGA-GM-A3XL 
       23.90         0.79         8.48        19.99       109.87        69.30 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-OL-A5DA TCGA-OL-A5S0 TCGA-OL-A97C TCGA-PL-A8LZ 
        2.63        15.68        58.62        20.38         8.91         9.93 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-WT-AB44 TCGA-Z7-A8R6 
       18.81        20.68        29.03       107.05 

$`XP GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        31.79         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       114.81        92.48        88.60       107.93        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        98.99       107.93        67.33        34.55 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72        89.36        80.28       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        27.12        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       44.28        17.52        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        18.21        50.47        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       48.46        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       19.20        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT 
       18.15        10.59        36.23        39.65        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       29.98        32.75        56.28        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE 
       24.39        21.30        23.21        26.96        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DC TCGA-A7-A13D 
       34.29        35.47        30.61        37.45        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       20.19        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZW 
       13.74        14.50        21.17        17.92        14.73        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O 
       11.05        10.29         9.37        10.42         8.75        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02         9.01        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A084 
       18.97        14.01        12.00         9.99         7.99        15.06 
TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       36.95         0.99        19.96        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A097 
        0.99        33.01        43.00        40.01        30.97        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98        33.07         1.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       22.95        73.91         1.48        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP 
       19.33        14.66        32.45         6.48        16.31        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU 
       23.24        24.79        29.26        16.80        19.33        14.96 
TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       11.44        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.17         6.90         0.33         0.36         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P 
        0.33         5.33         5.59        80.28        61.35        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        55.33       115.27        99.25       108.72 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      108.03        90.58        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       32.52         2.56        32.91        19.20       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       84.10       109.02        75.22        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       133.22       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW 
       93.90        99.32        17.23        37.81        94.29        86.53 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
        2.76       104.28       112.77        97.84       105.27        77.69 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
      105.30        32.58        98.76        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       85.64        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN 
       66.15        63.62        38.17        39.39        40.54        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       38.96        10.59        77.62        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK 
       50.70        65.72       146.50       112.37       233.62        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
      162.05       102.77       140.48       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      113.79       129.70        28.27        68.94        58.88        43.59 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       73.51       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       70.16        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       59.84        63.09        81.44        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       70.22        81.63        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW 
       72.23        75.48        74.14        53.95        45.57        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.05        41.75        44.02        89.06        90.97        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        23.44        38.01        29.98        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         3.22        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ 
       46.19        32.58        24.49        31.00        24.43        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        53.26        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       52.96        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R 
       20.12        90.84        26.66        72.56        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES 
       66.05         7.36        51.39        51.16        67.50       113.82 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 
       42.28        55.69        49.58        17.69        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       97.48        24.62       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O 
       72.07        28.14        38.60        83.31        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28        20.88        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 
       12.66        12.66        48.53        12.56        13.51         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.92         4.11         4.08        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       11.34        11.28         0.16        12.03        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.95        20.25        12.53        12.36        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         9.53         9.50        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.88        13.25        20.58        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE 
       14.17        17.49        16.50        55.50        15.78        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JN 
       12.03        53.00        14.01        18.97        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       21.01        12.20        14.70        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       23.90        27.58        18.15        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       14.73        14.50        19.92        17.69        55.30        15.85 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 
       16.31        16.64        12.99        15.16        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
        9.93        14.24        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P 
       14.43        48.03        16.41        13.48         4.80         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       10.09        13.08        33.37        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        44.68        38.24 
TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z 
       38.60        75.98        43.33        32.02        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       63.62        69.96        23.24        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       25.05        23.34        22.82        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       12.92        55.63        53.92        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 
       19.56        56.94        14.07        51.39        76.57        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
        3.88        22.19        60.99        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       73.64        19.66        24.59        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
      106.75       102.61         8.75        43.04        26.99        34.55 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       43.56        30.61        38.76        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE 
       36.82        34.16        36.56        39.55        41.62        35.77 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       32.09         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       38.37        41.03        41.72        40.73        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54Y 
        9.47        38.07        32.91        30.18        30.44        23.84 
TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
        7.86        18.90         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA 
       34.03        17.49        10.16        23.51        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30        33.21         7.40        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       79.10        83.34        75.02        70.85        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       25.05        17.06        15.32        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       22.26        16.08         7.46        14.50        19.53        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       58.52        31.99        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        22.32        26.70        23.47        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       42.77        26.04        17.36        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
       40.11        47.01        64.21        86.96         0.16         0.26 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       18.48        21.07        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.26        13.94        17.03         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       52.96        15.35        16.04       108.07 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.03              0.03 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           281.29            282.90 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           27.075            27.880 
[1] "0.0 - 281.3 (27.1)" "0.0 - 282.9 (27.9)"
[1] "hr=" "1"  
D40V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP GAIN MUTATED        12        8        2        2        55        33
  XP GAIN WILD-TYPE      77       77        4        4       298       219
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           0         21          4         10        4
  XP GAIN WILD-TYPE         2        133         25         55       16
                   vv
clus                STAGE TIS STAGE X
  XP GAIN MUTATED           0       0
  XP GAIN WILD-TYPE         1      13
D40V3, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 12                77
  STAGE IA                 8                77
  STAGE IB                 2                 4
  STAGE II                 2                 4
  STAGE IIA               55               298
  STAGE IIB               33               219
  STAGE III                0                 2
  STAGE IIIA              21               133
  STAGE IIIB               4                25
  STAGE IIIC              10                55
  STAGE IV                 4                16
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED    29  98  19   5
  XP GAIN WILD-TYPE 247 526 117  35
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              29               247
  T2              98               526
  T3              19               117
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP GAIN MUTATED    74  46  18  11
  XP GAIN WILD-TYPE 433 312 101  66
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              74               433
  N1              46               312
  N2              18               101
  N3              11                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED   129   5
  XP GAIN WILD-TYPE 760  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED    129    5
  XP GAIN WILD-TYPE  760   17
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0             129               760
  1               5                17
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED   150   1
  XP GAIN WILD-TYPE 918  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED    150    1
  XP GAIN WILD-TYPE  918   11
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE             150               918
  MALE                 1                11
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    57  79
  XP GAIN WILD-TYPE 372 439
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     57   79
  XP GAIN WILD-TYPE  372  439
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               57               372
  YES              79               439
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XP GAIN MUTATED                            1                           122
  XP GAIN WILD-TYPE                          0                           648
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XP GAIN MUTATED                               11                   3
  XP GAIN WILD-TYPE                            189                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XP GAIN MUTATED                       2                                3
  XP GAIN WILD-TYPE                     7                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XP GAIN MUTATED                    3              6
  XP GAIN WILD-TYPE                 14             41
D40V9, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                122               648
  INFILTRATING LOBULAR CARCINOMA                11               189
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 6                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  1     6
  XP GAIN WILD-TYPE                                0    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          31    92
  XP GAIN WILD-TYPE                       150   653
D40V11, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     31               150
  WHITE                                         92               653
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V12, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     3 118
  XP GAIN WILD-TYPE  36 757
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      3  118
  XP GAIN WILD-TYPE   36  757
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO             118               757
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED   117  16
  XQ GAIN WILD-TYPE 800 131
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              133               931 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               16               131 
$`XQ GAIN MUTATED`
TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A0CM TCGA-A2-A0CX TCGA-A2-A0D2 
       13.68        28.01        73.84        24.79        56.81        33.76 
TCGA-A2-A0EQ TCGA-A2-A0SW TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YJ 
       79.76        44.88         8.38        49.84        21.90        18.61 
TCGA-A2-A0YM TCGA-A2-A1G0 TCGA-A2-A25E TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S2 
       31.73        20.25       105.34        47.31        35.93        21.14 
TCGA-A7-A0CD TCGA-A7-A0DB TCGA-A7-A2KD TCGA-A7-A3J0 TCGA-A7-A425 TCGA-A7-A4SD 
       38.30        33.11        22.32        10.29        14.70        14.50 
TCGA-A7-A5ZV TCGA-A8-A076 TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W 
       12.10        53.98        32.05        10.98         8.98         9.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08T 
       45.07        13.02        38.01        28.96        33.01       112.08 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09Q TCGA-A8-A09W 
       33.01        17.95        41.98        12.00        25.02         0.99 
TCGA-AC-A2BK TCGA-AC-A3OD TCGA-AC-A5EI TCGA-AC-A62X TCGA-AN-A03Y TCGA-AN-A0FT 
       73.05        14.83        14.53        13.71         0.33         7.04 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.33         0.33        66.77        81.63        32.78        52.18 
TCGA-AO-A0JM TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12F TCGA-AO-A1KR TCGA-AR-A0TW 
       71.80       106.78        98.27        48.36        70.39        98.93 
TCGA-AR-A1AV TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24Z TCGA-AR-A254 TCGA-AR-A5QM 
       61.28       104.28       112.77        98.66        85.64        73.35 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A1KF TCGA-BH-A0AW 
      143.38       281.29       206.86       245.10       101.52        20.45 
TCGA-BH-A0AY TCGA-BH-A0DL TCGA-BH-A0DS TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0GY 
       25.55        78.28         2.56         9.63        24.43        30.35 
TCGA-BH-A0HQ TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A1EO 
       36.85        50.79        23.05        37.74        55.63        91.99 
TCGA-BH-A1ET TCGA-BH-A1F0 TCGA-BH-A1FC TCGA-BH-A202 TCGA-BH-A6R8 TCGA-C8-A12L 
       82.85        25.81       114.15        26.14         9.63        11.93 
TCGA-C8-A12M TCGA-C8-A1HG TCGA-C8-A274 TCGA-C8-A275 TCGA-D8-A142 TCGA-D8-A143 
       11.77        11.34         9.53         0.03        13.97        14.17 
TCGA-D8-A1JD TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1XQ TCGA-D8-A1XW TCGA-D8-A1XZ 
       18.15        13.32        18.58        16.41        43.04        15.32 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-E2-A10B TCGA-E2-A14P TCGA-E2-A14S 
       12.53        12.26        18.51        37.51        40.96        33.17 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A15D TCGA-E2-A1B0 TCGA-E2-A56Z 
       34.26        31.96        69.34        17.29        53.62         8.28 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1RC TCGA-E9-A2JS TCGA-E9-A54X TCGA-E9-A5FL 
       17.69        22.29        40.24        29.72        23.90         0.79 
TCGA-EW-A1IY TCGA-EW-A1P5 TCGA-EW-A1PB TCGA-GI-A2C9 TCGA-LL-A6FQ TCGA-LL-A73Y 
        8.48        23.11        19.99       109.87         2.63        15.68 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A97C TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z 
       20.38        23.47         8.91         9.93        18.81        20.68 
TCGA-Z7-A8R6 
      107.05 

$`XQ GAIN WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       99.12       114.81        92.48        88.60       107.93        77.19 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       75.25         5.19        98.99       107.93        67.33        34.55 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       61.58        25.22       101.72        89.36        80.28       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        27.12        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       44.28        17.52        17.13        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH 
       20.75        32.55        25.28        18.21        50.47        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC 
      107.70        42.44        17.19        18.15        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        91.07        29.98        32.75        56.28 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       26.96        21.90        35.31        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       37.45        35.67        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A3RF 
       21.73        20.61        11.34        10.59        11.28        13.41 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        14.93        13.74        21.17        17.92        14.73 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01         1.02        17.03         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O 
       19.99        18.97        18.97        14.01        12.00         9.99 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08G 
        7.99        24.99        15.06        36.95         0.99        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       12.00        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        43.00        40.01        30.97         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X 
       33.07         1.02         8.98        19.04        15.02        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45         6.48        16.31        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y 
       29.26        16.80        19.33        14.96        11.44        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 
       20.19         1.12         1.32         2.30         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.62         2.96         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        7.36         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        6.44         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        6.90         0.33         0.36         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R 
        5.33         5.59        80.28        61.35        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        58.95        29.13        21.40        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       72.00        76.77        65.10        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       55.33       115.27        99.25       108.72       108.03        90.58 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       61.87         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      140.55        98.33         5.26        84.10       109.02        75.22 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
       64.83        55.86       107.24        65.36       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       97.68        98.33        96.00        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       17.23        37.81        94.29        86.53        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
      160.90        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        2.76        97.84       105.27        77.69       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 
       98.76        89.00        99.62        93.30        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        57.27        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       10.59        77.62        12.13       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG 
       84.59       165.76       129.07       140.88       255.68        68.45 
TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      212.25       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      129.70        28.27        68.94        58.88        43.59        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
      139.17       170.17        37.87         7.07        85.35        70.16 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       68.12        18.84       103.63        71.15        62.93        59.84 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       63.09        81.44        40.83        39.55        39.16        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.63        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       43.53        61.51        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       75.48        74.14        76.60        53.95        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       77.95        49.05        41.75        44.02        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       17.26        15.65         3.22        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        24.49        31.00        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HW 
       20.38         5.85         2.50        13.61        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       32.91         4.90        35.93        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U 
       72.56        30.28        37.55        66.05         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.16        67.50       113.82        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 
       49.58        17.69        31.53        89.16        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       20.12        10.52       109.28        20.88        18.64        23.51 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N 
        5.26         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56         3.16        13.51         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF 
       12.59        12.92         4.11         4.08        12.33        10.92 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.28         0.16        12.03        10.42        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         9.50        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.25        20.58        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF 
       17.49        16.50        55.50        15.78        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       53.00        14.01        18.97        20.09        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 
       19.40        20.38        21.01        12.20        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        55.30        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       15.16        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         1.61        10.09        13.08 
TCGA-D8-A3Z5 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       33.37        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        46.59        40.41        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       28.87        47.15        44.68        38.24        38.60        75.98 
TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       43.33        32.02        18.51        63.62        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       22.82        20.71        21.63        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        14.07        51.39        76.57        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        75.81        28.90        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        26.99        34.55        43.56 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        38.76        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       35.77        35.24        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       48.23        45.01        32.09         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       37.74        39.09        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 
       40.50        20.12         0.69        38.99         1.94         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56        12.33         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       30.44        23.84        26.70        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       12.20        39.72        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       30.08         7.86        18.90         6.15        13.94        10.52 
TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV 
       14.43        34.55        19.96        55.00        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       22.09        34.03        17.49        10.16        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       16.77        24.99        31.30        33.21         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       13.55        18.12         2.60        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       32.75        29.23        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A740 
       14.47        14.79        22.26        16.08         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       19.53        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       34.92        36.36        28.87        24.72        22.32        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       28.21        19.73        40.11        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 
        0.16         0.26        18.48        21.07        19.27        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       18.87        17.39        17.26        13.94        17.03         3.81 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       66.84        11.41        52.96        29.03        15.35        16.04 
TCGA-Z7-A8R5 
      108.07 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.03              0.03 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           281.29            282.90 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            25.81             28.14 
[1] "0.0 - 281.3 (25.8)" "0.0 - 282.9 (28.1)"
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ GAIN MUTATED         8        8        2        2        54        28
  XQ GAIN WILD-TYPE      81       77        4        4       299       224
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           0         16          5          9        4
  XQ GAIN WILD-TYPE         2        138         24         56       16
                   vv
clus                STAGE TIS STAGE X
  XQ GAIN MUTATED           0       0
  XQ GAIN WILD-TYPE         1      13
D41V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  8                81
  STAGE IA                 8                77
  STAGE IB                 2                 4
  STAGE II                 2                 4
  STAGE IIA               54               299
  STAGE IIB               28               224
  STAGE III                0                 2
  STAGE IIIA              16               138
  STAGE IIIB               5                24
  STAGE IIIC               9                56
  STAGE IV                 4                16
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED    28  89  14   5
  XQ GAIN WILD-TYPE 248 535 122  35
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              28               248
  T2              89               535
  T3              14               122
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ GAIN MUTATED    68  41  15  11
  XQ GAIN WILD-TYPE 439 317 104  66
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              68               439
  N1              41               317
  N2              15               104
  N3              11                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED   115   5
  XQ GAIN WILD-TYPE 774  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    115    5
  XQ GAIN WILD-TYPE  774   17
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0             115               774
  1               5                17
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED   135   1
  XQ GAIN WILD-TYPE 933  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED    135    1
  XQ GAIN WILD-TYPE  933   11
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE             135               933
  MALE                 1                11
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    51  68
  XQ GAIN WILD-TYPE 378 450
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     51   68
  XQ GAIN WILD-TYPE  378  450
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               51               378
  YES              68               450
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ GAIN MUTATED                            1                           112
  XQ GAIN WILD-TYPE                          0                           658
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ GAIN MUTATED                                9                   2
  XQ GAIN WILD-TYPE                            191                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XQ GAIN MUTATED                       1                                1
  XQ GAIN WILD-TYPE                     8                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XQ GAIN MUTATED                    3              6
  XQ GAIN WILD-TYPE                 14             41
D41V9, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                112               658
  INFILTRATING LOBULAR CARCINOMA                 9               191
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 6                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  0     6
  XQ GAIN WILD-TYPE                                1    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          30    81
  XQ GAIN WILD-TYPE                       151   664
D41V11, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     30               151
  WHITE                                         81               664
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V12, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     3 104
  XQ GAIN WILD-TYPE  36 771
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      3  104
  XQ GAIN WILD-TYPE   36  771
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO             104               771
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   196  44
  1P LOSS WILD-TYPE 721 103
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              240               824 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               44               103 
$`1P LOSS MUTATED`
TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SN TCGA-A2-A04R TCGA-A2-A0CS TCGA-A2-A0CW 
      131.67         9.96        39.32       121.94        77.19       107.93 
TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SV 
       25.22        89.36        79.76        35.05        63.29        27.12 
TCGA-A2-A0T4 TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A1FW 
       20.52        18.21        50.47        21.90        21.67        17.36 
TCGA-A2-A1FX TCGA-A2-A25C TCGA-A2-A3KC TCGA-A2-A3XU TCGA-A2-A4S3 TCGA-A7-A0CJ 
       60.72        17.19        36.23        29.98        21.90        30.61 
TCGA-A7-A0DC TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06U 
       29.79        14.73        12.10        13.02        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07G 
       26.01        17.03         9.01        43.00        18.97        18.97 
TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08S 
        8.98        15.06        38.01        37.05        31.00        33.01 
TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       30.97         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 
       49.05        45.07         1.02        25.02        14.01        19.04 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FE 
       21.04        27.02        17.03        22.95        73.05        86.66 
TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A5EH TCGA-AC-A8OP TCGA-AN-A03X 
       26.04        32.45         6.48        16.80        20.19         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR 
        0.33         0.23         0.33         2.96         7.46         0.33 
TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU 
        6.44         7.00         7.17         0.30         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JA 
       80.28        66.77        95.70        26.04        20.32        21.53 
TCGA-AO-A0JI TCGA-AO-A12A TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AQ-A0Y5 
       50.24        90.58        82.62        61.87         0.53         5.65 
TCGA-AR-A0TQ TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R 
       98.33        83.87        93.90        86.53       160.90       112.77 
TCGA-AR-A24T TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LK TCGA-AR-A2LO TCGA-AR-A5QN 
      105.27        89.00        85.64        54.21        39.39        33.30 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE 
       12.13       129.57       146.50       233.62       165.76       255.68 
TCGA-B6-A0RL TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW 
       81.17       162.05       102.77       100.70        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A40B 
       21.47       113.79       101.52        73.51       139.17       103.63 
TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BV TCGA-BH-A0C0 
       40.83        70.22        81.63        37.22        49.94        41.75 
TCGA-BH-A0C1 TCGA-BH-A0E2 TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.02        14.30        46.19        24.49        30.35        10.78 
TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18K 
       23.08        12.89        51.32        23.93        32.91        90.84 
TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EU 
       26.66        30.28         7.36        51.39        67.50        42.28 
TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FM TCGA-BH-A204 
       12.00        24.62       114.15        74.73        45.63        83.31 
TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5J0 TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A131 
      130.16        10.52        23.51        11.77        12.66        13.51 
TCGA-C8-A138 TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 
        4.08        12.03        10.42        12.36         8.28         9.53 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JE TCGA-D8-A1JF 
       24.56        33.99        13.97        21.14        18.90        12.03 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XQ 
       18.97        20.09        19.40        15.22        14.73        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XZ TCGA-D8-A1Y1 
       15.85        16.31        12.99        15.16        15.32         9.93 
TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27T TCGA-D8-A27W TCGA-D8-A73U TCGA-E2-A107 
       14.14        14.43        13.08        12.26        16.18        34.42 
TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A15R TCGA-E2-A1IH TCGA-E2-A1LG 
       28.44        44.68        34.26        56.94        33.73        50.07 
TCGA-E2-A2P5 TCGA-E2-A576 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NH TCGA-E9-A1NI 
       26.99        34.29        36.56        41.62        18.94         9.86 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RC TCGA-E9-A1RG TCGA-E9-A22A TCGA-E9-A22E 
        2.56         3.02        40.24        21.27        39.09        41.72 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y 
        0.69        38.99         7.13        12.33        29.72        23.84 
TCGA-E9-A5FK TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 
       26.70        26.40        28.77        29.85        52.96        23.11 
TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW 
        6.15        10.52        19.96        55.00        25.91        22.09 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A3NW TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A5YL 
       33.21         7.40       110.50         2.60        11.57        17.06 
TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A9Q3 TCGA-OK-A5Q2 TCGA-OL-A5RZ TCGA-OL-A66K 
       15.32        22.26        17.49         2.10        22.32        41.92 
TCGA-OL-A66N TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-WT-AB41 TCGA-WT-AB44 TCGA-Z7-A8R5 
       26.04         0.16        18.81        52.96        29.03       108.07 

$`1P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U 
       18.21       143.15        18.02        78.41        73.84        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT 
       24.79       114.81        92.48        88.60       107.93        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19        98.99        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
       61.58       101.72        80.28       118.45        74.40        72.00 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU 
       34.29        31.82        61.94        24.72        99.19        54.64 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       49.84        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       49.48        18.61        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        42.44        18.15       105.34        10.59 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        91.07        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       35.93        50.37        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        26.96        21.14        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       35.47        37.45        35.67        33.11        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       25.15        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.74        14.50        21.17        17.92        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q 
       10.29         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07I 
       17.98        31.00         1.02        53.98        19.99        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
        9.99        45.07        36.95        13.02         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R 
       33.01        19.96        12.00         9.99        31.00         0.99 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
      112.08        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       12.00        29.98        33.07         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C 
        0.99        12.00        13.02         0.99        38.04         0.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF 
       73.91         5.72         1.48        99.35        40.57        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        74.14        33.04        19.33        14.66 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       16.57        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       14.53        19.33        14.96        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        1.12         1.32         2.30         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF 
        9.96         7.36         0.16         0.33         0.33         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        7.96         7.59         6.90         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.33         0.33         0.33         5.36         0.33        12.33 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        61.35        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       52.18        37.48        22.36        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL 
       72.00        76.77        65.10        26.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       115.27        99.25       108.72       106.78       108.03 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        64.04        57.30        48.36        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       14.73        70.39        17.79        24.79        26.93       130.09 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91        19.20       140.55 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       133.22       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      125.16       108.36       101.00       103.86        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       96.00        86.07        99.32        17.23        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       61.28        86.43        33.73        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U 
       99.78       118.59         2.76       104.28        97.84        77.69 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
      105.30        32.58        98.76        98.66        99.62        93.30 
TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL 
       71.05        93.83       166.42        20.25        86.53        66.15 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP 
       63.62        38.17        40.54        57.27        73.35        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC 
       10.59        77.62       143.38       281.29       275.87        50.70 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
       65.72       112.37        18.77       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      140.88        68.45       212.25       234.28        78.02       263.28 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48        89.46       282.90       157.41        97.48       188.68 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
       43.59       170.17        37.87         7.07        85.35        70.16 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       68.12        18.84        71.15        62.93        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 
       25.55        63.09        81.44        39.55        39.16        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       51.68        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       53.95        45.57        77.95        49.05        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       78.28        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 
       67.86        70.88        16.27         4.41        15.68         9.63 
TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 
       44.81        32.58        31.00        24.43        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        24.56        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        36.85        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G 
        5.59        24.95        42.35        44.81        23.05         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q TCGA-BH-A18R 
       35.93        20.12        72.56        37.74        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW 
       66.05        51.16        91.99       113.82        82.85        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 
       49.58        17.69        25.81        31.53        89.16        97.48 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62        33.17       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
       57.83        10.65         6.44        20.12       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       18.64         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
        9.44        11.93        11.77        11.77        12.66        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56         3.16 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        1.87        12.59        12.92         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.34        11.28         0.16        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
       20.25        12.53        12.95         9.67         0.03         9.50 
TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       14.43        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       56.81        20.88        13.25        20.58        14.17        13.48 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       18.15        53.00        14.01        20.12        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       17.16        21.80        14.50        19.92        17.69        55.30 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E 
       16.64        43.04        16.54        15.52        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       16.04        13.45        13.05        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         1.61        10.09        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 
       21.67        12.66        25.22        43.00        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       40.41        37.51        40.11        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W 
       38.24        38.60        33.17        75.98        43.33        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A 
       19.43        21.04        23.87        14.79        25.05        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        14.07        51.39        76.57        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       37.41        70.36        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        28.90       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       34.92        38.76        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF 
       22.29        34.16        36.20        39.55        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 
       25.84        24.82        28.27        34.95         6.12        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       48.23        45.01        32.09         1.12        46.65         6.58 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 
       38.37        41.03        40.73        40.50        20.12         1.94 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       23.90         0.79        25.81        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        22.82        29.95        40.41        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       29.82        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 
       13.94        14.43        34.55        52.73        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       10.16        23.51        15.22        16.77        24.99        31.30 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
      101.62        85.35        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U 
       72.03        13.55        18.12        62.47        11.84        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ 
       29.23        25.05        14.70        14.47        14.79         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       16.08        15.68         7.46        14.50        19.53        12.36 
TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       19.59        27.91        22.39        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O 
       20.38        26.70        23.47        65.62        42.77        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       64.21        86.96         0.26         9.93        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-XX-A899 
       13.94        17.03         3.81        66.84        11.41        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.16              0.03 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           255.68            282.90 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           25.960            28.885 
[1] "0.2 - 255.7 (26.0)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.5"
D42V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1P LOSS MUTATED        13       14        0        1        77        45
  1P LOSS WILD-TYPE      76       71        6        5       276       207
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           1         42         17         21        7
  1P LOSS WILD-TYPE         1        112         12         44       13
                   vv
clus                STAGE TIS STAGE X
  1P LOSS MUTATED           0       5
  1P LOSS WILD-TYPE         1       8
D42V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 13                76
  STAGE IA                14                71
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               77               276
  STAGE IIB               45               207
  STAGE III                1                 1
  STAGE IIIA              42               112
  STAGE IIIB              17                12
  STAGE IIIC              21                44
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED    50 141  29  22
  1P LOSS WILD-TYPE 226 483 107  18
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              50               226
  T2             141               483
  T3              29               107
  T4              22                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1P LOSS MUTATED    94  81  36  26
  1P LOSS WILD-TYPE 413 277  83  51
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              94               413
  N1              81               277
  N2              36                83
  N3              26                51
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   201   7
  1P LOSS WILD-TYPE 688  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    201    7
  1P LOSS WILD-TYPE  688   15
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0             201               688
  1               7                15
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   241   2
  1P LOSS WILD-TYPE 827  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    241    2
  1P LOSS WILD-TYPE  827   10
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE             241               827
  MALE                 2                10
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    94 117
  1P LOSS WILD-TYPE 335 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     94  117
  1P LOSS WILD-TYPE  335  401
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               94               335
  YES             117               401
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1P LOSS MUTATED                            1                           177
  1P LOSS WILD-TYPE                          0                           593
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1P LOSS MUTATED                               47                   2
  1P LOSS WILD-TYPE                            153                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1P LOSS MUTATED                       0                                5
  1P LOSS WILD-TYPE                     9                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1P LOSS MUTATED                    2              9
  1P LOSS WILD-TYPE                 15             38
D42V9, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                177               593
  INFILTRATING LOBULAR CARCINOMA                47               153
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                 9                38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0    14
  1P LOSS WILD-TYPE                                1    46
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          38   156
  1P LOSS WILD-TYPE                       143   589
D42V11, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         14                46
  BLACK OR AFRICAN AMERICAN                     38               143
  WHITE                                        156               589
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V12, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     7 186
  1P LOSS WILD-TYPE  32 689
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      7  186
  1P LOSS WILD-TYPE   32  689
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             186               689
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    41  10
  1Q LOSS WILD-TYPE 876 137
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               51              1013 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               10               137 
$`1Q LOSS MUTATED`
TCGA-A2-A0CW TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4S3 
      107.93        18.21        50.47        17.36        60.72        21.90 
TCGA-A7-A0DC TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A08J TCGA-A8-A08S TCGA-A8-A09N 
       29.79        29.03         9.01        37.05        33.01         1.02 
TCGA-AC-A3BB TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0XS TCGA-AN-A0XU 
       32.45         2.96         7.46         0.33         0.33         0.33 
TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AR-A0TQ TCGA-AR-A0U2 
       66.77        95.70        82.62         0.53        98.33        83.87 
TCGA-AR-A24H TCGA-AR-A24T TCGA-B6-A0IG TCGA-B6-A0RL TCGA-BH-A0B6 TCGA-BH-A0BV 
      160.90       105.27       146.50        81.17        81.63        49.94 
TCGA-BH-A0E2 TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0HW TCGA-BH-A1FC TCGA-BH-A1FE 
       14.30        30.35        10.78        51.32       114.15        74.73 
TCGA-BH-A204 TCGA-BH-A42T TCGA-C8-A138 TCGA-C8-A27A TCGA-D8-A1XQ TCGA-D8-A1XU 
       83.31        10.52         4.08        24.56        16.41        12.99 
TCGA-D8-A1XZ TCGA-E2-A15R TCGA-E9-A1ND TCGA-E9-A1RC TCGA-E9-A247 TCGA-EW-A1J6 
       15.32        56.94        41.62        40.24        38.99        28.77 
TCGA-EW-A6SD TCGA-HN-A2NL TCGA-OL-A5RZ 
       33.21         2.60        22.32 

$`1Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM 
       14.27        47.24        20.88        13.68        31.79         7.96 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
       39.32        28.01        19.20        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W 
       78.41       121.94        73.84        87.25        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       98.99        56.81        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.77        23.47        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       26.96        21.14        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E 
       30.61        37.45        35.67        33.11        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       25.15        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
       13.02        13.02         1.02        17.98        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E 
       26.01         1.02        17.03        53.98        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99        24.99         9.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        12.00         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
        0.99       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       17.95        41.98        12.00         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        1.02        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        1.48        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       14.66         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU 
       24.79        29.26        16.80        14.53        19.33        14.96 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       11.44        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS 
        1.78         1.71         9.96         7.36         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.17         6.90         7.04         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       81.63        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       65.10        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27        99.25       108.72       106.78       108.03        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       98.27        64.04        57.30        48.36        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       14.73        61.87        70.39        17.79        24.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
      130.09         5.65        15.62        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20       140.55         5.26        84.10       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.93        64.83        55.86       107.24        65.36       133.22 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      134.14       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ 
       97.68        98.33        96.00        86.07        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        94.29        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V 
        2.76       104.28       112.77        97.84        77.69       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       32.58        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       281.29        12.13       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       282.90       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        18.35        21.47       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      245.10        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       73.51       139.17       170.17        37.87         7.07        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       70.16        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        63.09        81.44        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        70.22        84.13        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        43.53        61.51        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       45.57        77.95        49.05        41.75        44.02        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        45.83        77.98        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        78.28        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       24.43        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       51.39        51.16        67.50        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       31.53        89.16        97.48        24.62       120.62        33.17 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN 
      122.89        36.92        63.35        55.00        45.63        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
      144.59        72.07        28.14        26.14        38.60        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V 
      130.16        10.65         6.44        20.12       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       18.64        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56         3.16        13.51         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       12.92         4.11        12.33        10.92        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
        0.16        12.03        10.42        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       20.25        12.53        12.36        12.95         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         0.03         9.50        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI 
       18.15        18.90        12.03        53.00        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       15.22        14.73        21.80        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       55.30        15.85        16.31        16.64        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.52         9.93        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       69.96        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       25.05        23.34        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        50.79        19.56        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        87.22        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        60.36        73.64        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        50.07       106.75       102.61         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 
       26.99        34.55        43.56         8.28        30.61        34.92 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 
       38.76        34.29        17.69        34.82        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE 
       22.29        34.16        36.20        36.56        39.55        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02        11.15        48.23 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       45.01        32.09         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       39.09        38.37        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.12         0.69         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       23.90        23.84        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       13.25        16.57        15.68        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       10.16        23.51        15.22        16.77        24.99        31.30 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC 
        7.40       109.87        59.57       216.76        79.10        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ 
       15.32        14.70        14.47        14.79        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       16.08        15.68         7.46        14.50        19.53        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW 
       58.52        31.99        58.62        40.08        34.92        36.36 
TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       28.87        24.72        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       41.92        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         9.93        18.81        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       13.94        17.03         3.81        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.33              0.03 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            160.9             282.9 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            32.45             27.12 
[1] "0.3 - 160.9 (32.5)" "0.0 - 282.9 (27.1)"
[1] "hr=" "1.3"
D43V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  1Q LOSS MUTATED         3        5        0        0        15        13
  1Q LOSS WILD-TYPE      86       80        6        6       338       239
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           0         10          2          3        1
  1Q LOSS WILD-TYPE         2        144         27         62       19
                   vv
clus                STAGE TIS STAGE X
  1Q LOSS MUTATED           0       0
  1Q LOSS WILD-TYPE         1      13
D43V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  3                86
  STAGE IA                 5                80
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               15               338
  STAGE IIB               13               239
  STAGE III                0                 2
  STAGE IIIA              10               144
  STAGE IIIB               2                27
  STAGE IIIC               3                62
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED    14  29   5   4
  1Q LOSS WILD-TYPE 262 595 131  36
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              14               262
  T2              29               595
  T3               5               131
  T4               4                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  1Q LOSS MUTATED    18  20   9   5
  1Q LOSS WILD-TYPE 489 338 110  72
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              18               489
  N1              20               338
  N2               9               110
  N3               5                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    48   1
  1Q LOSS WILD-TYPE 841  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     48    1
  1Q LOSS WILD-TYPE  841   21
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              48               841
  1               1                21
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                   0    1
  1Q LOSS MUTATED     52    0
  1Q LOSS WILD-TYPE 1016   12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     52    0
  1Q LOSS WILD-TYPE 1016   12
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              52              1016
  MALE                 0                12
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    22  21
  1Q LOSS WILD-TYPE 407 497
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     22   21
  1Q LOSS WILD-TYPE  407  497
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               22               407
  YES              21               497
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  1Q LOSS MUTATED                            0                            44
  1Q LOSS WILD-TYPE                          1                           726
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  1Q LOSS MUTATED                                6                   1
  1Q LOSS WILD-TYPE                            194                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  1Q LOSS MUTATED                       0                                1
  1Q LOSS WILD-TYPE                     9                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  1Q LOSS MUTATED                    0              0
  1Q LOSS WILD-TYPE                 17             47
D43V9, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 44               726
  INFILTRATING LOBULAR CARCINOMA                 6               194
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 0                47
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     3
  1Q LOSS WILD-TYPE                                1    57
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                          10    32
  1Q LOSS WILD-TYPE                       171   713
D43V11, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          3                57
  BLACK OR AFRICAN AMERICAN                     10               171
  WHITE                                         32               713
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V12, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  37
  1Q LOSS WILD-TYPE  37 838
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   37
  1Q LOSS WILD-TYPE   37  838
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                37
  NOT HISPANIC OR LATINO              37               838
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED   155  24
  2P LOSS WILD-TYPE 762 123
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              179               885 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               24               123 
$`2P LOSS MUTATED`
TCGA-3C-AAAU TCGA-4H-AAAK TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0EO 
      129.14        11.44        77.19        75.25        98.99        80.28 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0YH TCGA-A2-A1FW TCGA-A2-A1FX 
       35.05        34.29        27.12        21.67        17.36        60.72 
TCGA-A2-A25B TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A2KD 
       42.44        24.39        35.31        29.79        25.15        22.32 
TCGA-A7-A3J1 TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B 
       11.28        10.42        13.02        26.01         1.02        43.00 
TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08F 
       18.97        10.98         8.98         9.99        38.01        33.01 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C 
       37.05        31.00        33.01        30.97        12.00         1.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 
        1.02        25.02        19.04        19.04        21.04        27.02 
TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A3EH 
       17.03        22.95        99.35        90.71        26.04         6.48 
TCGA-AC-A62V TCGA-AC-A7VC TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK 
       11.44         0.03         0.33         9.96         0.33         7.00 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XT 
        7.59         7.04         0.36         0.33         0.30         0.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JI TCGA-AO-A12A 
       80.28        61.35        95.70        21.40        50.24        90.58 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54O TCGA-AR-A0TZ TCGA-AR-A0U3 
        0.53        17.79         5.65        32.91       107.24       134.14 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R 
       98.33        96.00        37.81       160.90        50.89       112.77 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A2LK TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RL 
      105.30        32.58        54.21       112.37       233.62        81.17 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A408 TCGA-BH-A0B2 TCGA-BH-A0BA TCGA-BH-A0BT 
       43.59        73.51        68.12        40.83        37.22        45.57 
TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0EB TCGA-BH-A0EE 
       49.94        90.97         4.41        14.30        24.49        31.00 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
       23.08        41.00        52.96        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1FN 
       50.79        35.93        55.63       113.82        42.28        72.07 
TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A138 TCGA-C8-A1HG 
       23.51         5.26        12.66        12.66         4.08        11.34 
TCGA-C8-A3M7 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JD TCGA-D8-A1JI TCGA-D8-A1JP 
       33.99        13.97        21.14        18.15        18.97        21.01 
TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XR TCGA-D8-A1XV 
       17.79        27.58        18.15        21.80        15.85        15.16 
TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27T TCGA-E2-A14O TCGA-E2-A14R 
       16.54         9.93        14.14        13.08        44.68        38.60 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15S 
       18.51        69.96        20.71        18.21        12.92        14.07 
TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IN TCGA-E2-A2P5 TCGA-E9-A1N4 
       76.57        37.25        33.73        22.19        26.99        32.88 
TCGA-E9-A1N6 TCGA-E9-A1NF TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE 
       22.29        35.24        11.15        45.01        32.09        46.65 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A249 
       21.27        47.64        42.25        41.03        40.73         7.13 
TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 
       38.07        30.44        23.84        26.40        18.90        28.77 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PE TCGA-EW-A2FV 
       22.82        29.85        23.11         7.86        10.52        25.91 
TCGA-EW-A2FW TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-GI-A2C8 TCGA-LL-A6FR 
       22.09        10.16        15.22        16.77         7.40        16.08 
TCGA-LL-A73Y TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-XX-A89A 
       15.68        64.21         0.16        21.07        16.04 

$`2P LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        42.81        40.14        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
      107.93         5.19       107.93        56.81        67.33        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       33.76        61.58        25.22       101.72        89.36       118.45 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       79.76        74.40        72.00        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.77        23.47        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        36.23        39.65        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA 
       38.30        34.29        35.47        30.61        37.45        35.67 
TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       33.11        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       24.26        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.59        10.29        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05        10.29         9.37         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 
        1.02        17.98        53.06        29.03        31.00        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       53.98         9.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 
       32.05         9.99         7.99        24.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I 
       36.95        13.02         0.99        28.96        19.96        12.00 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
        9.99        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       33.01        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R 
       50.04        49.05        45.07        29.98        33.07         8.98 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A7 
       15.02         0.99        14.01        12.00        13.02         0.99 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
       38.04         0.95        73.91         5.72         1.48        73.05 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       40.57        86.66        60.92        87.12        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       19.33        14.66        32.45        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       23.24        24.79        29.26        16.80        14.53        19.33 
TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        1.68         8.22        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.23         0.33         0.62         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        1.71         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV 
        6.44         5.65         7.96         7.17         6.90         0.33 
TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR 
        0.33         0.33         5.36         0.33        12.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        66.77        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 
       68.75        47.87        58.95        29.13        32.78        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      106.78       108.03        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        40.57        14.73        82.62        61.87        70.39 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
       24.79        26.93       130.09        15.62        32.52         2.56 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       19.20       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
       75.22        98.93        64.83        55.86        65.36       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
       83.87       107.21       125.16       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU 
       97.68        86.07        93.90        99.32        17.23        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M 
       61.28        86.53        86.43        33.73        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
       99.78       118.59         2.76       104.28        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 
       77.69        98.76        98.66        89.00        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       73.35        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        12.13       275.87       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      146.50        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      140.88       255.68        68.45       212.25       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.88       101.52       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        85.35        70.16        18.84       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        70.22        81.63        84.13        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        43.53        61.51        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       61.68        72.23        75.48        74.14        76.60        53.95 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       77.95        49.05        41.75        44.02        89.06        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        23.44        38.01        29.98        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
       70.88        16.27        15.68         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       53.26        24.56        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       13.61        36.85         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       44.81        23.05        32.91         4.90        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       26.66        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET 
        7.36        51.39        51.16        67.50        91.99        82.85 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ 
      109.28        20.88        18.64         9.63         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.16        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.28         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       24.56        14.43        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
       19.46        56.81        20.88        13.25        20.58        14.17 
TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       13.48        19.20        14.17        17.49        16.50        55.50 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ 
       15.78        18.90        12.03        53.00        14.01        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        19.40        20.38        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       14.70        18.58        16.73        25.74        23.90        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW 
       55.30        16.41        16.31        16.64        12.99        43.04 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.32        15.52        14.24        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43        48.03        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        1.61        10.09        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T 
       28.87        47.15        40.96        38.24        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 
       43.33        34.26        32.02        31.96        69.34        63.62 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J 
       23.34        22.82        17.29        21.63        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        50.79        19.56        56.94 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       16.47        77.65        37.41        70.36        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       59.18         3.88        60.99        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       73.64        19.66        24.59        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        43.04        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       34.82        36.82        34.16        36.20        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ 
       41.62        35.77        25.84        18.94         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       28.27        34.95         2.56         6.12         3.02        48.23 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
       40.24         1.12         6.58        46.59        34.45        32.05 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        38.37        41.72        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
        0.69        38.99         1.94        24.56        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
        9.47        32.91        30.18        23.90        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ 
       13.25        16.57        15.68        25.94        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99         6.15        13.94        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       19.96        55.00        52.73        34.03        17.49        23.51 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30        33.21       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       79.10        83.34        75.02        70.85        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
       38.20        43.73        69.30        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       29.23        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
       14.79        22.26         2.63         7.46        14.50        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       12.36        19.59        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z 
       86.96         0.26         9.93        18.81        18.48        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       19.27        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       17.03         3.81        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35       108.07       107.05 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.03              0.03 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           233.62            282.90 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            25.02             28.87 
[1] "0.0 - 233.6 (25.0)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.2"
D44V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2P LOSS MUTATED        12       12        0        1        56        38
  2P LOSS WILD-TYPE      77       73        6        5       297       214
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           1         32          6         14        7
  2P LOSS WILD-TYPE         1        122         23         51       13
                   vv
clus                STAGE TIS STAGE X
  2P LOSS MUTATED           0       3
  2P LOSS WILD-TYPE         1      10
D44V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 12                77
  STAGE IA                12                73
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               56               297
  STAGE IIB               38               214
  STAGE III                1                 1
  STAGE IIIA              32               122
  STAGE IIIB               6                23
  STAGE IIIC              14                51
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED    39 109  24   9
  2P LOSS WILD-TYPE 237 515 112  31
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              39               237
  T2             109               515
  T3              24               112
  T4               9                31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2P LOSS MUTATED    82  52  29  17
  2P LOSS WILD-TYPE 425 306  90  60
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              82               425
  N1              52               306
  N2              29                90
  N3              17                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED   145   8
  2P LOSS WILD-TYPE 744  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    145    8
  2P LOSS WILD-TYPE  744   14
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0             145               744
  1               8                14
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED   179   3
  2P LOSS WILD-TYPE 889   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED    179    3
  2P LOSS WILD-TYPE  889    9
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE             179               889
  MALE                 3                 9
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    71  92
  2P LOSS WILD-TYPE 358 426
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     71   92
  2P LOSS WILD-TYPE  358  426
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               71               358
  YES              92               426
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2P LOSS MUTATED                            0                           141
  2P LOSS WILD-TYPE                          1                           629
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2P LOSS MUTATED                               25                   0
  2P LOSS WILD-TYPE                            175                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2P LOSS MUTATED                       3                                6
  2P LOSS WILD-TYPE                     6                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2P LOSS MUTATED                    2              5
  2P LOSS WILD-TYPE                 15             42
D44V9, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                141               629
  INFILTRATING LOBULAR CARCINOMA                25               175
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                 5                42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0    12
  2P LOSS WILD-TYPE                                1    48
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                          21   124
  2P LOSS WILD-TYPE                       160   621
D44V11, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         12                48
  BLACK OR AFRICAN AMERICAN                     21               160
  WHITE                                        124               621
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V12, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    10 131
  2P LOSS WILD-TYPE  29 744
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10  131
  2P LOSS WILD-TYPE   29  744
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                29
  NOT HISPANIC OR LATINO             131               744
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED   178  30
  2Q LOSS WILD-TYPE 739 117
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              208               856 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               30               117 
$`2Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV 
      129.14        42.81        11.44        77.19        75.25        98.99 
TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0YH TCGA-A2-A1FW 
       80.28        35.05        34.29        27.12        21.67        17.36 
TCGA-A2-A1FX TCGA-A2-A3XS TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0DC TCGA-A7-A13E 
       60.72        33.93        24.39        35.31        29.79        20.19 
TCGA-A7-A13F TCGA-A7-A3J1 TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06T 
       25.15        11.28        10.42        13.02         1.02        53.06 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07F TCGA-A8-A07P TCGA-A8-A07R 
       26.01         1.02        43.00        18.97        10.98         8.98 
TCGA-A8-A07W TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
        9.99        38.01        33.01        12.00        37.05        31.00 
TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09N TCGA-A8-A09Q 
       33.01        30.97        12.00         1.02         1.02        25.02 
TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23E 
       19.04        19.04        21.04        27.02        17.03        22.95 
TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A3EH TCGA-AC-A62V TCGA-AC-A6IW 
       99.35        90.71        26.04         6.48        11.44        13.58 
TCGA-AC-A7VC TCGA-AN-A03Y TCGA-AN-A0AJ TCGA-AN-A0AS TCGA-AN-A0FK TCGA-AN-A0FL 
        0.03         0.33         9.96         0.33         7.00         7.59 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XT 
        7.04         0.36         0.33         0.33         0.30         0.33 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0JD TCGA-AO-A0JI 
       80.28        61.35        95.70        21.40        72.00        50.24 
TCGA-AO-A12A TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AQ-A54O 
       90.58         0.53        17.79         5.65         2.56        32.91 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0U3 TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AS 
       84.10        75.22       134.14        98.33        96.00        37.81 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W 
       33.73       160.90        50.89       112.77       105.30        32.58 
TCGA-AR-A2LK TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0RL TCGA-B6-A0RU 
       54.21        12.13       112.37       233.62        81.17       282.90 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0B2 TCGA-BH-A0BA 
       43.59        73.51       139.17        68.12        40.83        37.22 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C7 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 
       45.57        49.94        90.97         4.41        14.30         9.63 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HU 
       24.49        31.00        23.08        41.00        52.96        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A18I TCGA-BH-A18Q TCGA-BH-A1ES TCGA-BH-A1EU 
       51.32        27.25        35.93        55.63       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 
       12.00        97.48       114.15        45.63        72.07        26.14 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R9 TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A138 
       18.64        23.51         5.26        12.66        12.66         4.08 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HK TCGA-C8-A26Z TCGA-C8-A3M7 TCGA-D8-A13Z 
       10.92        11.34        12.03         8.28        33.99        20.88 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1JI TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB 
       13.97        21.14        18.97        17.79        27.58        18.15 
TCGA-D8-A1XJ TCGA-D8-A1XR TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       21.80        15.85        15.16        16.54         9.93        14.14 
TCGA-D8-A27T TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 
       13.08        44.68        38.60        31.96        18.51        69.96 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A1BD 
       20.71        18.21        12.92        14.07        76.57        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A2P5 TCGA-E9-A1N4 TCGA-E9-A1N6 
       33.73        33.70        22.19        26.99        32.88        22.29 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RE 
       35.24         9.86        11.15        45.01        32.09        46.65 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A228 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A249 
       21.27        47.64        42.25        41.03        40.73         7.13 
TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 
       38.07        30.44        23.84        26.40        18.90        28.77 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PE TCGA-EW-A2FV 
       22.82        29.85        23.11         7.86        10.52        25.91 
TCGA-EW-A2FW TCGA-EW-A423 TCGA-EW-A6S9 TCGA-GM-A2DF TCGA-GM-A4E0 TCGA-HN-A2NL 
       22.09        10.16        15.22        70.85        72.03         2.60 
TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A6VO TCGA-PE-A5DD 
       16.08        19.53        12.36        22.32        28.21        64.21 
TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-XX-A89A 
        0.16        21.07        17.39        16.04 

$`2Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
      131.67        40.14        48.56        48.36         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       13.68        31.79         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T 
       18.21       143.15        18.02        78.41       121.94        73.84 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19       107.93        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       61.58        25.22       101.72        89.36       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       74.40        72.00        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       49.48        18.61        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        39.65        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       21.30        23.21        26.96        21.14        21.90        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A13D TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G 
       31.73        23.61        29.56        31.36        24.26        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.80        21.73        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       10.29        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       14.50        21.17        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06R 
       11.05        10.29         9.37         8.75        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       29.03        31.00        17.03        53.98         9.01        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07S 
       18.97        14.01        12.00        32.05         9.99         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       24.99        45.07        15.06        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       28.96        19.96         9.99        31.00         0.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       43.00        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99         9.99        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       33.07         8.98        15.02         0.99        14.01        12.00 
TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H 
       13.02         0.99        38.04         0.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        73.05        40.57        86.66        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3HN 
       74.14        33.04        19.33        14.66        32.45        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       14.83        22.19        24.13        25.05        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       19.79        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       14.53        19.33        14.96        13.71        17.42        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
       12.26         1.68         8.22        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        2.30         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.78         1.71         7.36         7.46         0.16         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         6.44         5.65         7.96         7.17         6.90 
TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR 
        0.33         0.33         5.36         0.33        12.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        66.77        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 
       68.75        47.87        58.95        29.13        32.78        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       26.04        37.48        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ 
       50.70        50.86        76.77        65.10        26.24        62.04 
TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       55.33        71.80       115.27        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
      108.03        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       40.57        14.73        82.62        61.87        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP 
       26.93       130.09        15.62        32.52        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       98.33         5.26       109.02        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24        65.36       133.22        83.87       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP 
      108.36       101.00       103.86        97.68        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       99.32        17.23        94.29        61.28        86.53        86.43 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       97.84       105.27        77.69        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        66.15        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       281.29       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       65.72       146.50        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
       89.46       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
       68.94        58.88       101.52       170.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       85.35        70.16        18.84       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC 
       39.16        70.22        81.63        84.13        51.68        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW 
       72.23        75.48        74.14        76.60        53.95        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        41.75        44.02        89.06        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI 
       16.27        15.68        44.81        46.19        32.58        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       23.05        32.91         4.90        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       72.56        37.74        30.28        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EW 
       51.39        51.16        67.50        91.99        82.85        55.69 
TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       49.58        17.69        25.81        31.53        89.16        24.62 
TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      120.62        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 
       55.00       144.59        72.07        28.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
      109.28        20.88         9.63         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
        9.44        11.93        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE 
       13.51         1.87        12.59        12.92         4.11        12.33 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.28         0.16        10.42        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 
       20.25        12.53        12.36        12.95         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HP 
        0.03         9.50        24.56        14.43        12.95        13.02 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        19.46        56.81        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       14.17        13.48        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       55.50        15.78        18.15        18.90        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        20.09        20.12        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        18.58        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       25.74        23.90        12.39        17.16        15.22        14.73 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS 
       14.50        19.92        17.69        55.30        16.41        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 
       16.64        12.99        43.04        15.32        15.52        14.24 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48         4.80         1.61        10.09        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P 
       37.51        40.11        28.44        28.87        47.15        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       69.34        63.62        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       14.79        25.05        23.34        22.82        17.29        21.63 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        56.94        51.39        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18         3.88        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       60.36        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 
       50.07       106.75       102.61         8.75        43.04        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
       43.56         8.28        30.61        34.92        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       17.69        34.82        36.82        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ 
       39.55        41.62        35.77        25.84        18.94        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       28.27        34.95         2.56         6.12         3.02        48.23 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 
       40.24         1.12         6.58        46.59        34.45        32.05 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        38.37        41.72        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
        0.69        38.99         1.94        24.56        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
        9.47        32.91        30.18        23.90        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ 
       13.25        16.57        15.68        25.94        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99         6.15        13.94        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       19.96        55.00        52.73        34.03        17.49        23.51 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DH 
       59.57       216.76        79.10        83.34        75.02        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A5PV 
      110.50        38.20        43.73        69.30        66.38        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
       18.12        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       25.05        17.06        15.32        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
       22.26         2.63        15.68         7.46        14.50        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        26.04        17.36        14.07        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
        8.91        47.01        86.96         0.26         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 
       18.48        20.68        19.27        13.84        18.87        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       13.94        17.03         3.81        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35       108.07       107.05 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.03              0.03 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           282.90            281.29 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           25.085            28.930 
[1] "0.0 - 282.9 (25.1)" "0.0 - 281.3 (28.9)"
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  2Q LOSS MUTATED        14       14        0        1        66        43
  2Q LOSS WILD-TYPE      75       71        6        5       287       209
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           1         37          7         15        8
  2Q LOSS WILD-TYPE         1        117         22         50       12
                   vv
clus                STAGE TIS STAGE X
  2Q LOSS MUTATED           0       3
  2Q LOSS WILD-TYPE         1      10
D45V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 14                75
  STAGE IA                14                71
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               66               287
  STAGE IIB               43               209
  STAGE III                1                 1
  STAGE IIIA              37               117
  STAGE IIIB               7                22
  STAGE IIIC              15                50
  STAGE IV                 8                12
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED    46 123  30  11
  2Q LOSS WILD-TYPE 230 501 106  29
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              46               230
  T2             123               501
  T3              30               106
  T4              11                29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  2Q LOSS MUTATED    94  63  33  18
  2Q LOSS WILD-TYPE 413 295  86  59
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              94               413
  N1              63               295
  N2              33                86
  N3              18                59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED   170   8
  2Q LOSS WILD-TYPE 719  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    170    8
  2Q LOSS WILD-TYPE  719   14
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0             170               719
  1               8                14
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED   209   2
  2Q LOSS WILD-TYPE 859  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED    209    2
  2Q LOSS WILD-TYPE  859   10
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE             209               859
  MALE                 2                10
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    82 105
  2Q LOSS WILD-TYPE 347 413
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     82  105
  2Q LOSS WILD-TYPE  347  413
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               82               347
  YES             105               413
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  2Q LOSS MUTATED                            0                           164
  2Q LOSS WILD-TYPE                          1                           606
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  2Q LOSS MUTATED                               27                   2
  2Q LOSS WILD-TYPE                            173                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  2Q LOSS MUTATED                       3                                7
  2Q LOSS WILD-TYPE                     6                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  2Q LOSS MUTATED                    2              6
  2Q LOSS WILD-TYPE                 15             41
D45V9, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                164               606
  INFILTRATING LOBULAR CARCINOMA                27               173
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          3                 6
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             2                15
  OTHER  SPECIFY                                 6                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0    15
  2Q LOSS WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                          31   136
  2Q LOSS WILD-TYPE                       150   609
D45V11, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15                45
  BLACK OR AFRICAN AMERICAN                     31               150
  WHITE                                        136               609
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V12, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11 153
  2Q LOSS WILD-TYPE  28 722
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11  153
  2Q LOSS WILD-TYPE   28  722
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                28
  NOT HISPANIC OR LATINO             153               722
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   156  28
  3P LOSS WILD-TYPE 761 119
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              184               880 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               28               119 
$`3P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T 
      129.14       131.67        42.81        31.79        19.20        73.84 
TCGA-A2-A04U TCGA-A2-A0CL TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       87.25        99.12        75.25       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0T3 TCGA-A2-A0YE 
       34.55        25.22        80.28        79.76        49.84        18.21 
TCGA-A2-A0YT TCGA-A2-A1G1 TCGA-A2-A3XX TCGA-A2-A4S1 TCGA-A7-A0CE TCGA-A7-A0CJ 
       23.77        19.20        47.31        26.96        35.31        30.61 
TCGA-A7-A13D TCGA-A7-A26F TCGA-A7-A2KD TCGA-A7-A4SF TCGA-A7-A6VW TCGA-A7-A6VX 
       31.73        24.26        22.32        17.92         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A08O 
        8.75        29.03         1.02        18.97        12.00        31.00 
TCGA-A8-A09M TCGA-AC-A2BK TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A8OQ TCGA-AN-A041 
       33.07        73.05        74.14        14.83         1.12         0.23 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AR TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT 
        1.78         1.71         0.33         7.96         7.59         7.04 
TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 
        0.33        80.28        61.35        95.70        47.87        21.40 
TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A124 TCGA-AO-A1KS TCGA-AQ-A04L TCGA-AR-A0TP 
       21.53        26.24       115.27         0.53       130.09       140.55 
TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AQ 
      109.02        64.83       133.22        83.87       125.16        99.32 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LO 
       97.84       105.27        99.62        71.05        93.83        39.39 
TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0WS TCGA-B6-A0WW 
      129.57       146.50       112.37       233.62        97.48        18.35 
TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A409 TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BJ 
      113.79        73.51        18.84        51.68        61.51        21.70 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DI TCGA-BH-A0DL TCGA-BH-A0E0 
       77.95        49.05        44.02        29.98        78.28         4.41 
TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A18F TCGA-BH-A18L 
       52.96        12.89        51.32         5.59        32.91        26.66 
TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FU TCGA-BH-A208 
        7.36        67.50        24.62        45.63        72.07        57.83 
TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HF 
       10.52        18.64        11.93        12.92         4.11        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A8HP 
       11.34         0.16        12.03        12.33        12.53        13.02 
TCGA-C8-A8HQ TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ 
       12.49        14.17        17.49        18.15        53.00        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XJ TCGA-D8-A1XK 
       20.12        19.40        18.58        18.15        21.80        14.50 
TCGA-D8-A1XL TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 
       19.92        16.64        12.99        16.54        15.32         9.93 
TCGA-D8-A27M TCGA-D8-A27N TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A150 
       13.48         4.80        40.11        38.60        34.26        63.62 
TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 
       69.96        25.05        23.34        33.70        60.99        60.36 
TCGA-E2-A1LE TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1NC 
       28.90        38.76        34.29        17.69        34.16        39.55 
TCGA-E9-A1NF TCGA-E9-A1R4 TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22G TCGA-E9-A244 
       35.24         6.12        34.45        37.74        40.73         0.69 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-EW-A1OW TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PC 
       12.33        29.72        22.82        29.82        23.11         6.15 
TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A6S9 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DB 
       52.73        10.16        15.22         7.40       109.87        79.10 
TCGA-GM-A2DH TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A5YL TCGA-LL-A7T0 
       72.10         2.60        11.57         7.10        17.06        12.36 
TCGA-LL-A8F5 TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66K TCGA-OL-A66N TCGA-S3-A6ZG 
       19.59        24.72        20.38        41.92        26.04        18.48 
TCGA-S3-A6ZH TCGA-V7-A7HQ TCGA-XX-A89A TCGA-Z7-A8R5 
       21.07        66.84        16.04       108.07 

$`3P LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
       40.14        11.44        48.56        48.36         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N 
       13.68         7.96        39.32        28.01        18.21       143.15 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
       18.02        78.41       121.94        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
       36.13       136.73        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        77.19         5.19        98.99        33.76        61.58 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET 
      101.72        89.36       118.45        74.40        72.00        35.05 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST 
       34.29        31.82        61.94        24.72        63.29        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       54.64        27.12        44.88        50.43        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13         8.38        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        50.47        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW 
       18.61        19.33        48.46        31.73        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       56.28        35.93        50.37        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG 
       21.30        23.21        21.14        21.90        38.30        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E 
       35.47        37.45        35.67        33.11        29.79        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H 
       25.15        23.61        29.56        31.36        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        20.61        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       21.17        14.73        12.10        10.72        11.05        10.29 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X 
       13.02        13.02         1.02        17.98        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01        17.03        53.98         9.01        43.00        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99         9.99        45.07        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       13.02         0.99        38.01        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       12.00        37.05         9.99        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
      112.08        43.00        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q 
       50.04        49.05        45.07        29.98         1.02        25.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
        8.98        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95        22.95        73.91         5.72         1.48 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
       99.35        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       26.04        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       16.31        22.19        24.13        25.05        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       19.79        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       14.53        19.33        14.96        11.44        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
       20.19         1.32         2.30         0.33         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.62         2.96         9.96         7.36         7.46         0.16 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN 
        0.33         0.33         6.44         5.65         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.90         0.33         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        0.33         5.33         5.59        66.77        81.63        68.75 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       20.32        22.36        53.03        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        65.10        50.24        62.04        55.33        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J 
       82.62        61.87        70.39        17.79        24.79        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY 
       98.33         5.26        84.10        75.22        98.93        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ 
      107.24        65.36       134.14       107.21       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      103.86        97.68        98.33        96.00        86.07        93.90 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        94.29        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       33.73       160.90        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24U TCGA-AR-A24V 
      118.59         2.76       104.28       112.77        77.69       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 
       32.58        98.76        98.66        89.00        93.30        85.64 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        12.13       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
       50.70        65.72        18.77       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       282.90       157.41       188.68        79.63 
TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.88        43.59       101.52       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        85.35        70.16        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        70.22        81.63        84.13 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BM 
       37.22        32.02        18.21        43.53        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       72.23        75.48        74.14        76.60        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.94        41.75        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       23.44        38.01        13.91        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        67.86        70.88        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        24.56        23.08        41.00        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY 
        5.85         2.50        13.61        36.85        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        23.05         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       35.93        20.12        90.84        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       55.63        37.55        66.05        51.39        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX 
      113.82        82.85        42.28        12.00        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        97.48       120.62 
TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
      114.15        33.17        74.73       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       55.00        72.07       144.59        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       83.31       130.16        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 
       12.56         3.16        13.51         1.87        12.59         4.08 
TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       12.33        11.28        10.42        12.95        12.33        20.25 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HR 
        9.50        24.56        14.43        33.99        12.95        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       19.46        56.81        20.88        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        13.48        21.14        19.20        16.50        55.50 
TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL 
       15.78        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 
       20.38        21.01        12.20        13.32        14.70        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        27.58        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       15.22        14.73        17.69        55.30        16.41        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.31        15.16        43.04        15.52        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       16.41         1.61        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        75.98        43.33        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       18.51        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK 
       77.65        37.41        70.36        33.73        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 
        3.88        22.19        11.08        54.18        73.64        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        75.81        50.07       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        26.99        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 
       34.92        34.82        32.88        36.82        22.29        36.20 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       36.56        41.62        35.77        25.84        18.94         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 
       24.82        28.27        34.95         2.56         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 
        6.58        21.27        46.59        47.64        32.05        42.25 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       39.09        38.37        41.03        41.72        40.50        20.12 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO 
       38.99         1.94         7.13        24.56         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.79        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       28.77        25.94        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       39.78        52.96        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 
       55.00        25.91        22.09        34.03        17.49        23.51 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GM-A2D9 TCGA-GM-A2DA 
       16.77        24.99        31.30        33.21        59.57       216.76 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       83.34        75.02        70.85        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.84        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       32.75        29.23        25.05        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 
       14.50        19.53        17.49        27.91        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
       36.30        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       36.36        28.87        22.32        26.70        23.47        65.62 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
        8.91        47.01        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        9.93        18.81        20.68        19.27        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G 
       17.39        17.26        13.94        17.03         3.81        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       52.96        29.03        15.35       107.05 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.16              0.03 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           233.62            282.90 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            26.81             27.96 
[1] "0.2 - 233.6 (26.8)" "0.0 - 282.9 (28.0)"
[1] "hr=" "1.1"
D46V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3P LOSS MUTATED        11       12        1        0        63        55
  3P LOSS WILD-TYPE      78       73        5        6       290       197
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           0         24          3         11        3
  3P LOSS WILD-TYPE         2        130         26         54       17
                   vv
clus                STAGE TIS STAGE X
  3P LOSS MUTATED           0       3
  3P LOSS WILD-TYPE         1      10
D46V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 11                78
  STAGE IA                12                73
  STAGE IB                 1                 5
  STAGE II                 0                 6
  STAGE IIA               63               290
  STAGE IIB               55               197
  STAGE III                0                 2
  STAGE IIIA              24               130
  STAGE IIIB               3                26
  STAGE IIIC              11                54
  STAGE IV                 3                17
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED    32 130  20   3
  3P LOSS WILD-TYPE 244 494 116  37
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              32               244
  T2             130               494
  T3              20               116
  T4               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3P LOSS MUTATED    87  63  20  13
  3P LOSS WILD-TYPE 420 295  99  64
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              87               420
  N1              63               295
  N2              20                99
  N3              13                64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   149   3
  3P LOSS WILD-TYPE 740  19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    149    3
  3P LOSS WILD-TYPE  740   19
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             149               740
  1               3                19
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   186   0
  3P LOSS WILD-TYPE 882  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    186    0
  3P LOSS WILD-TYPE  882   12
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             186               882
  MALE                 0                12
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    61 101
  3P LOSS WILD-TYPE 368 417
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     61  101
  3P LOSS WILD-TYPE  368  417
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               61               368
  YES             101               417
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3P LOSS MUTATED                            0                           152
  3P LOSS WILD-TYPE                          1                           618
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3P LOSS MUTATED                               20                   1
  3P LOSS WILD-TYPE                            180                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3P LOSS MUTATED                       2                                3
  3P LOSS WILD-TYPE                     7                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3P LOSS MUTATED                    1              7
  3P LOSS WILD-TYPE                 16             40
D46V9, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                152               618
  INFILTRATING LOBULAR CARCINOMA                20               180
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             1                16
  OTHER  SPECIFY                                 7                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0    16
  3P LOSS WILD-TYPE                                1    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          41   119
  3P LOSS WILD-TYPE                       140   626
D46V11, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16                44
  BLACK OR AFRICAN AMERICAN                     41               140
  WHITE                                        119               626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V12, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2 163
  3P LOSS WILD-TYPE  37 712
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2  163
  3P LOSS WILD-TYPE   37  712
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                37
  NOT HISPANIC OR LATINO             163               712
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    85  17
  3Q LOSS WILD-TYPE 832 130
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              102               962 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               17               130 
$`3Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CT 
      129.14        42.81        31.79        19.20        73.84        75.25 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0EQ 
      107.93        56.81        34.55        25.22        80.28        79.76 
TCGA-A2-A0YE TCGA-A2-A0YT TCGA-A2-A3XX TCGA-A2-A4S1 TCGA-A7-A26F TCGA-A7-A2KD 
       18.21        23.77        47.31        26.96        24.26        22.32 
TCGA-A7-A4SF TCGA-A7-A6VY TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A08O 
       17.92         8.75        29.03         1.02        18.97        31.00 
TCGA-AC-A2FO TCGA-AC-A3OD TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A0AR TCGA-AN-A0FJ 
       74.14        14.83         1.12         1.78         0.33         7.96 
TCGA-AN-A0FT TCGA-AN-A0XU TCGA-AO-A03P TCGA-AO-A0JA TCGA-AO-A124 TCGA-AO-A1KS 
        7.04         0.33        95.70        21.53       115.27         0.53 
TCGA-AR-A0TT TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AQ TCGA-AR-A251 TCGA-B6-A0IG 
      109.02        83.87       125.16        99.32        99.62       146.50 
TCGA-B6-A1KI TCGA-B6-A409 TCGA-BH-A0B9 TCGA-BH-A0BJ TCGA-BH-A0BZ TCGA-BH-A0C1 
       73.51        18.84        51.68        21.70        49.05        44.02 
TCGA-BH-A0HW TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1FM 
       51.32        32.91        26.66         7.36        67.50        45.63 
TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12L TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG 
       72.07        57.83        11.93        12.92        10.92        11.34 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JD TCGA-D8-A1JG 
       12.03        12.33        14.17        17.49        18.15        53.00 
TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XB TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1XZ 
       20.09        19.40        18.15        16.64        16.54        15.32 
TCGA-D8-A1Y1 TCGA-D8-A27N TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A150 
        9.93         4.80        40.11        38.60        75.98        63.62 
TCGA-E2-A15A TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
       23.34        60.99        60.36        38.76        34.29        17.69 
TCGA-E9-A1R4 TCGA-E9-A226 TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A295 
        6.12        34.45        40.73         0.69        38.99        12.33 
TCGA-EW-A1P5 TCGA-EW-A6S9 TCGA-GI-A2C9 TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A7T0 
       23.11        15.22       109.87        11.57         7.10        12.36 
TCGA-OL-A66K TCGA-OL-A66N TCGA-S3-A6ZG TCGA-V7-A7HQ TCGA-XX-A89A TCGA-Z7-A8R5 
       41.92        26.04        18.48        66.84        16.04       108.07 

$`3Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      143.15        18.02        78.41       121.94        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU 
      114.81        92.48        88.60       107.93        77.19         5.19 
TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       98.99        67.33        33.76        61.58       101.72        89.36 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
      118.45        74.40        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC 
       49.84        20.52        17.46        18.90        20.75        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       25.28        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX 
       19.33        48.46        31.73        23.47        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       56.28        35.93        50.37        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       29.79        31.73        20.19        25.15        23.61        29.56 
TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       31.36        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        14.50        21.17        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O 
       10.72        11.05        10.29         9.37        10.42        13.02 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        53.06        31.00        26.01 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99         9.99        45.07        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       13.02         0.99        38.01        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       12.00        37.05         9.99        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
      112.08        43.00        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        1.48        73.05        99.35        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        26.04        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
       32.45         6.48        16.31        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       29.26        16.80        14.53        19.33        14.96        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        8.22         0.03        20.19         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT 
        9.96         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.00         7.59         7.17         6.90 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        61.35        66.77        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       98.33         5.26        84.10        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       133.22       134.14       107.21 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       86.53        86.43        33.73       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.66        89.00        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        57.27        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ 
      275.87       129.57        50.70        65.72       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B 
       37.87         7.07        85.35        70.16        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        62.93        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       81.44        40.83        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       84.13        37.22        32.02        18.21        43.53        61.51 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 
       53.95        45.57        49.94        77.95        41.75        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       90.97        45.83        77.98        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        78.28        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       14.30         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       27.25        50.79         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       44.81        23.05         4.90        35.93        20.12        90.84 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        51.16        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
      144.59        28.14        26.14        38.60        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       18.64        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.77        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 
       12.56         3.16        13.51         1.87        12.59         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HN 
        4.08        12.33        11.28         0.16        10.42        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       56.81        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        21.14        19.20        16.50        55.50        15.78 
TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL 
       18.90        12.03        14.01        18.97        20.12        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       17.69        55.30        16.41        15.85        16.31        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       15.16        43.04        15.52        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       13.48         1.61        10.09        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       18.51        69.96        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F 
       14.79        25.05        22.82        17.29        20.71        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        50.79        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.70        28.44        59.18         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       50.07       106.75       102.61         8.75        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E9-A1N3 
       34.55        43.56         8.28        30.61        34.92        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       32.88        36.82        22.29        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       39.55        41.62        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
        9.86        24.82        28.27        34.95         2.56         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
       11.15        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 
       46.65         6.58        21.27        46.59        47.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E 
       42.25        37.74        39.09        38.37        41.03        41.72 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS 
       40.50        20.12         1.94         7.13        24.56        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        26.70         0.79        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       16.57        15.68        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       18.48        30.08         7.86        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       52.73        25.91        22.09        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       23.51        16.77        24.99        31.30        33.21         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.47        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       21.24        13.22        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       29.23        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        19.53        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       34.92        36.36        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P 
       26.70        23.47        65.62        42.77        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       86.96         0.16         0.26         9.93        18.81        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-Z7-A8R6 
       15.35       107.05 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.33              0.03 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            146.5             282.9 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           25.630            28.175 
[1] "0.3 - 146.5 (25.6)" "0.0 - 282.9 (28.2)"
[1] "hr=" "1.3"
D47V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  3Q LOSS MUTATED         2        9        0        0        37        30
  3Q LOSS WILD-TYPE      87       76        6        6       316       222
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           0         16          1          5        2
  3Q LOSS WILD-TYPE         2        138         28         60       18
                   vv
clus                STAGE TIS STAGE X
  3Q LOSS MUTATED           0       1
  3Q LOSS WILD-TYPE         1      12
D47V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  2                87
  STAGE IA                 9                76
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               37               316
  STAGE IIB               30               222
  STAGE III                0                 2
  STAGE IIIA              16               138
  STAGE IIIB               1                28
  STAGE IIIC               5                60
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED    16  76   9   1
  3Q LOSS WILD-TYPE 260 548 127  39
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              16               260
  T2              76               548
  T3               9               127
  T4               1                39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  3Q LOSS MUTATED    48  33  14   6
  3Q LOSS WILD-TYPE 459 325 105  71
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              48               459
  N1              33               325
  N2              14               105
  N3               6                71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    86   2
  3Q LOSS WILD-TYPE 803  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     86    2
  3Q LOSS WILD-TYPE  803   20
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              86               803
  1               2                20
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED   103   0
  3Q LOSS WILD-TYPE 965  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED    103    0
  3Q LOSS WILD-TYPE  965   12
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE             103               965
  MALE                 0                12
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    36  50
  3Q LOSS WILD-TYPE 393 468
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     36   50
  3Q LOSS WILD-TYPE  393  468
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               36               393
  YES              50               468
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  3Q LOSS MUTATED                            0                            86
  3Q LOSS WILD-TYPE                          1                           684
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  3Q LOSS MUTATED                               12                   0
  3Q LOSS WILD-TYPE                            188                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  3Q LOSS MUTATED                       1                                1
  3Q LOSS WILD-TYPE                     8                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  3Q LOSS MUTATED                    0              3
  3Q LOSS WILD-TYPE                 17             44
D47V9, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 86               684
  INFILTRATING LOBULAR CARCINOMA                12               188
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 3                44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     9
  3Q LOSS WILD-TYPE                                1    51
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                          21    67
  3Q LOSS WILD-TYPE                       160   678
D47V11, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          9                51
  BLACK OR AFRICAN AMERICAN                     21               160
  WHITE                                         67               678
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V12, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  93
  3Q LOSS WILD-TYPE  39 782
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   93
  3Q LOSS WILD-TYPE   39  782
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                39
  NOT HISPANIC OR LATINO              93               782
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   294  54
  4P LOSS WILD-TYPE 623  93
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              348               716 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               54                93 
$`4P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN 
      129.14       131.67        42.81        20.88        31.79        39.32 
TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CV 
       28.01        18.02        99.12        24.79        77.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ TCGA-A2-A0SV TCGA-A2-A0T1 TCGA-A2-A0T3 
      107.93        67.33        79.76        27.12        17.13        49.84 
TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1G1 
       20.75        18.21        21.67        18.61        17.36        19.20 
TCGA-A2-A25C TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX 
       17.19        33.93        91.07        50.37         7.30        24.39 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.31        30.61        35.67        31.73        20.19        25.15 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZV 
       23.74        21.73        22.32        14.50        14.73        12.10 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06T 
       10.29         9.37        10.42         8.75         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A07B TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A084 
       31.00        26.01        43.00         9.99         8.98        15.06 
TCGA-A8-A085 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R 
       36.95        38.01        33.01        12.00         9.99         0.99 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09X 
       43.00        30.97         1.02        49.05        45.07        14.01 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH 
        0.95        22.95        73.05        19.33        32.45         6.48 
TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW 
       16.80        19.33        11.44        13.71        17.42        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.03         1.12         0.23         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        1.71         9.96         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW 
        6.44         7.96         7.00         7.04         0.33         0.36 
TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
        0.33         5.59        66.77        32.78        21.40        52.18 
TCGA-AO-A0J7 TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12A 
       20.32        76.77        71.80       115.27       108.03        90.58 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04J 
       64.04        48.36        61.87         0.53        17.79        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 
      130.09         5.65       140.55         5.26        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AM TCGA-AR-A1AN 
      133.22       134.14       125.16       108.36        98.33        96.00 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O 
       99.32        17.23        33.73       160.90        50.89       118.59 
TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 
      104.28       105.30        32.58        99.62        71.05        93.83 
TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA TCGA-B6-A0IB 
       39.39        33.30        10.59        77.62       275.87       129.57 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       233.62        18.77        84.59       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0RU 
      140.88       255.68       212.25        81.17       100.70       282.90 
TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A400 
       79.63        21.47       113.79        43.59        73.51         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AW 
       85.35        70.16        68.12        18.84       103.63        20.45 
TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BG 
       81.44        39.55        70.22        37.22        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV 
       21.70        74.89        75.48        76.60        45.57        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DX TCGA-BH-A0E0 TCGA-BH-A0E6 
       41.75        44.02        90.97        70.88         4.41         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HY 
       46.19        24.49        23.08        20.38        12.89        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q TCGA-BH-A18T 
        5.59        23.93        23.05        32.91        55.63         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F0 TCGA-BH-A1F6 
       51.39        51.16        42.28        12.00        25.81        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       24.62        33.17        72.07        38.60        57.83       130.16 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A12Z TCGA-C8-A135 
       18.64        23.51        11.93        11.77        12.56        12.92 
TCGA-C8-A138 TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26Y 
        4.08         0.16        12.03        10.42        12.33        12.95 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A8HP TCGA-D8-A13Y TCGA-D8-A13Z 
        0.03         9.50        14.43        13.02        56.81        20.88 
TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JA TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JJ 
       13.97        19.20        16.50        18.90        12.03        20.09 
TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       20.12        19.40        27.58        15.22        14.73        21.80 
TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XW TCGA-D8-A1Y3 
       14.50        55.30        15.85        12.99        43.04        14.14 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27T TCGA-D8-A73U TCGA-E2-A14N TCGA-E2-A14O 
       16.04        13.05        13.08        16.18        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 
       40.96        38.24        38.60        18.51        63.62        19.43 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1BD 
       14.79        25.05        12.92        76.57        53.62        37.25 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LH 
       33.73        33.70        60.36        73.64        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 
      102.61        34.92        38.76        17.69        22.29        34.16 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R3 
       39.55        41.62        35.24        18.94         9.86         2.56 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A244 
       48.23        45.01        32.09        41.72        40.73         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5FK 
        1.94         7.13        38.07        30.44        23.84        26.70 
TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY 
        0.79        39.72        18.90        25.94        22.82        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE 
       40.41        23.11         7.86         6.15        13.94        10.52 
TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       55.00        17.49        24.99        33.21         7.40       109.87 
TCGA-GM-A2DB TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A3XL 
       79.10        70.85        72.10        85.15       115.69        69.30 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YP 
        2.60        11.84        11.57        32.75        15.32        14.79 
TCGA-LL-A6FR TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 
       16.08         7.46        19.59        58.52        36.36        20.38 
TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LZ 
       23.47        41.92        28.21        86.96         0.16         9.93 
TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA14 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-WT-AB44 
       21.07        19.27        17.39        13.94        17.03        29.03 

$`4P LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
       40.14        11.44        48.56        48.36         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SJ 
       14.37        43.43        48.10        14.27        47.24        13.68 
TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R 
        7.96        19.20        18.21       143.15        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CT 
      136.73       114.81        92.48        88.60       107.93        75.25 
TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
        5.19        56.81        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      101.72        89.36        80.28       118.45        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        44.88        50.43        44.28        17.52 
TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
        8.38        20.52        17.46        18.90        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       50.47        21.90        49.48        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 
       23.77        23.47        60.72        22.45        20.25        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A25E 
       16.47        52.47       107.70        42.44        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        36.23        39.65        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       47.31        35.93        50.83        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.14        21.90        38.30        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       33.11        29.79        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       23.80        20.61        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       17.92        10.72        11.05        13.02        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       29.03         1.02        17.03        53.98         9.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P 
       18.97        18.97        14.01        12.00        32.05        10.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A 
        7.99        24.99         9.99        45.07        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S 
       28.96        19.96        37.05        31.00        31.00        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
      112.08        40.01        33.01        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09M 
        9.99         9.99        12.00        50.04        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
        1.02        25.02         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM 
       17.03        38.04        73.91         5.72         1.48        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       74.14        33.04        14.66        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XU TCGA-AC-A6IV 
       23.24        24.79        29.26        14.53        14.96        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0FF 
        0.33         0.33         1.78         7.36         7.46         5.65 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.59         7.17         6.90         0.33         0.33         5.36 
TCGA-AN-A0XR TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P 
        0.33         5.33        80.28        61.35        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J5 TCGA-AO-A0J6 
       68.75        47.87        58.95        29.13        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 
       65.10        26.24        50.24        62.04        55.33        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
      108.72       106.78        98.27        57.30        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       14.73        82.62        70.39        24.79        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT 
        2.56        32.91        19.20        98.33        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U4 
       75.22        98.93        64.83       107.24        83.87       107.21 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
      101.00       103.86        97.68        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M 
       94.29        61.28        86.53        86.43        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       99.78         2.76       112.77        97.84       105.27        77.69 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE 
       98.76        98.66        89.00        93.30        85.64       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 
       40.54        57.27        73.35        38.96       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG 
       12.13        50.70        65.72       127.33       129.07        68.45 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WZ 
       89.46       157.41        97.48       188.68        18.35       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      129.70       245.10        28.27        68.94        58.88       101.52 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
      139.17       170.17        37.87        71.15        62.93        59.84 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 
       25.55        63.09        40.83        39.16        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       51.68        32.02        18.21        61.68        72.23        74.14 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       53.95        77.95        49.05        89.06        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ 
       15.65         3.22         2.56        38.47        67.86        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       15.68        14.30        44.81        32.58        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        52.96        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       36.85        51.32        27.25        24.95        42.35        44.81 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A1EN TCGA-BH-A1EO 
       37.74        30.28        37.55        66.05        67.50        91.99 
TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F2 
      113.82        82.85        55.69        49.58        17.69        31.53 
TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       89.16       120.62       114.15        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       63.35        55.00        45.63        72.07       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       26.14        83.31        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
      109.28        20.88         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
       21.76         9.44        11.77        11.77        12.66        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 
       12.66        12.66        12.66        12.66        48.53         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       13.51         1.87        12.59         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       11.34        11.28        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A3M7 
       12.36         8.28         9.67         9.53        24.56        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 
       12.95        12.49        13.41        19.46        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JB 
       14.17        13.48        21.14        14.17        17.49        55.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL 
       15.78        18.15        53.00        14.01        18.97        20.09 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT 
       17.16        19.92        17.69        16.41        16.31        16.64 
TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        13.45        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         1.61        10.09        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       18.51        21.67        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       28.87        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 
       31.96        69.34        69.96        23.24        21.04        23.87 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        56.94        14.07        51.39        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        77.65        37.41        70.36 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK 
       54.18        19.66        24.59        75.81        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        26.99        34.55        43.56         8.28        30.61 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.29        34.82        32.88        36.82        36.20        36.56 
TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 
       35.77        25.84        24.82        28.27        34.95         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
        3.02        11.15        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        38.37        41.03        40.50        20.12 
TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
       38.99        24.56        12.33        29.72         9.47        32.91 
TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       30.18        23.90        25.81        26.40        27.85        12.20 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
        8.48        18.21        13.25        16.57        15.68        28.77 
TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 
       29.95        41.13        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       30.08        18.90        19.99        14.43        34.55        19.96 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       52.73        25.91        22.09        34.03        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       15.22        16.77        31.30        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       75.02        86.96       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.47        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       24.95        29.23        25.05        17.06        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
       22.26         2.63        15.68        14.50        19.53        12.36 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       17.49        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       26.70        65.62        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY 
       19.73        40.11         8.91        47.01        64.21         0.26 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 
       18.81        18.48        20.68        13.84        18.87        17.26 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
        3.81        66.84        11.41        52.96        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.03              0.26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           282.90            281.29 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           25.480            28.635 
[1] "0.0 - 282.9 (25.5)" "0.3 - 281.3 (28.6)"
[1] "hr=" "1.1"
D48V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4P LOSS MUTATED        26       17        1        1       123        85
  4P LOSS WILD-TYPE      63       68        5        5       230       167
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           0         54         10         21        7
  4P LOSS WILD-TYPE         2        100         19         44       13
                   vv
clus                STAGE TIS STAGE X
  4P LOSS MUTATED           0       4
  4P LOSS WILD-TYPE         1       9
D48V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 26                63
  STAGE IA                17                68
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA              123               230
  STAGE IIB               85               167
  STAGE III                0                 2
  STAGE IIIA              54               100
  STAGE IIIB              10                19
  STAGE IIIC              21                44
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  4                 9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED    71 226  39  15
  4P LOSS WILD-TYPE 205 398  97  25
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              71               205
  T2             226               398
  T3              39                97
  T4              15                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4P LOSS MUTATED   162 117  46  23
  4P LOSS WILD-TYPE 345 241  73  54
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0             162               345
  N1             117               241
  N2              46                73
  N3              23                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   298   7
  4P LOSS WILD-TYPE 591  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    298    7
  4P LOSS WILD-TYPE  591   15
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             298               591
  1               7                15
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   349   4
  4P LOSS WILD-TYPE 719   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    349    4
  4P LOSS WILD-TYPE  719    8
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE             349               719
  MALE                 4                 8
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   139 168
  4P LOSS WILD-TYPE 290 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    139  168
  4P LOSS WILD-TYPE  290  350
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              139               290
  YES             168               350
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4P LOSS MUTATED                            1                           291
  4P LOSS WILD-TYPE                          0                           479
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4P LOSS MUTATED                               34                   3
  4P LOSS WILD-TYPE                            166                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4P LOSS MUTATED                       4                                6
  4P LOSS WILD-TYPE                     5                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4P LOSS MUTATED                    0             13
  4P LOSS WILD-TYPE                 17             34
D48V9, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                291               479
  INFILTRATING LOBULAR CARCINOMA                34               166
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                13                34
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  1    20
  4P LOSS WILD-TYPE                                0    40
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                          79   228
  4P LOSS WILD-TYPE                       102   517
D48V11, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         20                40
  BLACK OR AFRICAN AMERICAN                     79               102
  WHITE                                        228               517
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V12, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    11 291
  4P LOSS WILD-TYPE  28 584
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     11  291
  4P LOSS WILD-TYPE   28  584
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                28
  NOT HISPANIC OR LATINO             291               584
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   261  46
  4Q LOSS WILD-TYPE 656 101
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              307               757 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               46               101 
$`4Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO 
      129.14        42.81        20.88        31.79        39.32        28.01 
TCGA-A2-A04P TCGA-A2-A04W TCGA-A2-A0CL TCGA-A2-A0CS TCGA-A2-A0CV TCGA-A2-A0CW 
       18.02       101.98        99.12        77.19        98.99       107.93 
TCGA-A2-A0D0 TCGA-A2-A0EQ TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T7 
       67.33        79.76        27.12        50.43        17.13        20.75 
TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A3XT 
       18.21        18.61        17.36        19.20        17.19        91.07 
TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       50.37        24.39        35.31        30.61        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF 
       25.15        23.74        21.73        14.50        21.17        17.92 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06Q TCGA-A8-A06T 
       14.73        10.29         9.37        10.42         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E 
       31.00        26.01         1.02        17.03        43.00        19.99 
TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L 
        8.98        15.06        38.01        33.01        12.00         9.99 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09R 
        0.99        43.00        30.97         1.02        49.05         8.98 
TCGA-A8-A09X TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH 
       14.01        22.95        73.05        19.33        32.45         6.48 
TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW 
       16.80        19.33        11.44        13.71        17.42        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.03         1.12         0.23         0.33         0.62         2.96 
TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        9.96         0.33         0.33         0.33         6.44         7.96 
TCGA-AN-A0FK TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AN-A0XP 
        7.00         0.33         0.36         0.33         0.33         0.30 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.33         0.33         5.59        66.77        32.78        52.18 
TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A129 
       20.32        72.00        76.77        71.80       115.27       108.03 
TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT 
       90.58        64.04        48.36        61.87         0.53        17.79 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TR TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
      130.09         5.65         5.26        55.86        65.36       133.22 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AY 
      134.14       125.16        98.33        96.00        99.32        33.73 
TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24V 
      160.90        50.89       118.59       104.28        97.84       105.30 
TCGA-AR-A24W TCGA-AR-A251 TCGA-AR-A256 TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IA 
       32.58        99.62        93.83        10.59        77.62       275.87 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO 
      129.57       112.37       233.62        18.77        84.59       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV 
      140.88       255.68       212.25        81.17       282.90        79.63 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A401 TCGA-B6-A408 
       21.47       113.79        43.59        73.51        85.35        68.12 
TCGA-B6-A40B TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B5 
      103.63        59.84        20.45        81.44        39.55        70.22 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR 
       37.22        43.53        21.70        74.89        75.48        76.60 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0E0 TCGA-BH-A0E6 
       45.57        49.94        41.75        44.02         4.41         9.63 
TCGA-BH-A0E9 TCGA-BH-A0EB TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0HI TCGA-BH-A0HU 
       46.19        24.49        10.78        23.08        20.38        12.89 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18Q 
       50.79         5.59        23.93        23.05        32.91        55.63 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1F6 
       51.39        51.16        67.50        42.28        12.00        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FU TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 
       24.62        33.17        72.07        38.60        57.83       130.16 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12L TCGA-C8-A12P TCGA-C8-A138 TCGA-C8-A1HJ 
       18.64        23.51        11.93        11.77         4.08         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A27B 
       12.03        10.42        12.33        12.95         9.50        14.43 
TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A1JA TCGA-D8-A1JE 
       13.02        13.41        56.81        20.88        16.50        18.90 
TCGA-D8-A1JF TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1XG 
       12.03        20.09        20.12        19.40        21.01        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A27H 
       21.80        14.50        55.30        15.85        12.99        13.05 
TCGA-D8-A27T TCGA-D8-A73U TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R 
       13.08        16.18        47.15        44.68        38.24        38.60 
TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1B0 
       63.62        19.43        25.05        12.92        14.07        53.62 
TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LG 
       37.25        33.73        33.70        60.36        73.64        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N6 
      106.75       102.61        34.92        38.76        17.69        22.29 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1NI 
       34.16        39.55        41.62        35.24        18.94         9.86 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A226 TCGA-E9-A22E 
        2.56         6.12        45.01        32.09        34.45        41.72 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A3HO TCGA-E9-A3X8 
       40.73         0.69         1.94         7.13        38.07        30.44 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OV 
       23.84        26.70         0.79        39.72        18.90        25.94 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PC 
       22.82        29.85        40.41        23.11         7.86         6.15 
TCGA-EW-A1PE TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-EW-A6SB 
       10.52        19.96        55.00        17.49        16.77        24.99 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A3XL 
       33.21         7.40        70.85        72.10        85.15        69.30 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FR 
        2.60        11.84        11.57        32.75        15.32        16.08 
TCGA-LL-A73Z TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K 
        7.46        19.59        58.52        36.36        20.38        41.92 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-S3-AA17 TCGA-UL-AAZ6 
       86.96         0.16        21.07        17.39        13.94        17.03 
TCGA-WT-AB44 
       29.03 

$`4Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       13.68         7.96        19.20        18.21       143.15        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        73.84        87.25        63.12        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
       75.25         5.19        56.81        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72        89.36        80.28       118.45        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       63.29        99.19        54.64        44.88        44.28        17.52 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
        8.38        49.84        20.52        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       25.28        50.47        21.90        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ 
       48.46        31.73        23.77        23.47        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 
       29.98        32.75        56.28        47.31        35.93        50.83 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       38.30        34.29        35.47        37.45        33.11        29.79 
TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       20.19        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A5ZV 
       13.41        14.70        11.97        14.93        13.74        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       10.72        11.05         8.75        13.02        13.02        17.98 
TCGA-A8-A06U TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       29.03        53.98         9.01        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
        9.99        45.07        36.95        13.02         0.99        28.96 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       19.96        37.05        31.00        31.00        33.01       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       40.01        33.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        9.99        12.00        50.04        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 
        1.02        25.02        19.04        15.02         0.99        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB 
       19.04        13.02        21.04         0.99        27.02        17.03 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM 
       38.04         0.95        73.91         5.72         1.48        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       74.14        33.04        14.66        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XU TCGA-AC-A6IV 
       23.24        24.79        29.26        14.53        14.96        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL 
        0.33         0.33         1.78         1.71         7.36         7.46 
TCGA-AN-A0AM TCGA-AN-A0FF TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        0.16         5.65         7.59         7.17         6.90         7.04 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XU 
        0.33         0.33         5.36        12.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.33        80.28        61.35        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        58.95        29.13        21.40        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JF 
       22.36        53.03        21.53        50.70        50.86        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        62.04        55.33        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
      106.78        98.27        57.30        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       82.62        70.39        24.79        26.93        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        2.56        32.91        19.20       140.55        98.33        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U2 
      109.02        75.22        98.93        64.83       107.24        83.87 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
      107.21       108.36       101.00       103.86        97.68        86.07 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        17.23        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24R 
       86.43        94.22       120.33        99.78         2.76       112.77 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
      105.27        77.69        98.76        98.66        89.00        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       85.64        71.05       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       73.35        33.30        38.96       143.38       281.29        12.13 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RG 
       50.70        65.72       146.50       127.33       129.07        68.45 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      100.70        89.46       157.41        97.48       188.68        18.35 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 
      101.52       139.17       170.17        37.87         7.07        70.16 
TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 
       18.84        71.15        62.93        25.55        63.09        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       39.16        81.63        84.13        51.68        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BW 
       61.51        61.68        72.23        74.14        53.95        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       49.05        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        29.98        13.91        78.28        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       15.68        14.30        44.81        32.58        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       30.35        15.16        37.78        53.26        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G 
       51.32        27.25        24.95        42.35        44.81         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       35.93        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EO TCGA-BH-A1ES 
       30.28        37.55        66.05         7.36        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       82.85        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       89.16       120.62       114.15        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 
       63.35        55.00        45.63        72.07       144.59        28.14 
TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       26.14        83.31        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
      109.28        20.88         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q 
       21.76         9.44        11.77        11.77        12.66        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 
        3.16        13.51         1.87        12.59        12.92         4.11 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A1HO 
       12.33        10.92        11.34        11.28        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       20.25        12.53        12.36         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A9FZ 
        0.03        24.56        33.99        12.95        12.49        19.46 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       19.20        14.17        17.49        55.50        15.78        18.15 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JS 
       53.00        14.01        18.97        20.09        20.38        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 
       13.32        14.70        18.58        17.79        16.73        25.74 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       23.90        27.58        18.15        12.39        17.16        15.22 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
       19.92        17.69        16.41        16.31        16.64        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       43.04        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
       14.14        17.42        16.04        13.45        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48         4.80         1.61        10.09        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X 
       12.26        33.37        18.51        21.67        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T 
       40.11        28.44        28.87        40.96        33.17        75.98 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       43.33        34.26        32.02        31.96        69.34        18.51 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A 
       69.96        23.24        21.04        23.87        14.79        23.34 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I 
       22.82        17.29        20.71        21.63        18.21        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       56.94        51.39        76.57        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ 
       28.50        16.47        77.65        37.41        70.36        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL 
       19.66        24.59        75.81        28.90         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
       26.99        34.55        43.56         8.28        30.61        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE 
       34.82        32.88        36.82        36.20        36.56        35.77 
TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 
       25.84        24.82        28.27        34.95         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       48.23        40.24         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A24A 
       38.37        41.03        40.50        20.12        38.99        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X 
       12.33        29.72         9.47        32.91        30.18        23.90 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        26.40        27.85        12.20         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX TCGA-EW-A1P0 
       13.25        16.57        15.68        28.77        29.95        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        29.82        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FV 
       19.99        13.94        14.43        34.55        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC 
       22.09        34.03        10.16        23.51        15.22        31.30 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.47        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       24.95        29.23        25.05        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ 
       14.79        22.26         2.63        15.68        14.50        19.53 
TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       12.36        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        40.08        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       22.32        26.70        23.47        65.62        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       47.01        64.21         0.26         9.93        18.81        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-UU-A93S 
       20.68        19.27        13.84        18.87        17.26         3.81 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       66.84        11.41        52.96        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.03              0.03 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           282.90            281.29 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            25.94             28.27 
[1] "0.0 - 282.9 (25.9)" "0.0 - 281.3 (28.3)"
[1] "hr=" "1"  
D49V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  4Q LOSS MUTATED        22       18        0        2       106        73
  4Q LOSS WILD-TYPE      67       67        6        4       247       179
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           0         49          9         18        7
  4Q LOSS WILD-TYPE         2        105         20         47       13
                   vv
clus                STAGE TIS STAGE X
  4Q LOSS MUTATED           0       5
  4Q LOSS WILD-TYPE         1       8
D49V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 22                67
  STAGE IA                18                67
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA              106               247
  STAGE IIB               73               179
  STAGE III                0                 2
  STAGE IIIA              49               105
  STAGE IIIB               9                20
  STAGE IIIC              18                47
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED    61 194  40  15
  4Q LOSS WILD-TYPE 215 430  96  25
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              61               215
  T2             194               430
  T3              40                96
  T4              15                25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  4Q LOSS MUTATED   143 103  39  21
  4Q LOSS WILD-TYPE 364 255  80  56
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0             143               364
  N1             103               255
  N2              39                80
  N3              21                56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   262   7
  4Q LOSS WILD-TYPE 627  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    262    7
  4Q LOSS WILD-TYPE  627   15
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             262               627
  1               7                15
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   309   3
  4Q LOSS WILD-TYPE 759   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    309    3
  4Q LOSS WILD-TYPE  759    9
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE             309               759
  MALE                 3                 9
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   122 148
  4Q LOSS WILD-TYPE 307 370
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    122  148
  4Q LOSS WILD-TYPE  307  370
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              122               307
  YES             148               370
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  4Q LOSS MUTATED                            0                           254
  4Q LOSS WILD-TYPE                          1                           516
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  4Q LOSS MUTATED                               32                   2
  4Q LOSS WILD-TYPE                            168                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  4Q LOSS MUTATED                       4                                6
  4Q LOSS WILD-TYPE                     5                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  4Q LOSS MUTATED                    0             13
  4Q LOSS WILD-TYPE                 17             34
D49V9, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                254               516
  INFILTRATING LOBULAR CARCINOMA                32               168
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                13                34
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  1    18
  4Q LOSS WILD-TYPE                                0    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                          68   199
  4Q LOSS WILD-TYPE                       113   546
D49V11, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         18                42
  BLACK OR AFRICAN AMERICAN                     68               113
  WHITE                                        199               546
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V12, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    10 249
  4Q LOSS WILD-TYPE  29 626
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10  249
  4Q LOSS WILD-TYPE   29  626
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                29
  NOT HISPANIC OR LATINO             249               626
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED   114  23
  5P LOSS WILD-TYPE 803 124
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              137               927 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               124 
$`5P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U 
        9.96        31.79        28.01        18.02        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0D0 TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ 
       24.79        67.33        63.29        50.43        21.67        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        19.20        33.93        91.07        47.31        35.93 
TCGA-A7-A0DA TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A6VY TCGA-A8-A06T 
       35.67        20.19        21.73        21.17         8.75        53.06 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08X 
       17.03        53.98         9.99         8.98        15.06        43.00 
TCGA-AC-A2BK TCGA-AC-A5XU TCGA-AC-A6IW TCGA-AN-A041 TCGA-AN-A0AK TCGA-AN-A0AL 
       73.05        14.96        13.58         0.23         7.36         7.46 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AO-A0J4 
        0.33         0.33         7.59         7.04         0.33        52.18 
TCGA-AO-A0J5 TCGA-AO-A0JB TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AQ-A04J 
       26.04        50.70       115.27       108.03        48.36        26.93 
TCGA-AQ-A04L TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AQ 
      130.09        65.36        83.87       125.16       101.00        99.32 
TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A250 TCGA-AR-A251 
       17.23        50.89       104.28        97.84        89.00        99.62 
TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IO TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A402 
      129.57       146.50       165.76       102.77       282.90        70.16 
TCGA-BH-A0B4 TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0HA 
       39.16        61.51        45.57        41.75         4.41        52.96 
TCGA-BH-A0WA TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN 
       23.05         7.36        51.16       114.15        74.73        72.07 
TCGA-BH-A1FU TCGA-BH-A209 TCGA-C8-A12O TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF 
       72.07       130.16        12.66        12.59         4.08        10.92 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A9FZ TCGA-D8-A147 
       12.53        12.36         9.50        24.56        19.46        19.20 
TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ 
       55.50        12.03        15.22        21.80        14.50        16.41 
TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27R TCGA-E2-A14N TCGA-E2-A159 TCGA-E2-A15A 
       15.32        14.14        10.09        47.15        25.05        23.34 
TCGA-E2-A1AZ TCGA-E2-A1B6 TCGA-E2-A1L7 TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       76.57        28.50        60.36       102.61         8.75        43.04 
TCGA-E2-A573 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A22D 
       34.92        34.16        39.55        41.62        35.24        41.03 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P0 
       40.73         0.69        30.18        22.82        29.85        41.13 
TCGA-EW-A1P8 TCGA-EW-A2FV TCGA-EW-A6S9 TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A3XL 
        7.86        25.91        15.22        75.02        70.85        69.30 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LL-A441 TCGA-OL-A5D7 TCGA-OL-A5RW 
        2.60        11.84         7.10        32.75        58.52        36.36 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A6VO TCGA-S3-AA10 TCGA-WT-AB41 
       23.47        65.62        28.21        19.27        52.96 

$`5P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W 
       18.21       143.15        78.41       121.94        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       36.23        39.65        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.83         7.30        24.39        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH 
       21.14        21.90        38.30        35.31        34.29        35.47 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F 
       30.61        37.45        33.11        29.79        31.73        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42        13.02        13.02         1.02        17.98 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B 
       29.03        31.00        26.01         1.02         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 
       10.98         7.99        24.99         9.99        45.07        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       13.02         0.99        38.01        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       12.00        37.05         9.99        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
       33.01       112.08        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V 
       24.79        29.26        16.80        14.53        19.33        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       13.71        17.42        18.67        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        9.96         0.16         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX 
        7.00         7.17         6.90         0.33         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         5.36         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L 
        0.33         0.33         0.33         5.33         5.59        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 
       58.95        29.13        32.78        21.40        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       22.36        53.03        21.53        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       65.10        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       99.25       108.72       106.78        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       70.39         0.53        17.79        24.79         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       32.52         2.56        32.91        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI 
       55.86       107.24       133.22       134.14       107.21       108.36 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      103.86        97.68        98.33        96.00        86.07        93.90 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        94.29        61.28        86.53        86.43        33.73 
TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
      160.90        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
      112.77       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       98.66        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        12.13       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.72       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
       84.59       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      234.28        81.17        78.02       263.28       162.05       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
      100.70        89.46       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       18.35        21.47       113.79       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 
      139.17       170.17        37.87         7.07        85.35        68.12 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       18.84       103.63        71.15        62.93        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 
       25.55        63.09        81.44        40.83        39.55        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.63        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       43.53        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       74.14        76.60        53.95        49.94        77.95        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        29.98        13.91        78.28        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 
       24.49        31.00        24.43        30.35        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB 
       37.78        53.26        24.56        23.08        41.00        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        32.91         4.90        35.93        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q 
       90.84        26.66        72.56        37.74        30.28        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05        51.39        67.50        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.62       120.62 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       33.17       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
      144.59        28.14        26.14        38.60        83.31        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       18.64        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P 
       21.76         9.44        11.93        11.77        11.77        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       12.66        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 
       12.56         3.16        13.51         1.87        12.92         4.11 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        12.95        12.33        20.25        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         9.53         0.03        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       13.02        12.49        13.41        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       20.58        13.97        14.17        13.48        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       17.49        16.50        15.78        18.15        18.90        53.00 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       12.39        17.16        14.73        19.92        17.69        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       16.54        15.52         9.93        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         1.61        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       34.42        27.52        46.59        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       69.34        18.51        63.62        69.96        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       21.04        23.87        14.79        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1BC 
       51.39        53.62        87.22        33.01        32.35        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
       50.07       106.75        26.99        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        38.76        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        22.29        36.20        36.56        35.77        25.84 
TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       18.94         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH 
       40.24         1.12        46.65         6.58        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 
       38.37        41.72        40.50        20.12        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       32.91        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       25.81        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       25.94        29.95        40.41        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48        30.08        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       52.73        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI 
       59.57       216.76        79.10        83.34        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       62.47        11.57        21.24        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       24.95        29.23        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        7.46        14.50        19.53        12.36        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91        22.39         2.10        36.30        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       40.08        34.92        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       26.70        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         9.93        18.81        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       20.68        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB44 TCGA-XX-A899 
       17.03         3.81        66.84        11.41        29.03        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             0.23              0.03 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           282.90            281.29 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            32.75             26.96 
[1] "0.2 - 282.9 (32.8)" "0.0 - 281.3 (27.0)"
[1] "hr=" "1.1"
D50V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5P LOSS MUTATED         9        7        0        0        56        33
  5P LOSS WILD-TYPE      80       78        6        6       297       219
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           0         19          3         10        2
  5P LOSS WILD-TYPE         2        135         26         55       18
                   vv
clus                STAGE TIS STAGE X
  5P LOSS MUTATED           0       0
  5P LOSS WILD-TYPE         1      13
D50V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  9                80
  STAGE IA                 7                78
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               56               297
  STAGE IIB               33               219
  STAGE III                0                 2
  STAGE IIIA              19               135
  STAGE IIIB               3                26
  STAGE IIIC              10                55
  STAGE IV                 2                18
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED    28  97  10   5
  5P LOSS WILD-TYPE 248 527 126  35
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1              28               248
  T2              97               527
  T3              10               126
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5P LOSS MUTATED    68  44  16  11
  5P LOSS WILD-TYPE 439 314 103  66
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              68               439
  N1              44               314
  N2              16               103
  N3              11                66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED   116   2
  5P LOSS WILD-TYPE 773  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    116    2
  5P LOSS WILD-TYPE  773   20
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0             116               773
  1               2                20
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED   139   1
  5P LOSS WILD-TYPE 929  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED    139    1
  5P LOSS WILD-TYPE  929   11
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE             139               929
  MALE                 1                11
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    58  67
  5P LOSS WILD-TYPE 371 451
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     58   67
  5P LOSS WILD-TYPE  371  451
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               58               371
  YES              67               451
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5P LOSS MUTATED                            0                           120
  5P LOSS WILD-TYPE                          1                           650
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5P LOSS MUTATED                                3                   4
  5P LOSS WILD-TYPE                            197                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5P LOSS MUTATED                       0                                4
  5P LOSS WILD-TYPE                     9                               25
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5P LOSS MUTATED                    0              8
  5P LOSS WILD-TYPE                 17             39
D50V9, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                120               650
  INFILTRATING LOBULAR CARCINOMA                 3               197
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               4                25
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 8                39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0    11
  5P LOSS WILD-TYPE                                1    49
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                          33    87
  5P LOSS WILD-TYPE                       148   658
D50V11, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         11                49
  BLACK OR AFRICAN AMERICAN                     33               148
  WHITE                                         87               658
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V12, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3 118
  5P LOSS WILD-TYPE  36 757
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3  118
  5P LOSS WILD-TYPE   36  757
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                36
  NOT HISPANIC OR LATINO             118               757
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED   191  33
  5Q LOSS WILD-TYPE 726 114
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              224               840 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33               114 
$`5Q LOSS MUTATED`
TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P 
      131.67         9.96        31.79        28.01        19.20        18.02 
TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CM TCGA-A2-A0D0 
       78.41        73.84        87.25       101.98        24.79        67.33 
TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0YH TCGA-A2-A0YJ 
       34.55        79.76        63.29        50.43        21.67        18.61 
TCGA-A2-A0YM TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XY 
       31.73        19.20        33.93        91.07        47.31        35.93 
TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E 
        7.30        21.90        30.61        35.67        31.73        20.19 
TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       23.74        21.73        21.17        17.92        14.73        12.10 
TCGA-A7-A6VY TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07O TCGA-A8-A07R 
        8.75        31.00        17.03        53.98         9.99         8.98 
TCGA-A8-A07U TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08X TCGA-A8-A09A TCGA-A8-A09K 
       24.99        15.06        33.01        43.00         9.99        29.98 
TCGA-AC-A2BK TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OQ TCGA-AN-A041 
       73.05        14.96        13.71        13.58         1.12         0.23 
TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FJ 
        1.78         7.36         7.46         0.33         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN 
        7.59         7.04         0.33         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A124 
        0.33        52.18        26.04        50.70        55.33       115.27 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A54N 
      108.03        48.36        70.39        26.93       130.09         2.56 
TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A1AH 
      140.55       109.02        75.22        65.36        83.87       125.16 
TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24Q 
      101.00        99.32        17.23        33.73        50.89       104.28 
TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-B6-A0IB 
       97.84        77.69        98.66        89.00        99.62       129.57 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RP TCGA-B6-A0RS 
       65.72       146.50       165.76       255.68       102.77       100.70 
TCGA-B6-A0RU TCGA-B6-A0WX TCGA-B6-A1KF TCGA-B6-A3ZX TCGA-B6-A402 TCGA-BH-A0AV 
      282.90        21.47       101.52        37.87        70.16        59.84 
TCGA-BH-A0B3 TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BW 
       39.55        43.53        61.51        75.48        45.57        77.95 
TCGA-BH-A0C0 TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0HA TCGA-BH-A0WA TCGA-BH-A18T 
       41.75         4.41         9.63        52.96        23.05         7.36 
TCGA-BH-A18V TCGA-BH-A1EV TCGA-BH-A1F2 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FN 
       51.16        12.00        31.53       114.15        74.73        72.07 
TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12O 
       72.07        57.83       130.16        18.64        11.93        12.66 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HJ 
        3.16        13.51        12.59         4.08        10.92         0.16 
TCGA-C8-A1HM TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       12.33        12.53        12.36         9.50        24.56        14.43 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A142 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JF 
       13.41        19.46        13.97        19.20        55.50        12.03 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XF TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XQ 
       20.12        20.09        15.22        14.50        19.92        16.41 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27H 
       16.64        43.04        15.32        14.14        16.04        13.05 
TCGA-D8-A27M TCGA-D8-A27R TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A150 TCGA-E2-A155 
       13.48        10.09        40.11        47.15        63.62        21.04 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B6 
       14.79        25.05        23.34        76.57        53.62        28.50 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA TCGA-E2-A1LI TCGA-E2-A1LK 
       33.70        60.99        60.36        24.59       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND 
       43.04        34.92        38.76        34.16        39.55        41.62 
TCGA-E9-A1RB TCGA-E9-A1RH TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A3QA 
       32.09        46.59        41.03        40.73         0.69        30.18 
TCGA-EW-A1OW TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PH TCGA-EW-A2FV 
       22.82        41.13         7.86        18.90        19.96        25.91 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DD 
       15.22        16.77        24.99        33.21       109.87        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A7W5 
       70.85        72.10        69.30         2.60        11.84         7.10 
TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FR TCGA-OL-A5D7 
       32.75        15.32        14.70        14.79        16.08        58.52 
TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I TCGA-OL-A66J TCGA-PL-A8LX 
       36.36        22.32        20.38        23.47        65.62         0.16 
TCGA-S3-AA10 TCGA-WT-AB41 
       19.27        52.96 

$`5Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04N 
       20.88        13.68         7.96        39.32        18.21       143.15 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
      121.94        63.12        55.43        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 
        5.19        98.99       107.93        56.81        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER 
       25.22       101.72        89.36        80.28       118.45        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       99.19        54.64        27.12        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XZ 
       36.23        39.65        29.98        32.75        56.28        50.37 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 
       50.83        24.39        21.30        23.21        26.96        21.14 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        20.61        22.32        11.34        10.59        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB 
       11.28        13.41        14.70        11.97        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.50        10.72        11.05        10.29         9.37        10.42 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02         9.01        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07S 
       18.97        14.01        12.00        32.05        10.98         7.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
        9.99        45.07        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O 
       28.96        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99        33.01       112.08        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B 
       30.97        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N 
        1.02        50.04        49.05        45.07        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       87.12        26.04        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V 
       24.79        29.26        16.80        14.53        19.33        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       17.42        18.67        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
       20.19         1.32         2.30         0.33         0.33         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
        0.62         2.96         1.71         9.96         0.16         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW 
        6.44         5.65         7.00         7.17         6.90         0.36 
TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.36        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       81.63        95.70        68.75        47.87        58.95        29.13 
TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       32.78        21.40        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       50.24        62.04        71.80        99.25       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       90.58        98.27        64.04        57.30        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87         0.53        17.79        24.79 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TQ 
        5.65        15.62        32.52        32.91        19.20        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        84.10        98.93        64.83        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL 
      133.22       134.14       107.21       108.36       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU 
       98.33        96.00        86.07        93.90        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       61.28        86.53        86.43       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V 
       99.78       118.59         2.76       112.77       105.27       105.30 
TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       32.58        98.76        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        57.27        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
      275.87        50.70       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       129.07       140.88        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT 
       81.17        78.02       263.28       162.05       140.48        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY 
      157.41        97.48       188.68        79.63        18.35       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 
       43.59        73.51       139.17       170.17         7.07        85.35 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       68.12        18.84       103.63        71.15        62.93        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 
       25.55        63.09        81.44        40.83        39.16        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.63        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        74.89        61.68        72.23        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       53.95        49.94        49.05        44.02        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       78.28        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 
       67.86        70.88        16.27        15.68        14.30        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.58        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N 
       35.93        20.12        90.84        26.66        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN 
       30.28        55.63        37.55        66.05        51.39        67.50 
TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX 
       91.99       113.82        82.85        42.28        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        89.16        97.48        24.62       120.62 
TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       33.17       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O 
      144.59        28.14        26.14        38.60        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 
        6.44        20.12        10.52       109.28        20.88        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A135 
       12.66        12.66        48.53        12.56         1.87        12.92 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL 
        4.11        12.33        11.34        11.28        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.95        12.33        20.25        12.95         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
        9.53         0.03        33.99        12.95        13.02        12.49 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 
       56.81        20.88        13.25        20.58        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD 
       21.14        14.17        17.49        16.50        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM 
       18.90        53.00        14.01        18.97        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO 
       12.39        17.16        14.73        21.80        17.69        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XY TCGA-D8-A1Y0 
       15.85        16.31        12.99        15.16        16.54        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
        9.93        14.24        17.42        13.45        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       16.41         4.80         1.61        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        28.87        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 
       69.34        18.51        69.96        23.24        19.43        23.87 
TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       22.82        17.29        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B1 TCGA-E2-A1B4 
       19.56        56.94        14.07        51.39        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       33.73        28.44        59.18         3.88        22.19        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       54.18        73.64        19.66        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
      106.75        26.99        34.55        43.56         8.28        30.61 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       36.20        36.56        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        24.82        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD 
        3.02        11.15        48.23        45.01        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 
       46.65         6.58        21.27        47.64        34.45        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       42.25        37.74        39.09        38.37        41.72        40.50 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.12        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X 
       29.72         9.47        38.07        32.91        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        26.70         0.79        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        28.77        25.94        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       40.41        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       10.16        23.51        31.30         7.40        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       79.10        83.34        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U 
       72.03        13.55        18.12        62.47        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       13.22        13.28        10.62        24.95        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       17.06        14.47        22.26         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        19.53        12.36        19.59        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39         2.10        36.30        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66K TCGA-OL-A66L 
       34.92        28.87        24.72        26.70        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ 
        8.91        47.01        64.21        86.96         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 
       18.81        18.48        21.07        20.68        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       17.39        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       11.41        29.03        15.35        16.04       108.07       107.05 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.16              0.03 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           282.90            281.29 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           28.255            27.715 
[1] "0.2 - 282.9 (28.3)" "0.0 - 281.3 (27.7)"
[1] "hr=" "1"  
D51V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  5Q LOSS MUTATED        16       11        0        2        93        54
  5Q LOSS WILD-TYPE      73       74        6        4       260       198
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           0         26          5         12        5
  5Q LOSS WILD-TYPE         2        128         24         53       15
                   vv
clus                STAGE TIS STAGE X
  5Q LOSS MUTATED           1       2
  5Q LOSS WILD-TYPE         0      11
D51V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 16                73
  STAGE IA                11                74
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA               93               260
  STAGE IIB               54               198
  STAGE III                0                 2
  STAGE IIIA              26               128
  STAGE IIIB               5                24
  STAGE IIIC              12                53
  STAGE IV                 5                15
  STAGE TIS                1                 0
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED    45 156  17   8
  5Q LOSS WILD-TYPE 231 468 119  32
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1              45               231
  T2             156               468
  T3              17               119
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  5Q LOSS MUTATED   117  71  24  13
  5Q LOSS WILD-TYPE 390 287  95  64
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0             117               390
  N1              71               287
  N2              24                95
  N3              13                64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   195   5
  5Q LOSS WILD-TYPE 694  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    195    5
  5Q LOSS WILD-TYPE  694   17
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0             195               694
  1               5                17
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED   227   1
  5Q LOSS WILD-TYPE 841  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED    227    1
  5Q LOSS WILD-TYPE  841   11
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE             227               841
  MALE                 1                11
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    94 108
  5Q LOSS WILD-TYPE 335 410
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     94  108
  5Q LOSS WILD-TYPE  335  410
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               94               335
  YES             108               410
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  5Q LOSS MUTATED                            1                           202
  5Q LOSS WILD-TYPE                          0                           568
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  5Q LOSS MUTATED                                5                   4
  5Q LOSS WILD-TYPE                            195                   2
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  5Q LOSS MUTATED                       0                                5
  5Q LOSS WILD-TYPE                     9                               24
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  5Q LOSS MUTATED                    0             10
  5Q LOSS WILD-TYPE                 17             37
D51V9, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                202               568
  INFILTRATING LOBULAR CARCINOMA                 5               195
  MEDULLARY CARCINOMA                            4                 2
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               5                24
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                10                37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0    18
  5Q LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                          63   130
  5Q LOSS WILD-TYPE                       118   615
D51V11, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18                42
  BLACK OR AFRICAN AMERICAN                     63               118
  WHITE                                        130               615
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V12, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     6 190
  5Q LOSS WILD-TYPE  33 685
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6  190
  5Q LOSS WILD-TYPE   33  685
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                33
  NOT HISPANIC OR LATINO             190               685
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED   161  23
  6P LOSS WILD-TYPE 756 124
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              184               880 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               23               124 
$`6P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SP TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04W 
      129.14        42.81        19.20       121.94        87.25       101.98 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 
       25.22        80.28        27.12        49.84        20.52        20.75 
TCGA-A2-A1FW TCGA-A2-A3KD TCGA-A2-A3XW TCGA-A2-A4RY TCGA-A7-A13D TCGA-A7-A2KD 
       17.36        39.65        56.28        21.30        31.73        22.32 
TCGA-A8-A06O TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07J TCGA-A8-A07S 
       13.02        26.01         1.02         9.01        12.00         7.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09C 
       33.01        19.96        12.00        31.00        12.00         1.02 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 
       29.98        33.07         1.02         8.98        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM 
       21.04        27.02        17.03        73.91        73.05        99.35 
TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A5EH TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AC-A8OR 
       26.04        32.45        16.80        17.42        20.19         1.32 
TCGA-AN-A04C TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XW TCGA-AO-A03T 
        1.78         5.65         0.33         0.33         5.59        47.87 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A1KR 
       37.48        20.32        22.36        26.24        62.04        70.39 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A1AP TCGA-AR-A1AU 
       17.79         2.56        32.91        98.33        93.90        94.29 
TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A252 TCGA-B6-A0IA 
       50.89         2.76       112.77       105.30        93.30       275.87 
TCGA-B6-A0IJ TCGA-B6-A0RO TCGA-B6-A0WV TCGA-B6-A401 TCGA-BH-A0AU TCGA-BH-A0B0 
      233.62       162.05        79.63        85.35        62.93        81.44 
TCGA-BH-A0B5 TCGA-BH-A0BP TCGA-BH-A0C3 TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 
       70.22        75.48        89.06        78.28        15.65        14.30 
TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0W3 
       24.43        23.08        52.96        51.32        27.25        23.93 
TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EY 
       35.93        26.66        66.05       113.82        42.28        17.69 
TCGA-BH-A1F5 TCGA-BH-A1FE TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A5J0 TCGA-BH-A8FZ 
       89.16        74.73        63.35        45.63        23.51        18.87 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A274 
       12.66        11.77        12.66         4.11        11.34         9.53 
TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A145 TCGA-D8-A1JC 
       24.56        13.02        13.41        19.46        13.48        15.78 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XU 
       18.90        53.00        19.40        27.58        15.22        12.99 
TCGA-D8-A1Y1 TCGA-D8-A27W TCGA-D8-A73W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A14V 
        9.93        12.26        12.66        34.42        46.59        34.26 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15R 
       69.96        23.24        20.71        21.63        12.92        56.94 
TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1L8 TCGA-E2-A1LE TCGA-E2-A1LL 
       76.57        37.25        77.65        73.64        28.90        43.04 
TCGA-E2-A9RU TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NF 
       17.69        22.29        34.16        36.56        35.77        35.24 
TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG 
       24.82         6.12        11.15        45.01        32.09        21.27 
TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS 
       47.64        37.74        39.09         1.94         7.13        29.72 
TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1P5 TCGA-EW-A6S9 
       30.44        26.40        18.90        28.77        23.11        15.22 
TCGA-EW-A6SD TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A3XL TCGA-LL-A5YM 
       33.21        79.10        83.34        75.02        69.30        15.32 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       19.53        19.59        22.39        28.21        19.73        40.11 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-UU-A93S 
       18.48        21.07        17.39         3.81 

$`6P LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       20.88        13.68        31.79         7.96        39.32        28.01 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04V 
       18.21       143.15        18.02        78.41        73.84        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
       92.48       107.93        56.81        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       61.58       101.72        89.36       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC 
       17.52        17.13         8.38        17.46        18.90        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        50.47        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        33.93        91.07        29.98        32.75 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       47.31        35.93        50.37        50.83         7.30        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY 
       24.26        23.74        23.80        21.73        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       12.10        10.72        11.05        10.29         9.37        10.42 
TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
        8.75        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        32.05         9.99        10.98         8.98 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
        0.99        38.01        28.96        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        17.95        41.98         9.99         9.99        12.00 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W 
       50.04        49.05        45.07        25.02        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C 
       14.01        12.00        19.04         0.99        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       22.95         5.72         1.48        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        74.14        33.04        19.33        14.66 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X 
       29.26        14.53        19.33        14.96        11.44        13.71 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.12         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        0.62         2.96         1.71         9.96         7.36         7.46 
TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        0.16         0.33         0.33         0.33         6.44         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW 
        7.00         7.59         7.17         6.90         7.04         0.36 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        0.33         0.33         5.36         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L 
        0.33         0.33         0.33         0.33         5.33        80.28 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03U 
       61.35        66.77        81.63        95.70        68.75        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J9 
       29.13        32.78        21.40        52.18        26.04        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       21.53        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
        0.53        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       32.52        19.20       140.55         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      133.22        83.87       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       99.32        17.23        37.81        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73       160.90        94.22       120.33        99.78       118.59 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
      104.28        97.84       105.27        77.69        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.66        89.00        99.62        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        57.27        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK 
      129.57        50.70        65.72       146.50       112.37        18.77 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE 
      127.33        84.59       165.76       129.07       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
       68.45       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ 
       97.48       188.68        18.35        21.47       113.79       206.86 
TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC 
      129.70       245.10        28.27        68.94        58.88        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
      101.52        73.51       139.17       170.17        37.87         7.07 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
       70.16        68.12        18.84       103.63        71.15        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        40.83        39.55        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.63        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       43.53        61.51        21.70        74.89        61.68        72.23 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW 
       74.14        76.60        53.95        45.57        49.94        77.95 
TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.05        41.75        44.02        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ 
       23.44        38.01        29.98        13.91        17.26         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        30.35        10.78        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        41.00        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 
       13.61        36.85        12.89        50.79         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J 
       42.35        44.81        23.05        32.91         4.90        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET 
        7.36        51.39        51.16        67.50        91.99        82.85 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 
       12.00        55.69        49.58        25.81        31.53        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH 
       24.62       120.62       114.15        33.17       122.89        36.92 
TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       55.00        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 
       20.12        10.52       109.28        20.88        18.64         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        5.26         9.70        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.56         3.16        13.51         1.87        12.59        12.92 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.08        12.33        10.92        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       10.42        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 
       12.36        12.95         8.28         9.67         0.03         9.50 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z 
       14.43        33.99        12.95        12.49        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 
       13.25        20.58        13.97        14.17        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JF 
       14.17        17.49        16.50        55.50        18.15        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       14.01        18.97        20.09        20.12        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.80        14.50        19.92        17.69        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       16.41        15.85        16.31        16.64        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E 
       16.54        15.32        15.52        14.24        14.14        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73X TCGA-E2-A105 
       33.37        18.51        21.67        16.18        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       75.98        43.33        32.02        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       63.62        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J 
       23.34        22.82        17.29        18.21        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S 
        9.04        20.58        11.05        50.79        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       16.47        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH 
       60.36        19.66        24.59        75.81        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        26.99        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        38.76        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NG TCGA-E9-A1NH 
       36.82        36.20        39.55        41.62        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R7 
        9.86        28.27        34.95         2.56         3.02        48.23 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A226 
       40.24         1.12        46.65         6.58        46.59        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       32.05        42.25        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 
       40.50        20.12         0.69        38.99        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y 
        9.47        38.07        32.91        30.18        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70         0.79        25.81        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
        8.48        18.21        13.25        16.57        15.68        25.94 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       22.82        29.95        29.85        40.41        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        29.82        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        10.16        23.51        16.77        24.99        31.30 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DF TCGA-GM-A2DH 
        7.40       109.87        59.57       216.76        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       18.12         2.60        62.47        11.84        11.57        21.24 
TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       13.22         7.10        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP 
       29.23        25.05        17.06        14.70        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       22.26         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       12.36        17.49        27.91         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       24.72        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A97C 
       41.92        42.77        26.04        17.36        14.07         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ 
       47.01        64.21        86.96         0.16         0.26         9.93 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 
       18.81        20.68        19.27        13.84        18.87        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.33              0.03 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           275.87            282.90 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           26.530            28.355 
[1] "0.3 - 275.9 (26.5)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6P LOSS MUTATED        15       16        1        0        63        46
  6P LOSS WILD-TYPE      74       69        5        6       290       206
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           0         25          6          8        4
  6P LOSS WILD-TYPE         2        129         23         57       16
                   vv
clus                STAGE TIS STAGE X
  6P LOSS MUTATED           0       3
  6P LOSS WILD-TYPE         1      10
D52V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 15                74
  STAGE IA                16                69
  STAGE IB                 1                 5
  STAGE II                 0                 6
  STAGE IIA               63               290
  STAGE IIB               46               206
  STAGE III                0                 2
  STAGE IIIA              25               129
  STAGE IIIB               6                23
  STAGE IIIC               8                57
  STAGE IV                 4                16
  STAGE TIS                0                 1
  STAGE X                  3                10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    52 109  17   8
  6P LOSS WILD-TYPE 224 515 119  32
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              52               224
  T2             109               515
  T3              17               119
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6P LOSS MUTATED    87  66  20  12
  6P LOSS WILD-TYPE 420 292  99  65
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              87               420
  N1              66               292
  N2              20                99
  N3              12                65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED   159   4
  6P LOSS WILD-TYPE 730  18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    159    4
  6P LOSS WILD-TYPE  730   18
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0             159               730
  1               4                18
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED   186   1
  6P LOSS WILD-TYPE 882  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    186    1
  6P LOSS WILD-TYPE  882   11
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE             186               882
  MALE                 1                11
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    67 100
  6P LOSS WILD-TYPE 362 418
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     67  100
  6P LOSS WILD-TYPE  362  418
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               67               362
  YES             100               418
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6P LOSS MUTATED                            0                           143
  6P LOSS WILD-TYPE                          1                           627
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6P LOSS MUTATED                               24                   1
  6P LOSS WILD-TYPE                            176                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6P LOSS MUTATED                       1                                7
  6P LOSS WILD-TYPE                     8                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6P LOSS MUTATED                    5              6
  6P LOSS WILD-TYPE                 12             41
D52V9, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                143               627
  INFILTRATING LOBULAR CARCINOMA                24               176
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             5                12
  OTHER  SPECIFY                                 6                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0    13
  6P LOSS WILD-TYPE                                1    47
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                          35   116
  6P LOSS WILD-TYPE                       146   629
D52V11, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         13                47
  BLACK OR AFRICAN AMERICAN                     35               146
  WHITE                                        116               629
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V12, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     5 149
  6P LOSS WILD-TYPE  34 726
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5  149
  6P LOSS WILD-TYPE   34  726
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                34
  NOT HISPANIC OR LATINO             149               726
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   241  32
  6Q LOSS WILD-TYPE 676 115
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              273               791 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               32               115 
$`6Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SE TCGA-A1-A0SN 
      129.14       131.67        42.81         9.96        43.43        39.32 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CQ TCGA-A2-A0CR 
      121.94        73.84        87.25       101.98        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0D4 TCGA-A2-A0EO 
       77.19        75.25         5.19        98.99        25.22        80.28 
TCGA-A2-A0ET TCGA-A2-A0SV TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 
       35.05        27.12        49.84        20.52        18.90        20.75 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KD 
       23.77        17.36       107.70        42.44       105.34        39.65 
TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A4RY TCGA-A7-A13D TCGA-A7-A13F 
       33.93        32.75        56.28        21.30        31.73        25.15 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J1 TCGA-A7-A426 TCGA-A8-A06O TCGA-A8-A06Y 
       20.61        11.34        11.28        11.97        13.02        26.01 
TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07J TCGA-A8-A07S TCGA-A8-A08F 
        1.02        53.98         9.01        12.00         7.99        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A097 TCGA-A8-A09A 
       19.96        12.00        37.05        31.00        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AB 
        8.98        19.04        13.02        21.04        27.02        17.03 
TCGA-AC-A23G TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A3BB TCGA-AC-A3TM 
       73.91        73.05        99.35        26.04        32.45        25.05 
TCGA-AC-A3W5 TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62Y TCGA-AC-A8OP TCGA-AC-A8OR 
       16.57        29.26        16.80        17.42        20.19         1.32 
TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AS TCGA-AN-A0FF TCGA-AN-A0FV TCGA-AN-A0FX 
        0.23         1.78         0.33         5.65         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J3 TCGA-AO-A0J6 
        5.59        66.77        68.75        47.87        21.40        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       20.32        22.36        26.24        50.24        62.04        55.33 
TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR 
       70.39        17.79         2.56        32.91        98.33         5.26 
TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A1AU TCGA-AR-A24K TCGA-AR-A24P TCGA-AR-A24R 
      107.24        83.87        94.29        50.89         2.76       112.77 
TCGA-AR-A24V TCGA-AR-A252 TCGA-AR-A255 TCGA-B6-A0IA TCGA-B6-A0IJ TCGA-B6-A0RG 
      105.30        93.30        71.05       275.87       233.62        68.45 
TCGA-B6-A0RO TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KN 
      162.05       282.90        79.63       113.79        43.59       139.17 
TCGA-B6-A2IU TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B0 
      170.17        85.35        68.12        71.15        62.93        81.44 
TCGA-BH-A0B5 TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BW 
       70.22        21.70        61.68        75.48        74.14        77.95 
TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E2 
       89.06        77.98        38.01        78.28        15.65        14.30 
TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0HX 
       24.43        15.16        23.08        52.96        51.32        27.25 
TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18S 
       23.93        32.91        35.93        90.84        26.66        66.05 
TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1F5 TCGA-BH-A1FC TCGA-BH-A1FE 
       67.50       113.82        42.28        89.16       114.15        74.73 
TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A8FZ TCGA-C8-A12M TCGA-C8-A12O 
       63.35        45.63        28.14        18.87        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HO TCGA-C8-A26Y 
       11.77        12.66         4.11        11.34        12.33        12.95 
TCGA-C8-A273 TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A145 
        9.67        24.56        13.02        13.41        19.46        13.48 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI TCGA-D8-A1JM 
       55.50        18.15        18.90        53.00        18.97        19.40 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XT 
       27.58        18.15        15.22        19.92        17.69        16.64 
TCGA-D8-A1XU TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27W 
       12.99        15.52         9.93        10.09        13.08        12.26 
TCGA-D8-A73W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10F TCGA-E2-A14V TCGA-E2-A152 
       12.66        34.42        46.59        28.87        34.26        69.96 
TCGA-E2-A153 TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15P TCGA-E2-A15R 
       23.24        20.71        21.63        12.92        19.56        56.94 
TCGA-E2-A1AZ TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IL TCGA-E2-A1L8 
       76.57        16.47        37.25        77.65         3.88        73.64 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1N5 
       28.90        50.07        43.04        17.69        32.88        36.82 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1QZ TCGA-E9-A1R0 
       22.29        34.16        36.56        35.77        24.82        28.27 
TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A1RH 
        6.12        11.15        45.01        32.09        21.27        46.59 
TCGA-E9-A1RI TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A2JS 
       47.64        37.74        39.09         1.94         7.13        29.72 
TCGA-E9-A3X8 TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J5 
       30.44        25.81        26.40        18.90        13.25        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P5 TCGA-EW-A3E8 TCGA-EW-A6S9 
       28.77        29.85        41.13        23.11        34.03        15.22 
TCGA-EW-A6SD TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A3XL 
       33.21        79.10        83.34        75.02        70.85        69.30 
TCGA-GM-A3XN TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A740 
       66.38        21.24        13.28        10.62        15.32        14.50 
TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A6VO 
       19.53        19.59        22.39        42.77        17.36        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-PE-A5DC TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
       19.73        40.11        47.01        18.81        18.48        21.07 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-UU-A93S 
       18.87        17.39         3.81 

$`6Q LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD 
       40.14        11.44        48.56        48.36         8.52        14.37 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK 
       48.10        14.27        47.24        20.88        13.68        31.79 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P 
        7.96        28.01        19.20        18.21       143.15        18.02 
TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       78.41        63.12        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 
       24.79       114.81        92.48       107.93        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       34.55        33.76        61.58       101.72        89.36       118.45 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       79.76        74.40        72.00        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0YC 
       44.28        17.52        17.13         8.38        17.46        32.55 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       25.28        18.21        50.47        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX 
       18.61        19.33        48.46        31.73        23.47        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XT TCGA-A2-A3XU 
       17.19        18.15        10.59        36.23        91.07        29.98 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       47.31        35.93        50.37        50.83         7.30        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        20.19        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.74        23.80        21.73        22.32        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       13.41        14.70        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
        9.37        10.42         8.75        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07E 
       53.06        29.03        31.00        17.03        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        18.97        14.01        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        8.98        24.99         9.99        45.07        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08P 
       13.02         0.99        38.01        28.96         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D 
       30.97        17.95        41.98         9.99        12.00        50.04 
TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       25.02        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A7 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H TCGA-AC-A2B8 
        0.99        38.04         0.95        22.95         5.72         1.48 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO 
       40.57        86.66        90.71        60.92        87.12        74.14 
TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       33.04        19.33        14.66         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       22.19        24.13        14.99        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X 
       24.79        14.53        19.33        14.96        11.44        13.71 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       18.67        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.12         2.30         0.33         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        2.96         1.71         9.96         7.36         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         0.33         6.44         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.90         7.04         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O 
        0.33         0.33         5.33        80.28        61.35        81.63 
TCGA-AO-A03P TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 
       95.70        58.95        29.13        32.78        52.18        26.04 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       53.03        21.53        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       65.10        71.80       115.27        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.03        90.58        98.27        64.04        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS 
       41.62        40.57        14.73        82.62        61.87         0.53 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW 
       19.20       140.55        84.10       109.02        75.22        98.93 
TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       64.83        55.86        65.36       133.22       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      125.16       108.36       101.00       103.86        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       96.00        86.07        93.90        99.32        17.23        37.81 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        86.53        86.43        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
      120.33        99.78       118.59       104.28        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 
       77.69        32.58        98.76        98.66        89.00        99.62 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       85.64        93.83       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       73.35        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
      281.29        12.13       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      112.37        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      140.88       255.68       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
      263.28       102.77       140.48       100.70        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       97.48       188.68        18.35        21.47       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      245.10        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AV 
       37.87         7.07        70.16        18.84       103.63        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        63.09        40.83        39.55        39.16 
TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD 
       81.63        84.13        51.68        37.22        32.02        18.21 
TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BR TCGA-BH-A0BS 
       43.53        61.51        74.89        72.23        76.60        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       45.57        49.94        49.05        41.75        44.02        90.97 
TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DQ 
       45.83        23.44        29.98        13.91        17.26         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB 
       15.68         9.63        44.81        46.19        32.58        24.49 
TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       31.00        30.35        10.78        37.78        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       41.00        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       36.85        12.89        50.79         5.59        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18M TCGA-BH-A18N 
       44.81        23.05         4.90        20.12        72.56        37.74 
TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       30.28        55.63        37.55         7.36        51.39        51.16 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       91.99        82.85        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       25.81        31.53        97.48        24.62       120.62        33.17 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
      122.89        36.92        55.00        72.07       144.59        72.07 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28        20.88        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-BH-AB28 
       23.51         9.63         5.26         9.70        21.76         9.44 
TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X 
       11.93        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       48.53        12.56         3.16        13.51         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.92         4.08        12.33        10.92        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42        12.33        12.95        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B 
       12.36         8.28         9.53         0.03         9.50        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 
       33.99        12.95        12.49        56.81        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       20.58        13.97        14.17        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JJ 
       17.49        16.50        15.78        12.03        14.01        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XO 
       12.39        17.16        14.73        21.80        14.50        55.30 
TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY 
       16.41        15.85        16.31        15.16        43.04        16.54 
TCGA-D8-A1XZ TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.32        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43        48.03        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
        1.61        12.53        33.37        18.51        21.67        16.18 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       25.22        43.00        27.52        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.44        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       33.17        75.98        43.33        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       18.51        63.62        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15I 
       25.05        23.34        22.82        17.29        18.21        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15S 
       53.92         9.04        20.58        11.05        50.79        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L9 
       22.19        60.99        11.08        54.18        60.36        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 
       24.59        75.81       106.75       102.61         8.75        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
       34.55        43.56         8.28        30.61        34.92        38.76 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NF 
       34.29        34.82        36.20        39.55        41.62        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       25.84        18.94         9.86        34.95         2.56         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A226 
       48.23        40.24         1.12        46.65         6.58        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G 
       32.05        42.25        38.37        41.03        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A24A TCGA-E9-A295 
       40.50        20.12         0.69        38.99        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y 
        9.47        38.07        32.91        30.18        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       26.70         0.79        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J3 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ 
       18.21        16.57        25.94        22.82        29.95        40.41 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       39.78        52.96        29.82        18.48        30.08         7.86 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       17.49        10.16        23.51        16.77        24.99        31.30 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DH TCGA-GM-A2DI 
        7.40       109.87        59.57       216.76        72.10        85.15 
TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       86.96       115.69       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       38.20        43.73        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LL-A440 
       62.47        11.84        11.57        13.22         7.10        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       32.75        29.23        25.05        17.06        14.70        14.47 
TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.79        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       12.36        17.49        27.91         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J 
       24.72        22.32        20.38        26.70        23.47        65.62 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE 
       41.92        26.04        14.07         8.91        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.16         0.26         9.93        20.68        19.27        13.84 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       17.26        13.94        17.03        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.23              0.03 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           282.90            281.29 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            28.27             26.99 
[1] "0.2 - 282.9 (28.3)" "0.0 - 281.3 (27.0)"
[1] "hr=" "1.2"
D53V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  6Q LOSS MUTATED        20       25        1        0        88        73
  6Q LOSS WILD-TYPE      69       60        5        6       265       179
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           0         38          9         13        5
  6Q LOSS WILD-TYPE         2        116         20         52       15
                   vv
clus                STAGE TIS STAGE X
  6Q LOSS MUTATED           0       4
  6Q LOSS WILD-TYPE         1       9
D53V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 20                69
  STAGE IA                25                60
  STAGE IB                 1                 5
  STAGE II                 0                 6
  STAGE IIA               88               265
  STAGE IIB               73               179
  STAGE III                0                 2
  STAGE IIIA              38               116
  STAGE IIIB               9                20
  STAGE IIIC              13                52
  STAGE IV                 5                15
  STAGE TIS                0                 1
  STAGE X                  4                 9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    78 156  29  12
  6Q LOSS WILD-TYPE 198 468 107  28
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              78               198
  T2             156               468
  T3              29               107
  T4              12                28
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  6Q LOSS MUTATED   121 102  30  18
  6Q LOSS WILD-TYPE 386 256  89  59
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0             121               386
  N1             102               256
  N2              30                89
  N3              18                59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   230   6
  6Q LOSS WILD-TYPE 659  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    230    6
  6Q LOSS WILD-TYPE  659   16
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             230               659
  1               6                16
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   275   1
  6Q LOSS WILD-TYPE 793  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    275    1
  6Q LOSS WILD-TYPE  793   11
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE             275               793
  MALE                 1                11
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    93 156
  6Q LOSS WILD-TYPE 336 362
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     93  156
  6Q LOSS WILD-TYPE  336  362
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               93               336
  YES             156               362
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  6Q LOSS MUTATED                            0                           202
  6Q LOSS WILD-TYPE                          1                           568
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  6Q LOSS MUTATED                               43                   2
  6Q LOSS WILD-TYPE                            157                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  6Q LOSS MUTATED                       1                               10
  6Q LOSS WILD-TYPE                     8                               19
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  6Q LOSS MUTATED                    7             11
  6Q LOSS WILD-TYPE                 10             36
D53V9, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                202               568
  INFILTRATING LOBULAR CARCINOMA                43               157
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)              10                19
  MUCINOUS CARCINOMA                             7                10
  OTHER  SPECIFY                                11                36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0    16
  6Q LOSS WILD-TYPE                                1    44
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          52   180
  6Q LOSS WILD-TYPE                       129   565
D53V11, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         16                44
  BLACK OR AFRICAN AMERICAN                     52               129
  WHITE                                        180               565
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V12, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     8 224
  6Q LOSS WILD-TYPE  31 651
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      8  224
  6Q LOSS WILD-TYPE   31  651
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                31
  NOT HISPANIC OR LATINO             224               651
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED    96  14
  7P LOSS WILD-TYPE 821 133
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
              110               954 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               14               133 
$`7P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A1-A0SO TCGA-A2-A04T TCGA-A2-A0CT TCGA-A2-A0D4 
        9.96        31.79        28.01        73.84        75.25        25.22 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FW 
       79.76        35.05        50.43        49.84        23.77        17.36 
TCGA-A2-A1G1 TCGA-A2-A4RX TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DC 
       19.20        24.39        21.90        38.30        30.61        29.79 
TCGA-A7-A26I TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A079 
       21.73        10.42        13.02        29.03        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07G TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08L 
       43.00        18.97         8.98        38.01        33.01         9.99 
TCGA-A8-A08S TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A09Q TCGA-A8-A0A2 TCGA-A8-A0A9 
       33.01        33.01        30.97        25.02        19.04        27.02 
TCGA-AC-A23E TCGA-AC-A2QH TCGA-AC-A62X TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0AS 
       22.95        33.04        13.71         1.78         0.16         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 TCGA-AO-A12F 
        0.33         0.33         0.33        80.28        20.32        48.36 
TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AQ TCGA-AR-A255 
        0.53         2.56       107.21       108.36        99.32        71.05 
TCGA-AR-A2LK TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0WY 
       54.21       233.62       165.76        68.45       100.70       113.79 
TCGA-B6-A402 TCGA-B6-A408 TCGA-BH-A0BG TCGA-BH-A0C0 TCGA-BH-A0HI TCGA-BH-A18F 
       70.16        68.12        61.51        41.75        20.38        32.91 
TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1F8 TCGA-BH-A42T TCGA-C8-A1HF 
       26.66        55.63        51.39        24.62        10.52        10.92 
TCGA-C8-A1HM TCGA-C8-A274 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JM 
       12.33         9.53        19.20        17.49        18.90        19.40 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XK TCGA-D8-A1XQ 
       14.70        18.58        27.58        18.15        14.50        16.41 
TCGA-D8-A27M TCGA-E2-A14Z TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1L7 TCGA-E9-A1N6 
       13.48        18.51        12.92        14.07        60.36        22.29 
TCGA-E9-A1RF TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A54Y 
        6.58        38.37        40.73         0.69         1.94        23.84 
TCGA-E9-A5UP TCGA-EW-A1PC TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 
       26.40         6.15        16.77        24.99        33.21       109.87 
TCGA-GM-A2DI TCGA-GM-A3XL TCGA-LL-A5YP TCGA-LL-A7T0 TCGA-OL-A5RY TCGA-S3-A6ZG 
       85.15        69.30        14.79        12.36        24.72        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 
       20.68        19.27 

$`7P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        39.32        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U 
       18.21       143.15        18.02        78.41       121.94        87.25 
TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       63.12       101.98        55.43        36.13       136.73        99.12 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       24.79       114.81        92.48        88.60       107.93        77.19 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
        5.19        98.99       107.93        56.81        67.33        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP 
       33.76        61.58       101.72        89.36        80.28       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       74.40        72.00        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY 
       63.29        99.19        54.64        27.12        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU 
       10.59        36.23        39.65        33.93        91.07        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CE 
        7.30        21.30        23.21        26.96        21.14        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       34.29        35.47        37.45        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       20.19        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       13.74        14.50        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05        10.29         9.37         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
        1.02        17.98        53.06        31.00        26.01         1.02 
TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       53.98        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99        24.99         9.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G 
       15.06        36.95        13.02         0.99        28.96        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T 
       12.00        37.05        31.00        31.00         0.99       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
       43.00        40.01        17.95        41.98        12.00         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I 
        9.99        12.00         1.02        50.04        49.05        45.07 
TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       29.98        33.07         1.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
        0.99        14.01        12.00        13.02        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       17.03        38.04         0.95        73.91         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       87.12        26.04        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       29.26        16.80        14.53        19.33        14.96        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       17.42        18.67        13.58        12.26         1.68         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        9.96         7.36         7.46         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV 
        0.33        12.33         0.30         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 
       47.87        58.95        29.13        32.78        21.40        52.18 
TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       26.04        37.48        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR 
       41.62        40.57        14.73        82.62        61.87        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AH 
      107.24        65.36       133.22        83.87       134.14       125.16 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       93.90        17.23        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.43        33.73       160.90        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      105.27        77.69       105.30        32.58        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        99.62        93.30        85.64        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        66.15        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB 
       77.62       143.38       281.29        12.13       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70        65.72       146.50       112.37        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       129.07       140.88       255.68       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A409 TCGA-B6-A40B 
      170.17        37.87         7.07        85.35        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       71.15        62.93        59.84        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       81.44        40.83        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        74.89        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG 
       44.02        89.06        90.97        45.83        77.98        23.44 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       38.01        29.98        13.91        78.28        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        53.26        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I 
       24.95        42.35        44.81        23.05         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R 
       20.12        90.84        72.56        37.74        30.28        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.16        67.50        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        97.48       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 
       45.63        72.07       144.59        72.07        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12       109.28        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        48.53        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       13.51         1.87        12.59        12.92         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y 
       12.95        12.33        20.25        12.53        12.36        12.95 
TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        8.28         9.67         0.03         9.50        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       33.99        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       56.81        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       13.48        21.14        14.17        16.50        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ 
       18.15        12.03        53.00        14.01        18.97        20.09 
TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.12        20.09        20.38        21.01        12.20        13.32 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD 
       17.79        16.73        25.74        23.90        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        21.80        19.92        17.69        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 
       34.26        32.02        31.96        69.34        63.62        69.96 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 
       23.24        19.43        21.04        23.87        14.79        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        56.94        51.39        76.57        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE 
       33.01        32.35        28.50        16.47        37.25        77.65 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
        3.88        22.19        60.99        11.08        54.18        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       19.66        24.59        75.81        28.90        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       39.55        41.62        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 
        9.86        24.82        28.27        34.95         2.56         6.12 
TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
        3.02        11.15        48.23        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
        1.12        46.65        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E 
       32.05        42.25        37.74        39.09        41.03        41.72 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       40.50        20.12        38.99         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW 
       23.90        26.70         0.79        25.81        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD 
       18.48        30.08         7.86        18.90        19.99        13.94 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       15.22        31.30         7.40        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL 
       83.34        75.02        70.85        72.10        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       15.32        14.70        14.47        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 
       15.68         7.46        14.50        19.53        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ 
       58.62        40.08        34.92        36.36        28.87        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       26.04        17.36        14.07        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
        8.91        47.01        64.21        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        9.93        18.81        21.07        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.26        13.94        17.03         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.16              0.03 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           233.62            282.90 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           24.115            28.870 
[1] "0.2 - 233.6 (24.1)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7P LOSS MUTATED         7        8        1        2        43        25
  7P LOSS WILD-TYPE      82       77        5        4       310       227
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           1         15          5          4        0
  7P LOSS WILD-TYPE         1        139         24         61       20
                   vv
clus                STAGE TIS STAGE X
  7P LOSS MUTATED           0       0
  7P LOSS WILD-TYPE         1      13
D54V3, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  7                82
  STAGE IA                 8                77
  STAGE IB                 1                 5
  STAGE II                 2                 4
  STAGE IIA               43               310
  STAGE IIB               25               227
  STAGE III                1                 1
  STAGE IIIA              15               139
  STAGE IIIB               5                24
  STAGE IIIC               4                61
  STAGE IV                 0                20
  STAGE TIS                0                 1
  STAGE X                  0                13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED    22  74  11   5
  7P LOSS WILD-TYPE 254 550 125  35
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1              22               254
  T2              74               550
  T3              11               125
  T4               5                35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7P LOSS MUTATED    60  29  17   5
  7P LOSS WILD-TYPE 447 329 102  72
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0              60               447
  N1              29               329
  N2              17               102
  N3               5                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED   102   0
  7P LOSS WILD-TYPE 787  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    102    0
  7P LOSS WILD-TYPE  787   22
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0             102               787
  1               0                22
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED   111   1
  7P LOSS WILD-TYPE 957  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED    111    1
  7P LOSS WILD-TYPE  957   11
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE             111               957
  MALE                 1                11
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED    40  58
  7P LOSS WILD-TYPE 389 460
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     40   58
  7P LOSS WILD-TYPE  389  460
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO               40               389
  YES              58               460
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7P LOSS MUTATED                            0                            96
  7P LOSS WILD-TYPE                          1                           674
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7P LOSS MUTATED                                5                   2
  7P LOSS WILD-TYPE                            195                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7P LOSS MUTATED                       2                                3
  7P LOSS WILD-TYPE                     7                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7P LOSS MUTATED                    0              4
  7P LOSS WILD-TYPE                 17             43
D54V9, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 96               674
  INFILTRATING LOBULAR CARCINOMA                 5               195
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 4                43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     6
  7P LOSS WILD-TYPE                                1    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                          25    65
  7P LOSS WILD-TYPE                       156   680
D54V11, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     25               156
  WHITE                                         65               680
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V12, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2  89
  7P LOSS WILD-TYPE  37 786
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2   89
  7P LOSS WILD-TYPE   37  786
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                37
  NOT HISPANIC OR LATINO              89               786
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED   101  17
  7Q LOSS WILD-TYPE 816 130
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
              118               946 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               17               130 
$`7Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SO TCGA-A2-A0CT TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ET 
        9.96        28.01        75.25        25.22        79.76        35.05 
TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1G1 TCGA-A2-A4RX 
       50.43        49.84        23.77        17.36        19.20        24.39 
TCGA-A7-A0CD TCGA-A7-A0CJ TCGA-A7-A0DC TCGA-A7-A26I TCGA-A7-A6VX TCGA-A8-A06O 
       38.30        30.61        29.79        21.73        10.42        13.02 
TCGA-A8-A06U TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07I 
       29.03        17.03        53.98         9.01        18.97        14.01 
TCGA-A8-A07R TCGA-A8-A08B TCGA-A8-A08S TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09I 
        8.98        38.01        33.01        30.97         9.99        45.07 
TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A9 TCGA-AC-A23E TCGA-AC-A2QH 
        0.99        12.00        19.04        27.02        22.95        33.04 
TCGA-AC-A62V TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A0AJ TCGA-AN-A0AM TCGA-AN-A0AS 
       11.44         0.62         1.78         9.96         0.16         0.33 
TCGA-AN-A0FT TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A0J7 
        7.04         0.33         0.33         0.33        80.28        20.32 
TCGA-AO-A0JE TCGA-AO-A1KS TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A24H TCGA-AR-A24W 
       76.77         0.53        83.87       107.21       160.90        32.58 
TCGA-AR-A255 TCGA-AR-A2LK TCGA-B6-A0IC TCGA-B6-A0IO TCGA-B6-A0RS TCGA-B6-A0WY 
       71.05        54.21        50.70       165.76       100.70       113.79 
TCGA-B6-A408 TCGA-BH-A0AZ TCGA-BH-A0BG TCGA-BH-A0DZ TCGA-BH-A0HI TCGA-BH-A0W7 
       68.12        63.09        61.51        16.27        20.38        44.81 
TCGA-BH-A18F TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18U TCGA-BH-A1EV TCGA-BH-A1FN 
       32.91        26.66        55.63        51.39        12.00        72.07 
TCGA-BH-A42T TCGA-BH-A5J0 TCGA-C8-A12W TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HM 
       10.52        23.51        12.66         4.08        10.92        12.33 
TCGA-D8-A1JE TCGA-D8-A1JJ TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XB 
       18.90        20.09        14.70        18.58        27.58        18.15 
TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A27M TCGA-E2-A14Z TCGA-E2-A15H 
       14.50        16.41        12.99        13.48        18.51        12.92 
TCGA-E2-A15M TCGA-E2-A1BC TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LB TCGA-E9-A1N6 
       11.05        16.47        60.36        73.64        75.81        22.29 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RF TCGA-E9-A22B TCGA-E9-A244 
        2.56         6.12        48.23         6.58        38.37         0.69 
TCGA-E9-A248 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A54Y TCGA-E9-A5UP TCGA-EW-A1PC 
        1.94        24.56        38.07        23.84        26.40         6.15 
TCGA-EW-A6SA TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DI TCGA-LL-A5YP TCGA-LL-A7SZ 
       16.77        33.21       109.87        85.15        14.79        19.53 
TCGA-OL-A5RY TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
       24.72        18.48        20.68        19.27 

$`7Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        77.19         5.19        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       67.33        34.55        33.76        61.58       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV 
       80.28       118.45        74.40        72.00        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 
       44.88        44.28        17.52        17.13         8.38        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       17.46        18.90        20.75        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK 
       50.47        21.90        21.67        49.48        18.61        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       48.46        31.73        23.47        60.72        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         7.30        21.30        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       21.14        21.90        35.31        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J 
       29.56        31.36        24.26        23.74        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        9.37         8.75        13.02         1.02        17.98        53.06 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01         1.02        43.00        19.99        18.97 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        15.06        36.95        13.02         0.99 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z 
       31.00        31.00         0.99       112.08        43.00        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B 
       33.01        17.95        41.98        12.00         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
        1.02        50.04        49.05        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A4 
       25.02         8.98        19.04        15.02        14.01        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23G 
       21.04         0.99        17.03        38.04         0.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI 
       90.71        60.92        87.12        26.04        74.14        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       23.24        24.79        29.26        16.80        14.53        19.33 
TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A 
        2.30         0.33         0.33         0.23         0.33         2.96 
TCGA-AN-A04D TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        1.71         7.36         7.46         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.90 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.30         0.33         0.33         5.33         5.59 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T 
       61.35        66.77        81.63        95.70        68.75        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       58.95        29.13        32.78        21.40        52.18        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       72.00        65.10        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       115.27        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT 
       40.57        14.73        82.62        61.87        70.39        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       84.10       109.02        75.22        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI 
      107.24        65.36       133.22       134.14       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       93.90        99.32        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
      105.27        77.69       105.30        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH 
       99.62        93.30        85.64        93.83       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       86.53        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       57.27        73.35        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IE 
      143.38       281.29        12.13       275.87       129.57        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35        21.47       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       68.94        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 
      170.17        37.87         7.07        85.35        70.16        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        62.93        59.84        20.45        25.55 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       81.44        40.83        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        74.89        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 
        4.41        15.68        14.30         9.63        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       32.58        24.49        31.00        24.43        30.35        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 
       15.16        37.78        53.26        24.56        23.08        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       12.89        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       24.95        42.35        23.05         4.90        35.93        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18S 
       90.84        72.56        37.74        30.28        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.16        67.50        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       42.28        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       57.83       130.16        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        18.64         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       12.56         3.16        13.51         1.87        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
        4.11        12.33        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       10.42        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ 
       24.56        14.43        33.99        12.95        13.02        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       13.41        19.46        56.81        20.88        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 
       13.97        14.17        13.48        21.14        19.20        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JF 
       17.49        16.50        55.50        15.78        18.15        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       53.00        14.01        18.97        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1X6 TCGA-D8-A1X7 
       20.38        21.01        12.20        13.32        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       25.74        23.90        12.39        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       21.80        19.92        17.69        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.64        15.16        43.04        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
        9.93        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43        48.03        16.41         4.80         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        63.62        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        18.21        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       20.58        50.79        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       54.18        19.66        24.59        28.90        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU 
        8.28        30.61        34.92        38.76        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH 
       39.55        41.62        35.77        35.24        25.84        18.94 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R5 TCGA-E9-A1R6 
        9.86        24.82        28.27        34.95         3.02        11.15 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG 
       45.01        32.09        40.24         1.12        46.65        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        41.03        41.72        40.73        40.50        20.12 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
       38.99         7.13        12.33        29.72         9.47        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO 
       30.18        30.44        23.90        26.70         0.79        25.81 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.82        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       55.00        52.73        25.91        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 
       10.16        23.51        15.22        24.99        31.30         7.40 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       72.10        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 
      110.50        38.20        43.73        69.30        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       13.55        18.12         2.60        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       32.75        29.23        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        12.36        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        36.36        28.87        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       14.07        28.21        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       21.07        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       17.03         3.81        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.16              0.03 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           165.76            282.90 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           21.205            29.080 
[1] "0.2 - 165.8 (21.2)" "0.0 - 282.9 (29.1)"
[1] "hr=" "1.5"
D55V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  7Q LOSS MUTATED         7       11        1        1        41        27
  7Q LOSS WILD-TYPE      82       74        5        5       312       225
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           1         20          4          4        1
  7Q LOSS WILD-TYPE         1        134         25         61       19
                   vv
clus                STAGE TIS STAGE X
  7Q LOSS MUTATED           0       2
  7Q LOSS WILD-TYPE         1      11
D55V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  7                82
  STAGE IA                11                74
  STAGE IB                 1                 5
  STAGE II                 1                 5
  STAGE IIA               41               312
  STAGE IIB               27               225
  STAGE III                1                 1
  STAGE IIIA              20               134
  STAGE IIIB               4                25
  STAGE IIIC               4                61
  STAGE IV                 1                19
  STAGE TIS                0                 1
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED    25  79  12   4
  7Q LOSS WILD-TYPE 251 545 124  36
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1              25               251
  T2              79               545
  T3              12               124
  T4               4                36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  7Q LOSS MUTATED    58  35  18   7
  7Q LOSS WILD-TYPE 449 323 101  70
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0              58               449
  N1              35               323
  N2              18               101
  N3               7                70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED   106   1
  7Q LOSS WILD-TYPE 783  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    106    1
  7Q LOSS WILD-TYPE  783   21
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0             106               783
  1               1                21
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED   118   2
  7Q LOSS WILD-TYPE 950  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED    118    2
  7Q LOSS WILD-TYPE  950   10
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE             118               950
  MALE                 2                10
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED    42  63
  7Q LOSS WILD-TYPE 387 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     42   63
  7Q LOSS WILD-TYPE  387  455
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO               42               387
  YES              63               455
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  7Q LOSS MUTATED                            0                           100
  7Q LOSS WILD-TYPE                          1                           670
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  7Q LOSS MUTATED                               11                   0
  7Q LOSS WILD-TYPE                            189                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  7Q LOSS MUTATED                       2                                3
  7Q LOSS WILD-TYPE                     7                               26
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  7Q LOSS MUTATED                    0              4
  7Q LOSS WILD-TYPE                 17             43
D55V9, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                100               670
  INFILTRATING LOBULAR CARCINOMA                11               189
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          2                 7
  MIXED HISTOLOGY (PLEASE SPECIFY)               3                26
  MUCINOUS CARCINOMA                             0                17
  OTHER  SPECIFY                                 4                43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     6
  7Q LOSS WILD-TYPE                                1    54
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                          22    73
  7Q LOSS WILD-TYPE                       159   672
D55V11, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          6                54
  BLACK OR AFRICAN AMERICAN                     22               159
  WHITE                                         73               672
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V12, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1  95
  7Q LOSS WILD-TYPE  38 780
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1   95
  7Q LOSS WILD-TYPE   38  780
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                38
  NOT HISPANIC OR LATINO              95               780
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   332  64
  8P LOSS WILD-TYPE 585  83
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              396               668 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               64                83 
$`8P LOSS MUTATED`
TCGA-3C-AALJ TCGA-4H-AAAK TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       42.81        11.44        31.79        39.32        28.01        19.20 
TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y 
       18.02        78.41        73.84        87.25        63.12        36.13 
TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D1 
       99.12       114.81        92.48         5.19       107.93        34.55 
TCGA-A2-A0D4 TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0SX 
       25.22        34.29        31.82        61.94        24.72        50.43 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YT 
       17.52        17.13        49.84        21.67        19.33        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G4 TCGA-A2-A25B TCGA-A2-A25D TCGA-A2-A3XT 
       17.36        60.72        19.56        42.44        18.15        91.07 
TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4S3 TCGA-A7-A0D9 TCGA-A7-A13D 
       29.98        50.37         7.30        21.90        37.45        31.73 
TCGA-A7-A13E TCGA-A7-A26G TCGA-A7-A26J TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SE 
       20.19        23.74        20.61        10.59        11.28        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
       17.92        14.73        12.10        13.02        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       53.06        17.03        19.99        32.05         9.99        10.98 
TCGA-A8-A07S TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A08J 
        7.99         9.99        15.06        36.95        19.96        37.05 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A097 TCGA-A8-A09D 
       31.00        33.01        43.00        33.01        12.00        50.04 
TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A0A7 
       29.98         1.02        25.02         8.98        19.04         0.99 
TCGA-AC-A23H TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A5EH 
        5.72        74.14        33.04        14.99        16.57        16.80 
TCGA-AC-A5XU TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 
       14.96         8.22        20.19         0.33         0.23         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        2.96         1.78         0.16         0.33         0.33         6.44 
TCGA-AN-A0FS TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        6.90         0.33         0.33         5.36         0.33        12.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        0.33         0.33         0.33        66.77        81.63        95.70 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       29.13        32.78        21.40        52.18        26.04        37.48 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL 
       53.03        21.53        50.70        76.77        26.24        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A126 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A1KR 
       71.80       115.27       108.72        64.04        41.62        70.39 
TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AR-A0TP TCGA-AR-A0TS 
       17.79       130.09         5.65        15.62       140.55        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 
      109.02        75.22        98.93        64.83        55.86       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AM TCGA-AR-A1AP 
       83.87       134.14       101.00       103.86        98.33        93.90 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       17.23        37.81        86.53        86.43       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A2LE 
       94.22        77.69       105.30        98.66        89.00       166.42 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IG TCGA-B6-A0IJ 
       10.59        77.62       143.38        12.13       146.50       233.62 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0RU 
       18.77       127.33       140.88        68.45       100.70       282.90 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0X5 TCGA-B6-A0X7 
       97.48       188.68        18.35       113.79        68.94        58.88 
TCGA-B6-A1KN TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
      139.17        68.12        18.84        71.15        59.84        25.55 
TCGA-BH-A0B2 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR 
       40.83        81.63        84.13        74.89        75.48        76.60 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DL TCGA-BH-A0E6 
       49.94        41.75        90.97        23.44        78.28         9.63 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H7 TCGA-BH-A0HK TCGA-BH-A0HW 
       24.49        31.00        24.43        23.08         5.85        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18F 
       27.25        50.79        23.93        42.35        23.05        32.91 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18S TCGA-BH-A18T 
       35.93        20.12        90.84        37.74        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       51.39        51.16        67.50        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FH TCGA-BH-A1FN TCGA-BH-A1FU 
       31.53        24.62        33.17        36.92        72.07        72.07 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42V TCGA-BH-A8FZ 
       28.14        38.60        57.83       130.16        20.88        18.87 
TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12Z TCGA-C8-A131 
        9.44        11.77        11.77        11.77        12.56        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HG TCGA-C8-A1HI 
        1.87        12.59         4.11         4.08        11.34        11.28 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26W 
       12.03        10.42        12.33        12.95        12.33        12.53 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR 
        9.50        24.56        14.43        12.95        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A143 TCGA-D8-A145 
       19.46        56.81        20.88        13.25        14.17        13.48 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ 
       14.17        17.49        15.78        18.15        53.00        20.09 
TCGA-D8-A1JK TCGA-D8-A1JT TCGA-D8-A1X8 TCGA-D8-A1XD TCGA-D8-A1XJ TCGA-D8-A1XM 
       20.12        13.32        25.74        17.16        21.80        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A27F TCGA-D8-A27H 
       16.41        16.31        15.52        14.24        16.04        13.05 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A73U 
       16.41        13.48        10.09        12.26        18.51        16.18 
TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14S 
       43.00        27.52        40.41        40.11        47.15        33.17 
TCGA-E2-A14T TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 
       75.98        34.26        32.02        31.96        18.51        63.62 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15H TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15R 
       23.34        22.82        12.92        53.92         9.04        56.94 
TCGA-E2-A1B0 TCGA-E2-A1B5 TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       53.62        32.35        77.65        37.41        70.36        33.73 
TCGA-E2-A1II TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LE 
       33.70        60.99        54.18        60.36        73.64        28.90 
TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A574 
       50.07       102.61         8.75        43.04         8.28        38.76 
TCGA-E2-A9RU TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH 
       17.69        34.16        36.20        41.62        35.24        18.94 
TCGA-E9-A1NI TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
        9.86         3.02        48.23        46.65         6.58        46.59 
TCGA-E9-A226 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A244 
       34.45        37.74        39.09        41.03        41.72         0.69 
TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A54Y TCGA-EW-A1IX TCGA-EW-A1OV TCGA-EW-A1OW 
        1.94        30.18        23.84        39.72        25.94        22.82 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PE 
       29.85        40.41        52.96         7.86        18.90        10.52 
TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3U0 
       14.43        19.96        55.00        52.73        25.91        17.49 
TCGA-EW-A424 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       23.51        24.99        33.21       109.87        59.57       216.76 
TCGA-GM-A3NW TCGA-GM-A3XL TCGA-GM-A5PV TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
      110.50        69.30        13.55        62.47        11.84        11.57 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YM 
        7.10        13.28        24.95        32.75        25.05        15.32 
TCGA-LL-A5YN TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-OL-A5RW 
       14.70        16.08        12.36        19.59        17.49        36.36 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66P TCGA-PE-A5DC 
       24.72        22.32        20.38        65.62        14.07        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZH TCGA-S3-AA14 TCGA-S3-AA17 TCGA-UL-AAZ6 
       64.21        86.96        21.07        17.39        13.94        17.03 
TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
        3.81        66.84        29.03        15.35        16.04       107.05 

$`8P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14       131.67        40.14        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04R 
       20.88        13.68         7.96        18.21       143.15       121.94 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CQ TCGA-A2-A0CR 
      101.98        55.43       136.73        24.79        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
       77.19        75.25        98.99        56.81        67.33        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       61.58       101.72        89.36        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       74.40        72.00        35.05        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 
       27.12        44.88        44.28         8.38        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       21.90        49.48        18.61        48.46        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.20        16.47        52.47       107.70 
TCGA-A2-A25C TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       17.19       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RX 
       32.75        56.28        47.31        35.93        50.83        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        26.96        21.14        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       34.29        35.47        30.61        35.67        33.11        29.79 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       25.15        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       21.73        22.32        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        14.93        13.74        14.50        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06U 
       10.29         9.37        10.42         8.75         1.02        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00        26.01         1.02        53.98         9.01        43.00 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07R TCGA-A8-A07U 
       18.97        18.97        14.01        12.00         8.98        24.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       45.07        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z 
       12.00         9.99        31.00         0.99       112.08        40.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B 
       30.97        17.95        41.98         9.99         9.99        12.00 
TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09V TCGA-A8-A09W 
        1.02        49.05        45.07        33.07        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 
       14.01        12.00        19.04        13.02        21.04        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       17.03        38.04         0.95        22.95        73.91         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       87.12        26.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3W6 
       16.31        14.83        22.19        24.13        25.05        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XS 
       15.48        23.24        24.79        29.26        14.53        19.33 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       11.44        13.71        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        1.68         0.03         1.12         1.32         2.30         0.33 
TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        0.33         1.71         9.96         7.36         7.46         0.33 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FT 
        5.65         7.96         7.00         7.59         7.17         7.04 
TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XV 
        0.36         0.33         0.33         0.30         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        80.28        61.35        68.75        47.87        58.95 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JI 
       20.32        22.36        50.86        72.00        65.10        50.24 
TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       62.04        99.25       106.78       108.03        90.58        98.27 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        48.36        40.57        14.73        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
        0.53        24.79        26.93        32.52         2.56        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U4 
       19.20        98.33         5.26       107.24        65.36       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
      125.16       108.36        97.68        96.00        86.07        99.32 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       94.29        61.28        33.73       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24W 
        2.76       104.28       112.77        97.84       105.27        32.58 
TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.76        99.62        93.30        85.64        71.05        93.83 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH 
      281.29       275.87       129.57        50.70        65.72       112.37 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       165.76       129.07       255.68       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WV TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
       89.46       157.41        79.63        21.47       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
      245.10        28.27        43.59       101.52        73.51       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AU 
       37.87         7.07        85.35        70.16       103.63        62.93 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       20.45        63.09        81.44        39.55        39.16        70.22 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       21.70        61.68        72.23        74.14        53.95        45.57 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       77.95        49.05        44.02        89.06        45.83        77.98 
TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       38.01        29.98        13.91        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0GY 
       15.68        14.30        44.81        46.19        32.58        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       10.78        15.16        37.78        53.26        24.56        41.00 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       52.96        26.50        20.38         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18L 
       12.89         5.59        24.95        44.81         4.90        26.66 
TCGA-BH-A18M TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A1EO TCGA-BH-A1ES 
       72.56        30.28        55.63        37.55        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1F6 
       82.85        42.28        12.00        49.58        89.16        97.48 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL 
      120.62       114.15        74.73       122.89        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
       45.63       144.59        26.14        83.31        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       20.12        10.52       109.28        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8G0 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12Q 
        5.26         9.70        21.76        11.93        12.66        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 
       12.66        12.66        12.66        12.66        48.53         3.16 
TCGA-C8-A135 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HJ TCGA-C8-A26V TCGA-C8-A26X 
       12.92        12.33        10.92         0.16        20.25        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M7 
       12.95         8.28         9.67         9.53         0.03        33.99 
TCGA-C8-A8HP TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA 
       13.02        20.58        13.97        21.14        19.20        16.50 
TCGA-D8-A1JB TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JL 
       55.50        18.90        12.03        14.01        18.97        20.09 
TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X5 
       19.40        20.38        21.01        12.20        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       17.79        16.73        23.90        27.58        18.15        12.39 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR 
       15.22        14.73        14.50        19.92        55.30        15.85 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y1 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K 
        9.93        14.14        17.42        13.45        14.43        48.03 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A4Z1 
        4.80         1.61        13.08        12.53        33.37        21.67 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10B TCGA-E2-A10E 
       12.66        25.22        34.42        46.59        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14U 
       28.87        44.68        40.96        38.24        38.60        43.33 
TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       69.34        69.96        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       14.79        25.05        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15S 
       55.63        20.58        11.05        50.79        19.56        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       51.39        76.57        87.22        33.01        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU 
       37.25        28.44        59.18         3.88        22.19        11.08 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH TCGA-E2-A2P5 TCGA-E2-A2P6 
       19.66        24.59        75.81       106.75        26.99        34.55 
TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 
       43.56        30.61        34.92        34.29        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG 
       36.82        22.29        36.56        39.55        35.77        25.84 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R6 
       24.82        28.27        34.95         2.56         6.12        11.15 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A1RI 
       45.01        32.09        40.24         1.12        21.27        47.64 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       32.05        42.25        38.37        40.73        40.50        20.12 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       38.99         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL 
       38.07        32.91        30.44        23.90        26.70         0.79 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ 
       25.81        26.40        27.85        12.20         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX 
       18.90        13.25        16.57        15.68        28.77        29.95 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        29.82        23.11        18.48        30.08 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PG TCGA-EW-A2FW TCGA-EW-A3E8 
       19.99         6.15        13.94        34.55        22.09        34.03 
TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2DB 
       10.16        15.22        16.77        31.30         7.40        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       83.34        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62        85.35        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PX TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A74U 
       66.38        72.03        18.12         2.60        21.24        13.22 
TCGA-LD-A9QF TCGA-LL-A442 TCGA-LL-A5YL TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       10.62        29.23        17.06        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LQ-A4E4 
        2.63        15.68         7.46        14.50        19.53        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66K 
       40.08        34.92        28.87        26.70        23.47        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        26.04        17.36        28.21        19.73        40.11 
TCGA-OL-A97C TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
        8.91         0.16         0.26         9.93        18.81        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-W8-A86G 
       20.68        19.27        13.84        18.87        17.26        11.41 
TCGA-WT-AB41 TCGA-Z7-A8R5 
       52.96       108.07 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.16              0.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           282.90            281.29 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           26.745            28.240 
[1] "0.2 - 282.9 (26.7)" "0.0 - 281.3 (28.2)"
[1] "hr=" "1.3"
D56V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8P LOSS MUTATED        32       31        2        1       132        94
  8P LOSS WILD-TYPE      57       54        4        5       221       158
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED           0         61          9         24        7
  8P LOSS WILD-TYPE         2         93         20         41       13
                   vv
clus                STAGE TIS STAGE X
  8P LOSS MUTATED           0       5
  8P LOSS WILD-TYPE         1       8
D56V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 32                57
  STAGE IA                31                54
  STAGE IB                 2                 4
  STAGE II                 1                 5
  STAGE IIA              132               221
  STAGE IIB               94               158
  STAGE III                0                 2
  STAGE IIIA              61                93
  STAGE IIIB               9                20
  STAGE IIIC              24                41
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED   103 240  40  16
  8P LOSS WILD-TYPE 173 384  96  24
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1             103               173
  T2             240               384
  T3              40                96
  T4              16                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8P LOSS MUTATED   186 127  52  27
  8P LOSS WILD-TYPE 321 231  67  50
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0             186               321
  N1             127               231
  N2              52                67
  N3              27                50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   338   7
  8P LOSS WILD-TYPE 551  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    338    7
  8P LOSS WILD-TYPE  551   15
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             338               551
  1               7                15
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   396   3
  8P LOSS WILD-TYPE 672   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    396    3
  8P LOSS WILD-TYPE  672    9
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE             396               672
  MALE                 3                 9
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   163 196
  8P LOSS WILD-TYPE 266 322
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    163  196
  8P LOSS WILD-TYPE  266  322
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              163               266
  YES             196               322
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8P LOSS MUTATED                            1                           316
  8P LOSS WILD-TYPE                          0                           454
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8P LOSS MUTATED                               50                   2
  8P LOSS WILD-TYPE                            150                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8P LOSS MUTATED                       1                                7
  8P LOSS WILD-TYPE                     8                               22
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8P LOSS MUTATED                    3             18
  8P LOSS WILD-TYPE                 14             29
D56V9, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     1                 0
  INFILTRATING DUCTAL CARCINOMA                316               454
  INFILTRATING LOBULAR CARCINOMA                50               150
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               7                22
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                18                29
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  1    31
  8P LOSS WILD-TYPE                                0    29
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          73   260
  8P LOSS WILD-TYPE                       108   485
D56V11, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 0
  ASIAN                                         31                29
  BLACK OR AFRICAN AMERICAN                     73               108
  WHITE                                        260               485
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V12, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    12 331
  8P LOSS WILD-TYPE  27 544
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12  331
  8P LOSS WILD-TYPE   27  544
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  12                27
  NOT HISPANIC OR LATINO             331               544
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    79  14
  8Q LOSS WILD-TYPE 838 133
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               93               971 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               14               133 
$`8Q LOSS MUTATED`
TCGA-3C-AALJ TCGA-A1-A0SO TCGA-A2-A0CU TCGA-A2-A3XZ TCGA-A7-A0D9 TCGA-A7-A13E 
       42.81        28.01         5.19        50.37        37.45        20.19 
TCGA-A7-A4SF TCGA-A8-A07L TCGA-A8-A097 TCGA-A8-A09D TCGA-AC-A2FO TCGA-AC-A3W5 
       17.92        32.05        12.00        50.04        74.14        16.57 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0FD TCGA-AN-A0XO 
       16.80        14.96         0.23         2.96         6.44        12.33 
TCGA-AO-A03P TCGA-AO-A0J2 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JL TCGA-AO-A0JM 
       95.70        32.78        53.03        21.53        55.33        71.80 
TCGA-AO-A124 TCGA-AQ-A0Y5 TCGA-AR-A0TY TCGA-AR-A0U3 TCGA-AR-A24H TCGA-AR-A24K 
      115.27         5.65        55.86       134.14       160.90        50.89 
TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RS TCGA-B6-A0WS TCGA-B6-A0X5 
       18.77       140.88        68.45       100.70        97.48        68.94 
TCGA-B6-A408 TCGA-BH-A0B7 TCGA-BH-A0BR TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0EB 
       68.12        84.13        76.60        90.97        23.44        24.49 
TCGA-BH-A0EE TCGA-BH-A0W3 TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1F8 
       31.00        23.93        66.05         7.36        67.50        24.62 
TCGA-BH-A1FD TCGA-C8-A12P TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
       33.17        11.77         1.87        12.59         4.11         4.08 
TCGA-C8-A1HI TCGA-C8-A1HL TCGA-C8-A26W TCGA-C8-A8HQ TCGA-D8-A140 TCGA-D8-A145 
       11.28        10.42        12.53        12.49        13.25        13.48 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A14V 
       14.17        17.49        12.26        18.51        16.18        34.26 
TCGA-E2-A15K TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A1LG TCGA-E2-A1LL 
        9.04        70.36        33.73        73.64        50.07        43.04 
TCGA-E9-A1N8 TCGA-E9-A1NH TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A22D TCGA-E9-A244 
       34.16        18.94         3.02        48.23        41.03         0.69 
TCGA-EW-A1PE TCGA-EW-A3U0 TCGA-EW-A424 TCGA-LL-A440 TCGA-LL-A8F5 TCGA-OL-A5RW 
       10.52        17.49        23.51        24.95        19.59        36.36 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66P TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZH 
       22.32        20.38        14.07        64.21        86.96        21.07 
TCGA-S3-AA14 TCGA-WT-AB44 TCGA-XX-A899 
       17.39        29.03        15.35 

$`8Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        77.19        75.25        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW 
       39.65        33.93        91.07        29.98        32.75        56.28 
TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       47.31        35.93        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       34.29        35.47        30.61        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       31.73        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.74        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        14.50        21.17        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       13.02        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 
       31.00        26.01         1.02        17.03        53.98         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       43.00        19.99        18.97        18.97        14.01        12.00 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L 
       28.96        33.01        19.96        12.00        37.05         9.99 
TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       31.00        31.00         0.99        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
        9.99        12.00         1.02        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
        0.99        27.02        17.03        38.04         0.95        22.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       73.91         5.72         1.48        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        26.04        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 
       22.19        24.13        25.05        14.99        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V 
       23.24        24.79        29.26        14.53        19.33        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
        8.22         0.03        20.19         1.12         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.33         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        9.96         7.36         7.46         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         5.65         7.96         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.36         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V 
       66.77        81.63        68.75        47.87        58.95        29.13 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       21.40        52.18        26.04        37.48        20.32        22.36 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       50.24        62.04        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79        26.93       130.09        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
        2.56        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ 
       84.10       109.02        75.22        98.93        64.83       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       65.36       133.22        83.87       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       93.90        99.32        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.53        86.43        33.73        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       77.69       105.30        32.58        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        12.13       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
      129.57        50.70        65.72       146.50       112.37       233.62 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH 
      127.33        84.59       165.76       129.07       255.68       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WT TCGA-B6-A0WV 
      140.48        89.46       282.90       157.41       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       18.35        21.47       113.79       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN 
       28.27        58.88        43.59       101.52        73.51       139.17 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 
      170.17        37.87         7.07        85.35        70.16        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        62.93        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 
       63.09        81.44        40.83        39.55        39.16        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       81.63        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       61.51        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       74.14        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH 
       41.75        44.02        89.06        45.83        77.98        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       29.98        13.91        78.28        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI 
       24.56        23.08        41.00        52.96        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW 
        5.85         2.50        13.61        36.85        12.89        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25        50.79         5.59        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        51.16        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        97.48       120.62       114.15        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 
       72.07        28.14        26.14        38.60        83.31        57.83 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
       20.88        18.64        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N 
       18.87        21.76         9.44        11.93        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       12.66        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A1HE 
       48.53        12.56         3.16        13.51        12.92        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       10.92        11.34         0.16        12.03        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.36        12.95         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 
        9.53         0.03         9.50        24.56        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       12.95        13.02        13.41        19.46        56.81        20.88 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1JA 
       20.58        13.97        14.17        21.14        19.20        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       55.50        15.78        18.15        18.90        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       14.01        18.97        20.09        20.12        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB 
       17.79        16.73        25.74        23.90        27.58        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.80        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS 
       19.92        17.69        55.30        16.41        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ 
       16.64        12.99        15.16        43.04        16.54        15.32 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 
        4.80         1.61        10.09        13.08        12.53        33.37 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 
       21.67        12.66        25.22        43.00        34.42        27.52 
TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       46.59        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       47.15        44.68        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z 
       75.98        43.33        32.02        31.96        69.34        18.51 
TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       63.62        69.96        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       14.79        25.05        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L 
       21.63        18.21        12.92        55.63        53.92        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        50.79        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       76.57        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ 
       16.47        37.25        77.65        37.41        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       60.36        19.66        24.59        75.81        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z 
      102.61         8.75        26.99        34.55        43.56         8.28 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        38.76        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       32.88        36.82        22.29        36.20        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       41.62        35.77        35.24        25.84         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1RA 
       28.27        34.95         2.56         6.12        11.15        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        40.24         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 
       39.09        38.37        41.72        40.73        40.50        20.12 
TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS 
       38.99         1.94         7.13        24.56        12.33        29.72 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.84        26.70         0.79        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       16.57        15.68        28.77        25.94        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.85        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
        6.15        13.94        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A6S9 
       52.73        25.91        22.09        34.03        10.16        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.57        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       32.75        29.23        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       14.47        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
        7.46        14.50        19.53        12.36        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66I 
       40.08        34.92        28.87        24.72        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A6VO 
       65.62        41.92        42.77        26.04        17.36        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LX TCGA-PL-A8LY 
       19.73        40.11         8.91        47.01         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.81        18.48        20.68        19.27        13.84 
TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       18.87        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       11.41        52.96        16.04       108.07       107.05 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.23              0.03 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            160.9             282.9 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            23.93             28.27 
[1] "0.2 - 160.9 (23.9)" "0.0 - 282.9 (28.3)"
[1] "hr=" "1.2"
D57V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  8Q LOSS MUTATED         6        7        0        0        28        30
  8Q LOSS WILD-TYPE      83       78        6        6       325       222
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0         13          3          5        0
  8Q LOSS WILD-TYPE         2        141         26         60       20
                   vv
clus                STAGE TIS STAGE X
  8Q LOSS MUTATED           0       1
  8Q LOSS WILD-TYPE         1      12
D57V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  6                83
  STAGE IA                 7                78
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               28               325
  STAGE IIB               30               222
  STAGE III                0                 2
  STAGE IIIA              13               141
  STAGE IIIB               3                26
  STAGE IIIC               5                60
  STAGE IV                 0                20
  STAGE TIS                0                 1
  STAGE X                  1                12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED    19  60  11   3
  8Q LOSS WILD-TYPE 257 564 125  37
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              19               257
  T2              60               564
  T3              11               125
  T4               3                37
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  8Q LOSS MUTATED    40  37   9   5
  8Q LOSS WILD-TYPE 467 321 110  72
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              40               467
  N1              37               321
  N2               9               110
  N3               5                72
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    74   0
  8Q LOSS WILD-TYPE 815  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     74    0
  8Q LOSS WILD-TYPE  815   22
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              74               815
  1               0                22
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    93   0
  8Q LOSS WILD-TYPE 975  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     93    0
  8Q LOSS WILD-TYPE  975   12
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              93               975
  MALE                 0                12
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    44  41
  8Q LOSS WILD-TYPE 385 477
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     44   41
  8Q LOSS WILD-TYPE  385  477
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               44               385
  YES              41               477
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  8Q LOSS MUTATED                            0                            72
  8Q LOSS WILD-TYPE                          1                           698
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  8Q LOSS MUTATED                               15                   0
  8Q LOSS WILD-TYPE                            185                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  8Q LOSS MUTATED                       0                                1
  8Q LOSS WILD-TYPE                     9                               28
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  8Q LOSS MUTATED                    3              2
  8Q LOSS WILD-TYPE                 14             45
D57V9, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                 72               698
  INFILTRATING LOBULAR CARCINOMA                15               185
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               1                28
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 2                45
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0    10
  8Q LOSS WILD-TYPE                                1    50
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                          23    56
  8Q LOSS WILD-TYPE                       158   689
D57V11, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         10                50
  BLACK OR AFRICAN AMERICAN                     23               158
  WHITE                                         56               689
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V12, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     4  79
  8Q LOSS WILD-TYPE  35 796
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      4   79
  8Q LOSS WILD-TYPE   35  796
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                35
  NOT HISPANIC OR LATINO              79               796
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   260  49
  9P LOSS WILD-TYPE 657  98
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              309               755 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               49                98 
$`9P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A0CL 
      129.14       131.67        13.68        28.01        18.02        99.12 
TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EU 
       75.25        67.33        80.28        79.76        35.05        34.29 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0T0 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH 
       27.12        44.88        17.52        18.21        21.90        21.67 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25E 
       23.77        17.36        60.72        19.20        42.44       105.34 
TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A7-A0CJ 
       33.93        32.75        47.31        35.93        26.96        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G 
       37.45        35.67        29.79        31.73        25.15        23.74 
TCGA-A7-A2KD TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06O 
       22.32        14.93        13.74        17.92        10.29        13.02 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B 
       17.98        29.03         1.02        17.03         9.01        43.00 
TCGA-A8-A07G TCGA-A8-A07W TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O 
       18.97         9.99        19.96        12.00        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       31.00         0.99        12.00         9.99        12.00         1.02 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R 
       49.05        45.07        33.07         1.02        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09W TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       19.04         0.99        19.04        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       17.03        99.35        90.71        33.04        19.33        14.66 
TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OP 
       16.80        14.96        11.44        13.58         0.03        20.19 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C 
        0.33         0.33         0.23         0.62         2.96         1.78 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FJ TCGA-AN-A0FW 
        9.96         7.36         7.46         0.16         7.96         0.36 
TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N 
        0.33         0.33         0.33         5.59        80.28        66.77 
TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0JA TCGA-AO-A0JD 
       81.63        29.13        52.18        26.04        21.53        72.00 
TCGA-AO-A0JE TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04L 
       76.77        48.36        61.87         0.53        17.79       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
        5.65        15.62        32.91        98.33         5.26        84.10 
TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 
       75.22        55.86       107.24       133.22        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AW 
      107.21       125.16       108.36        93.90        99.32        86.53 
TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V TCGA-AR-A24W 
       50.89        99.78       112.77        97.84       105.30        32.58 
TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL 
       98.66        99.62        93.30        71.05        54.21        66.15 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RO TCGA-B6-A0RP 
       12.13       129.57        18.77       165.76       162.05       102.77 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AU 
       79.63        18.35        85.35        68.12        18.84        62.93 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0BF 
       20.45        63.09        39.55        70.22        84.13        43.53 
TCGA-BH-A0BL TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 
       74.89        75.48        76.60        49.94        77.95        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DQ TCGA-BH-A0E6 TCGA-BH-A0EB 
       90.97        29.98        13.91         3.22         9.63        24.49 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HY 
       30.35        10.78        23.08        41.00        52.96        50.79 
TCGA-BH-A0W3 TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       23.93        90.84        26.66         7.36        51.39        67.50 
TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A1FN 
      113.82        17.69        31.53        24.62        45.63        72.07 
TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-AB28 TCGA-C8-A12L 
       72.07        57.83       130.16        10.52         9.44        11.93 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 
       12.66        11.77        12.66        12.66        12.66         3.16 
TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A26V 
       13.51         4.11        11.34        10.42        12.33        20.25 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A27B TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z 
       12.95         9.67        14.43        13.41        56.81        20.88 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JK 
       14.17        13.48        15.78        53.00        20.09        20.12 
TCGA-D8-A1JM TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XQ 
       19.40        18.58        17.79        27.58        17.16        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27N 
       16.31        16.64        16.54        14.14        16.04         4.80 
TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14T 
       10.09        12.26        46.59        44.68        38.60        75.98 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A15A TCGA-E2-A15E 
       32.02        31.96        18.51        69.96        23.34        20.71 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LH 
       21.63        12.92        14.07        24.59        75.81       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NF 
      102.61         8.75        34.92        36.20        36.56        35.24 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 
        9.86        24.82        34.95         6.12        11.15        48.23 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A22A 
       32.09        40.24        46.65        21.27        46.59        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1J6 TCGA-EW-A1OV 
       38.37        41.72        25.81        26.40        28.77        25.94 
TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1PA 
       22.82        29.85        52.96        29.82        23.11        18.90 
TCGA-EW-A1PD TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 
       13.94        55.00        52.73        25.91        34.03        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 
       23.51        15.22        16.77        24.99        33.21       109.87 
TCGA-GM-A2DB TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A441 TCGA-LL-A5YP 
       79.10         2.60        11.57         7.10        32.75        14.79 
TCGA-LL-A6FQ TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5D6 TCGA-OL-A5RZ TCGA-OL-A66N 
        2.63        19.53        12.36        36.30        22.32        26.04 
TCGA-OL-A66P TCGA-PE-A5DC TCGA-S3-A6ZH 
       14.07        47.01        21.07 

$`9P LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       20.88        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      143.15        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO 
      101.98        55.43        36.13       136.73        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV 
       92.48        88.60       107.93        77.19         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
      107.93        56.81        34.55        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV 
      101.72        89.36       118.45        74.40        72.00        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SX 
       61.94        24.72        63.29        99.19        54.64        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI 
       18.90        20.75        32.55        25.28        50.47        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       18.61        19.33        48.46        31.73        23.47        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C 
       20.25        19.56        16.47        52.47       107.70        17.19 
TCGA-A2-A25D TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU 
       18.15        10.59        36.23        39.65        91.07        29.98 
TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        50.37        50.83         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       35.47        33.11        20.19        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       24.26        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD 
       10.29        11.28        13.41        14.70        11.97        14.50 
TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       21.17        14.73        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X 
       10.42         8.75        13.02         1.02        53.06        31.00 
TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J 
       26.01        53.98        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       32.05         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X 
       28.96        33.01         9.99        33.01       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09D TCGA-A8-A09K TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 
       50.04        29.98        15.02        14.01        12.00        13.02 
TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 
       38.04         0.95        22.95        73.91         5.72         1.48 
TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       73.05        40.57        86.66        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       74.14        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X 
       23.24        24.79        29.26        14.53        19.33        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OQ 
       17.42        18.67        12.26         1.68         8.22         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A04D TCGA-AN-A0AR TCGA-AN-A0AS 
        1.32         2.30         0.33         1.71         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         6.44         5.65         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL 
        6.90         7.04         0.33         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV 
        0.33        12.33         0.30         0.33         0.33         5.33 
TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 
       61.35        95.70        68.75        47.87        58.95        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB 
       21.40        37.48        20.32        22.36        53.03        50.70 
TCGA-AO-A0JC TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL 
       50.86        65.10        26.24        50.24        62.04        55.33 
TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       71.80       115.27        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       90.58        98.27        64.04        57.30        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 
       14.73        82.62        70.39        24.79        26.93        32.52 
TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX 
        2.56        19.20       140.55       109.02        98.93        64.83 
TCGA-AR-A0U0 TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       65.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX 
       86.07        17.23        37.81        94.29        61.28        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P 
       33.73       160.90        94.22       120.33       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 
      104.28       105.27        77.69        98.76        89.00        85.64 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC 
       10.59        77.62       143.38       281.29       275.87        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37       233.62       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
       81.17        78.02       263.28       140.48       100.70        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WY 
      282.90       157.41        97.48       188.68        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX 
       43.59       101.52        73.51       139.17       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AY 
        7.07        70.16       103.63        71.15        59.84        25.55 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA 
       81.44        40.83        39.16        81.63        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO 
       32.02        18.21        61.51        21.70        61.68        72.23 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       74.14        53.95        45.57        49.05        41.75        44.02 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DO 
       45.83        77.98        23.44        38.01        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
        4.41        15.68        14.30        44.81        46.19        32.58 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       31.00        24.43        15.16        37.78        53.26        24.56 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       12.89        51.32        27.25         5.59        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05        32.91         4.90        35.93        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       51.16        91.99        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC 
       49.58        25.81        89.16        97.48       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O 
      144.59        28.14        26.14        38.60        83.31        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
        6.44        20.12       109.28        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A12M 
        9.63         5.26         9.70        18.87        21.76        11.77 
TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 
       11.77        12.66        12.66        48.53        12.56         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI 
       12.59        12.92         4.08        12.33        10.92        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26W TCGA-C8-A26X 
        0.16        12.03        12.95        12.33        12.53        12.36 
TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 
        8.28         9.53         0.03         9.50        24.56        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A140 TCGA-D8-A141 
       12.95        13.02        12.49        19.46        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.97        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       55.50        18.15        18.90        12.03        14.01        18.97 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XF 
       16.73        25.74        23.90        18.15        12.39        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       14.73        21.80        14.50        19.92        17.69        55.30 
TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 
       15.85        12.99        15.16        43.04        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I 
        9.93        14.24        17.42        13.45        13.05        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       48.03        16.41        13.48         1.61        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C 
       43.00        34.42        27.52        40.41        37.51        40.11 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S 
       28.44        28.87        47.15        40.96        38.24        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       43.33        34.26        69.34        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        25.05        22.82        17.29 
TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       18.21        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       50.79        19.56        56.94        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL 
       60.36        73.64        19.66        28.90        50.07        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
       26.99        34.55        43.56         8.28        30.61        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH 
       34.16        39.55        41.62        35.77        25.84        18.94 
TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RD TCGA-E9-A1RF 
       28.27         2.56         3.02        45.01         1.12         6.58 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D 
       47.64        34.45        32.05        42.25        37.74        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       40.73        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
        0.79        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OZ 
       18.90        13.25        16.57        15.68        29.95        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB 
       41.13        39.78        18.48        30.08         7.86        19.99 
TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FW 
        6.15        10.52        14.43        34.55        19.96        22.09 
TCGA-EW-A3U0 TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       17.49        31.30         7.40        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       11.84        21.24        13.22        13.28        10.62        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO 
       29.23        25.05        17.06        15.32        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 
       22.26        16.08        15.68         7.46        14.50        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 
       17.49        27.91        22.39         2.10        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       20.38        26.70        23.47        65.62        41.92        42.77 
TCGA-OL-A66O TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD 
       17.36        28.21        19.73        40.11         8.91        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       86.96         0.16         0.26         9.93        18.81        18.48 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       13.94        17.03         3.81        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.03              0.03 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           165.76            282.90 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            25.81             28.90 
[1] "0.0 - 165.8 (25.8)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.4"
D58V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9P LOSS MUTATED        21       15        0        2       105        64
  9P LOSS WILD-TYPE      68       70        6        4       248       188
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1         54         16         19       10
  9P LOSS WILD-TYPE         1        100         13         46       10
                   vv
clus                STAGE TIS STAGE X
  9P LOSS MUTATED           0       5
  9P LOSS WILD-TYPE         1       8
D58V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 21                68
  STAGE IA                15                70
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA              105               248
  STAGE IIB               64               188
  STAGE III                1                 1
  STAGE IIIA              54               100
  STAGE IIIB              16                13
  STAGE IIIC              19                46
  STAGE IV                10                10
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED    57 202  35  18
  9P LOSS WILD-TYPE 219 422 101  22
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              57               219
  T2             202               422
  T3              35               101
  T4              18                22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9P LOSS MUTATED   142  92  50  24
  9P LOSS WILD-TYPE 365 266  69  53
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0             142               365
  N1              92               266
  N2              50                69
  N3              24                53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   259  11
  9P LOSS WILD-TYPE 630  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    259   11
  9P LOSS WILD-TYPE  630   11
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             259               630
  1              11                11
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   306   7
  9P LOSS WILD-TYPE 762   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    306    7
  9P LOSS WILD-TYPE  762    5
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE             306               762
  MALE                 7                 5
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   125 153
  9P LOSS WILD-TYPE 304 365
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    125  153
  9P LOSS WILD-TYPE  304  365
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO              125               304
  YES             153               365
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9P LOSS MUTATED                            0                           263
  9P LOSS WILD-TYPE                          1                           507
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9P LOSS MUTATED                               25                   3
  9P LOSS WILD-TYPE                            175                   3
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9P LOSS MUTATED                       4                                9
  9P LOSS WILD-TYPE                     5                               20
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9P LOSS MUTATED                    3              6
  9P LOSS WILD-TYPE                 14             41
D58V9, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                263               507
  INFILTRATING LOBULAR CARCINOMA                25               175
  MEDULLARY CARCINOMA                            3                 3
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 6                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0    21
  9P LOSS WILD-TYPE                                1    39
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          57   197
  9P LOSS WILD-TYPE                       124   548
D58V11, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         21                39
  BLACK OR AFRICAN AMERICAN                     57               124
  WHITE                                        197               548
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V12, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    13 245
  9P LOSS WILD-TYPE  26 630
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     13  245
  9P LOSS WILD-TYPE   26  630
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                  13                26
  NOT HISPANIC OR LATINO             245               630
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   240  40
  9Q LOSS WILD-TYPE 677 107
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              280               784 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               40               107 
$`9Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
      129.14        13.68         7.96        28.01        18.02       101.98 
TCGA-A2-A0CL TCGA-A2-A0CT TCGA-A2-A0D0 TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0ET 
       99.12        75.25        67.33        80.28        79.76        35.05 
TCGA-A2-A0EU TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
       34.29        50.43        18.21        21.90        21.67        23.77 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XV TCGA-A2-A3XX 
       17.36        60.72        19.20        33.93        32.75        47.31 
TCGA-A2-A3XY TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA 
       35.93        26.96        21.90        35.31        37.45        35.67 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A2KD TCGA-A7-A4SB 
       29.79        31.73        25.15        23.74        22.32        13.74 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R 
       14.50        17.92        10.29        13.02         1.02        17.98 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07G 
       53.06        31.00         1.02         9.01        43.00        18.97 
TCGA-A8-A07R TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
        8.98        33.01        12.00        37.05        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09I 
        0.99        43.00        12.00        12.00         1.02        45.07 
TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A0A2 TCGA-A8-A0A6 TCGA-A8-A0A7 
       33.07        25.02        19.04        19.04        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A2BM TCGA-AC-A2FF TCGA-AC-A2QH TCGA-AC-A2QI 
       27.02        17.03        99.35        90.71        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A62V TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X 
       14.66        11.44        13.58         0.03        20.19         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0FJ 
        0.33         0.23         1.78         7.36         0.16         7.96 
TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03L 
        0.36         0.33         0.33         0.33         5.59        80.28 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       66.77        81.63        29.13        21.40        52.18        26.04 
TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       72.00        55.33        48.36        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O 
       17.79       130.09         5.65        15.62         2.56        32.91 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 
       98.33        84.10        55.86       107.24        65.36       133.22 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AP TCGA-AR-A1AQ 
      134.14       107.21       125.16       108.36        93.90        99.32 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24N TCGA-AR-A24R TCGA-AR-A24S 
       86.53        33.73        50.89        99.78       112.77        97.84 
TCGA-AR-A24V TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A2LK TCGA-AR-A2LL 
      105.30        98.66        99.62        93.30        54.21        66.15 
TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0RO 
       12.13       129.57       165.76       255.68        81.17       162.05 
TCGA-B6-A0RP TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A1KC TCGA-B6-A401 
      102.77        79.63        18.35        21.47        43.59        85.35 
TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0B3 TCGA-BH-A0B5 
       70.16        68.12        18.84        62.93        39.55        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BV 
       84.13        51.68        43.53        74.89        45.57        49.94 
TCGA-BH-A0C3 TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY 
       89.06         3.22         4.41         9.63        24.49        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0W3 TCGA-BH-A18K 
       10.78        23.08        41.00        52.96        23.93        90.84 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1F8 TCGA-BH-A1FD 
       55.63         7.36        67.50       113.82        24.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FU TCGA-BH-A208 TCGA-BH-A209 
       74.73        45.63        72.07        72.07        57.83       130.16 
TCGA-BH-A42T TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U 
       10.52         9.44        11.93        12.66        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HJ 
       12.66        12.66         3.16        13.51         4.11         0.16 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A27B TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A143 
       12.36         8.28        14.43        13.41        20.88        14.17 
TCGA-D8-A145 TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1X5 
       13.48        15.78        18.97        20.09        20.12        18.58 
TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XY 
       17.79        27.58        17.16        16.41        16.31        16.54 
TCGA-D8-A1Y3 TCGA-D8-A27F TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A109 TCGA-E2-A14O 
       14.14        16.04        10.09        12.26        46.59        44.68 
TCGA-E2-A14R TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 
       38.60        32.02        31.96        18.51        63.62        69.96 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A1AZ TCGA-E2-A1LB 
       25.05        23.34        20.71        21.63        76.57        75.81 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E9-A1N9 TCGA-E9-A1NA 
      106.75       102.61         8.75        34.92        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1R6 TCGA-E9-A1R7 
       39.55         9.86        24.82         6.12        11.15        48.23 
TCGA-E9-A1RC TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A22B TCGA-E9-A5UO TCGA-E9-A5UP 
       40.24        21.27        46.59        38.37        25.81        26.40 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 
       28.77        25.94        22.82        29.85        52.96        23.11 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 
       55.00        52.73        25.91        34.03        17.49        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 
       23.51        15.22        16.77        24.99        33.21       109.87 
TCGA-GM-A2DB TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A5YP 
       79.10         2.60        11.57        32.75        15.32        14.79 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-OL-A5RZ TCGA-OL-A5S0 
        2.63        16.08        19.53        12.36        22.32        20.38 
TCGA-OL-A66N TCGA-OL-A66P TCGA-S3-A6ZF TCGA-S3-A6ZH 
       26.04        14.07        18.81        21.07 

$`9Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       47.24        20.88        31.79        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      143.15        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
       88.60       107.93        77.19         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW 
       89.36       118.45        74.40        72.00        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       49.48        18.61        19.33        48.46        31.73        23.47 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       22.45        20.25        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XZ TCGA-A2-A3Y0 
       39.65        91.07        29.98        56.28        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
        7.30        24.39        21.30        23.21        21.14        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G 
       34.29        35.47        30.61        33.11        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        31.36        24.26        23.80        21.73        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        21.17        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06U 
       11.05         9.37        10.42         8.75        13.02        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       26.01        17.03        53.98        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99        10.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A08S TCGA-A8-A08T 
       38.01        28.96        19.96         9.99        33.01       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A09R 
        9.99        50.04        49.05        29.98         1.02         8.98 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0AD 
       15.02         0.99        14.01        12.00        13.02        38.04 
TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK 
        0.95        22.95        73.91         5.72         1.48        73.05 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO 
       40.57        86.66        60.92        87.12        26.04        74.14 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU 
       24.79        29.26        16.80        14.53        19.33        14.96 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB 
       13.71        17.42        18.67        12.26         1.68         8.22 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        1.12         1.32         2.30         0.33         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        1.71         9.96         7.46         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN 
        7.04         0.33         0.33         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03M 
       12.33         0.30         0.33         0.33         5.33        61.35 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J6 
       95.70        68.75        47.87        58.95        32.78        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC 
       20.32        22.36        53.03        21.53        50.70        50.86 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       76.77        65.10        26.24        50.24        62.04        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27        99.25       108.72       106.78       108.03        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       98.27        64.04        57.30        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP 
       82.62        24.79        26.93        32.52        19.20       140.55 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U2 
        5.26       109.02        75.22        98.93        64.83        83.87 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H 
       17.23        37.81        94.29        61.28        86.43       160.90 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T 
       94.22       120.33       118.59         2.76       104.28       105.27 
TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 
       77.69        32.58        98.76        89.00        85.64        71.05 
TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       93.83       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC 
       10.59        77.62       143.38       281.29       275.87        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       65.72       146.50       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       129.07       140.88        68.45       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU 
       78.02       263.28       140.48       100.70        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF TCGA-B6-A1KI 
      245.10        28.27        68.94        58.88       101.52        73.51 
TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A40B TCGA-B6-A40C 
      139.17       170.17        37.87         7.07       103.63        71.15 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        63.09        81.44        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG 
       39.16        81.63        37.22        32.02        18.21        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 
       53.95        77.95        49.05        41.75        44.02        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        17.26        15.65         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       70.88        16.27        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.58        31.00        24.43        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       24.56        26.50        20.38         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       36.85        12.89        51.32        27.25        50.79         5.59 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       35.93        20.12        26.66        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       37.55        66.05        51.39        51.16        91.99        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FG 
       31.53        89.16        97.48       120.62       114.15       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 
       36.92        63.35        55.00       144.59        28.14        26.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       38.60        83.31        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
       20.88        18.64        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V 
       18.87        21.76        11.77        11.77        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 
       48.53        12.56         1.87        12.59        12.92         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL 
       12.33        10.92        11.34        11.28        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y 
       12.33        12.95        12.33        20.25        12.53        12.95 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 
        9.67         9.53         0.03         9.50        24.56        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       12.95        13.02        12.49        19.46        56.81        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       20.58        13.97        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       16.50        55.50        18.15        18.90        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS 
       14.01        20.09        19.40        20.38        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       13.32        14.70        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       12.39        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV 
       17.69        55.30        15.85        16.64        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       43.04        15.32        15.52         9.93        14.24        17.42 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       13.45        13.05        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         1.61        13.08        12.53        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F 
       27.52        40.41        37.51        40.11        28.44        28.87 
TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       47.15        40.96        38.24        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 
       34.26        69.34        23.24        19.43        21.04        23.87 
TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I 
       14.79        22.82        17.29        18.21        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        14.07        51.39        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF 
       32.35        28.50        16.47        37.25        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       70.36        33.73        33.70        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 
       19.66        24.59        28.90        50.07        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56         8.28        30.61        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       17.69        34.82        32.88        36.82        22.29        34.16 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 
       41.62        35.77        35.24        25.84        18.94        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD 
       34.95         2.56         3.02        45.01        32.09         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       46.65         6.58        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       37.74        39.09        41.03        41.72        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.12         0.69        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       12.33        29.72         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE 
       30.44        23.90        23.84        26.70         0.79        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       16.57        15.68        29.95        40.41        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       29.82        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
        6.15        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FW TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DC 
       22.09        31.30         7.40        59.57       216.76        83.34 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       75.02        70.85        72.10        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO 
       24.95        29.23        25.05        17.06        14.70        14.47 
TCGA-LL-A6FP TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       22.26        15.68         7.46        14.50        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O 
       26.70        23.47        65.62        41.92        42.77        17.36 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z 
       86.96         0.16         0.26         9.93        18.48        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       19.27        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       17.03         3.81        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.03              0.03 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           255.68            282.90 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            25.99             28.44 
[1] "0.0 - 255.7 (26.0)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.1"
D59V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  9Q LOSS MUTATED        19       16        0        2        99        56
  9Q LOSS WILD-TYPE      70       69        6        4       254       196
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1         46         12         19        7
  9Q LOSS WILD-TYPE         1        108         17         46       13
                   vv
clus                STAGE TIS STAGE X
  9Q LOSS MUTATED           0       5
  9Q LOSS WILD-TYPE         1       8
D59V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 19                70
  STAGE IA                16                69
  STAGE IB                 0                 6
  STAGE II                 2                 4
  STAGE IIA               99               254
  STAGE IIB               56               196
  STAGE III                1                 1
  STAGE IIIA              46               108
  STAGE IIIB              12                17
  STAGE IIIC              19                46
  STAGE IV                 7                13
  STAGE TIS                0                 1
  STAGE X                  5                 8
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED    54 176  35  16
  9Q LOSS WILD-TYPE 222 448 101  24
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              54               222
  T2             176               448
  T3              35               101
  T4              16                24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  9Q LOSS MUTATED   135  81  40  23
  9Q LOSS WILD-TYPE 372 277  79  54
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0             135               372
  N1              81               277
  N2              40                79
  N3              23                54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   234   8
  9Q LOSS WILD-TYPE 655  14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    234    8
  9Q LOSS WILD-TYPE  655   14
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             234               655
  1               8                14
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   276   7
  9Q LOSS WILD-TYPE 792   5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    276    7
  9Q LOSS WILD-TYPE  792    5
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE             276               792
  MALE                 7                 5
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   105 142
  9Q LOSS WILD-TYPE 324 376
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    105  142
  9Q LOSS WILD-TYPE  324  376
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO              105               324
  YES             142               376
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  9Q LOSS MUTATED                            0                           235
  9Q LOSS WILD-TYPE                          1                           535
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  9Q LOSS MUTATED                               22                   2
  9Q LOSS WILD-TYPE                            178                   4
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  9Q LOSS MUTATED                       4                                9
  9Q LOSS WILD-TYPE                     5                               20
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  9Q LOSS MUTATED                    3              8
  9Q LOSS WILD-TYPE                 14             39
D59V9, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                235               535
  INFILTRATING LOBULAR CARCINOMA                22               178
  MEDULLARY CARCINOMA                            2                 4
  METAPLASTIC CARCINOMA                          4                 5
  MIXED HISTOLOGY (PLEASE SPECIFY)               9                20
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 8                39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0    18
  9Q LOSS WILD-TYPE                                1    42
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          59   174
  9Q LOSS WILD-TYPE                       122   571
D59V11, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         18                42
  BLACK OR AFRICAN AMERICAN                     59               122
  WHITE                                        174               571
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V12, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    12 220
  9Q LOSS WILD-TYPE  27 655
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     12  220
  9Q LOSS WILD-TYPE   27  655
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  12                27
  NOT HISPANIC OR LATINO             220               655
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED   142  29
  10P LOSS WILD-TYPE 775 118
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               171                893 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                29                118 
$`10P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN 
      129.14       131.67         9.96        13.68        31.79        39.32 
TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       19.20        73.84        77.19        75.25         5.19       107.93 
TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0YE TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A4RW 
       67.33        25.22        18.21        17.36        60.72         7.30 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A13F TCGA-A7-A26E 
       24.39        26.96        21.90        30.61        25.15        31.36 
TCGA-A7-A2KD TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A8-A06R TCGA-A8-A076 TCGA-A8-A07I 
       22.32        13.74        21.17        17.98        53.98        14.01 
TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A097 TCGA-A8-A09B 
       15.06        33.01        12.00         9.99        12.00        12.00 
TCGA-A8-A09R TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23H TCGA-AC-A2QH 
        8.98        21.04        17.03        38.04         5.72        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A4ZE TCGA-AC-A5XU TCGA-AC-A62Y 
       19.33        14.66         6.48        29.26        14.96        17.42 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AT 
       13.58        12.26         0.03         0.62         7.36         0.33 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU 
        0.33         0.36         0.33         0.30         0.33         0.33 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A0JD TCGA-AO-A12F TCGA-AQ-A04J 
       61.35        66.77        58.95        72.00        48.36        26.93 
TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0U2 TCGA-AR-A1AN TCGA-AR-A24L TCGA-AR-A24Q 
        5.26        75.22        83.87        96.00        94.22       104.28 
TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK 
      112.77        32.58        89.00        85.64        93.83        54.21 
TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS 
       39.39        57.27        10.59        18.77        81.17       100.70 
TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A408 TCGA-BH-A0AU TCGA-BH-A0B3 
      282.90        73.51       139.17        68.12        62.93        39.55 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ 
       84.13        37.22        21.70        45.57        49.94        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0EB TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HW 
       44.02        90.97        24.49        41.00        52.96        51.32 
TCGA-BH-A0WA TCGA-BH-A18I TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F8 
       23.05        35.93        51.16        91.99        42.28        24.62 
TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A5IZ 
       36.92        45.63        72.07        26.14        57.83        18.64 
TCGA-C8-A12L TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK 
       11.93         1.87        12.59         4.08        11.28        12.03 
TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Y TCGA-D8-A1J8 TCGA-D8-A1JE 
       12.95        20.25        12.53        12.95        14.17        18.90 
TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1XB TCGA-D8-A1XQ TCGA-D8-A1XV TCGA-D8-A27F 
       53.00        20.12        18.15        16.41        15.16        16.04 
TCGA-D8-A27I TCGA-D8-A27T TCGA-E2-A10C TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A15F 
       14.43        13.08        40.11        75.98        18.51        21.63 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LG TCGA-E2-A56Z 
       56.94        14.07        22.19        60.36        50.07         8.28 
TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RF 
       41.62        35.24         9.86         2.56        40.24         6.58 
TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A54Y 
       21.27        34.45        38.37        41.72         1.94        23.84 
TCGA-E9-A5FK TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A6S9 TCGA-EW-A6SD 
       26.70        23.11         7.86        18.90        15.22        33.21 
TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-OL-A5RW TCGA-OL-A66I 
       69.30         2.60        22.26        12.36        36.36        23.47 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZG 
       86.96         0.16        18.48 

$`10P LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
        7.96        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        98.99        56.81        34.55        33.76        61.58 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       63.29        99.19        54.64        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       17.46        18.90        20.75        32.55        25.28        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.77        23.47        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
       18.15       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       91.07        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
       50.37        50.83        21.30        23.21        21.14        38.30 
TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        34.29        35.47        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F 
       29.79        31.73        20.19        23.61        29.56        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.50        17.92        14.73        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       10.29         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
        1.02        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G 
       17.03         9.01        43.00        19.99        18.97        18.97 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
       24.99         9.99        45.07        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P 
       38.01        28.96        19.96        37.05        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       30.97        17.95        41.98         9.99         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N 
       50.04        49.05        45.07        29.98        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 
       25.02        19.04        15.02         0.99        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C TCGA-AC-A23E 
       19.04        13.02         0.99        27.02         0.95        22.95 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB 
       90.71        60.92        87.12        26.04        74.14        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EH 
       16.57        19.79        15.48        23.24        24.79        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6NO 
       14.53        19.33        11.44        13.71        18.67         1.68 
TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        8.22        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0FD 
        9.96         7.46         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XO 
        7.04         0.33         0.33         0.33         5.36        12.33 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        80.28        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       95.70        68.75        47.87        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 
       70.39         0.53        17.79        24.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP 
       15.62        32.52         2.56        32.91        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       98.33        84.10       109.02        98.93        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH 
      107.24        65.36       133.22       134.14       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO 
      108.36       101.00       103.86        97.68        98.33        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       93.90        99.32        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24M 
       86.53        86.43        33.73       160.90        50.89       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       99.78       118.59         2.76        97.84       105.27        77.69 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 
      105.30        98.76        98.66        99.62        93.30        71.05 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        66.15        63.62        38.17 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        73.35        33.30        38.96        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        12.13       275.87       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       233.62       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       263.28       162.05       102.77       140.48        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      157.41        97.48       188.68        79.63        18.35        21.47 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 
       58.88        43.59       101.52       170.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AV 
       85.35        70.16        18.84       103.63        71.15        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       70.22        81.63        51.68        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       61.51        74.89        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0DD 
       76.60        53.95        77.95        41.75        89.06        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        23.44        38.01        29.98        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       44.81        46.19        32.58        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ 
       26.50        20.38         5.85         2.50        13.61        36.85 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       12.89        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K 
       42.35        44.81        32.91         4.90        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05         7.36        51.39        67.50       113.82        82.85 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE 
       89.16        97.48       120.62       114.15        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
      122.89        63.35        55.00       144.59        72.07        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       38.60        83.31       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       109.28        20.88        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12M TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.77        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 
       12.66        48.53        12.56         3.16        13.51        12.92 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL 
        4.11        12.33        10.92        11.34         0.16        10.42 
TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       12.33        12.33        12.36         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        0.03         9.50        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       13.02        12.49        13.41        19.46        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       13.25        20.58        13.97        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD 
       19.20        17.49        16.50        55.50        15.78        18.15 
TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        14.01        18.97        20.09        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC 
       17.79        16.73        25.74        23.90        27.58        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL 
       17.16        15.22        14.73        21.80        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        55.30        15.85        16.31        16.64        12.99 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       43.04        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L 
       14.14        17.42        13.45        13.05        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         1.61        10.09        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       28.44        28.87        47.15        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        63.62        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1AZ 
       20.58        11.05        50.79        19.56        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        87.22        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18         3.88        60.99        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH 
       73.64        19.66        24.59        75.81        28.90       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      102.61         8.75        43.04        26.99        34.55        43.56 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 
       30.61        34.92        38.76        34.29        17.69        34.82 
TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       32.88        36.82        22.29        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ TCGA-E9-A1R0 
       39.55        35.77        25.84        18.94        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         6.12         3.02        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 
       32.09         1.12        46.65        46.59        47.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H 
       42.25        37.74        39.09        41.03        40.73        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.12         0.69        38.99         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       23.90         0.79        25.81        26.40        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       15.68        28.77        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 
       40.41        41.13        39.78        52.96        29.82        18.48 
TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB 
       34.03        17.49        10.16        23.51        16.77        24.99 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK 
       83.34        75.02        70.85        72.10        85.15        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       43.73        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       11.84        11.57        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
       15.32        14.70        14.47        14.79         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 
       15.68         7.46        14.50        19.53        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       27.91        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       58.62        40.08        34.92        28.87        24.72        22.32 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       20.38        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZH 
       47.01        64.21         0.26         9.93        18.81        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       13.94        17.03         3.81        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.03               0.03 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            282.90             281.29 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             24.39              28.50 
[1] "0.0 - 282.9 (24.4)" "0.0 - 281.3 (28.5)"
[1] "hr=" "1.6"
D60V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10P LOSS MUTATED        11        4        0        1        60        42
  10P LOSS WILD-TYPE      78       81        6        5       293       210
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           1         32          6         12        3
  10P LOSS WILD-TYPE         1        122         23         53       17
                    vv
clus                 STAGE TIS STAGE X
  10P LOSS MUTATED           0       1
  10P LOSS WILD-TYPE         1      12
D60V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                  4                 81
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                60                293
  STAGE IIB                42                210
  STAGE III                 1                  1
  STAGE IIIA               32                122
  STAGE IIIB                6                 23
  STAGE IIIC               12                 53
  STAGE IV                  3                 17
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED    27 115  21   9
  10P LOSS WILD-TYPE 249 509 115  31
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               27                249
  T2              115                509
  T3               21                115
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10P LOSS MUTATED    71  59  26  13
  10P LOSS WILD-TYPE 436 299  93  64
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               71                436
  N1               59                299
  N2               26                 93
  N3               13                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   153   3
  10P LOSS WILD-TYPE 736  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    153    3
  10P LOSS WILD-TYPE  736   19
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0              153                736
  1                3                 19
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED   173   0
  10P LOSS WILD-TYPE 895  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED    173    0
  10P LOSS WILD-TYPE  895   12
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE              173                895
  MALE                  0                 12
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    67  80
  10P LOSS WILD-TYPE 362 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     67   80
  10P LOSS WILD-TYPE  362  438
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                67                362
  YES               80                438
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10P LOSS MUTATED                            0                           129
  10P LOSS WILD-TYPE                          1                           641
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10P LOSS MUTATED                               22                   0
  10P LOSS WILD-TYPE                            178                   6
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10P LOSS MUTATED                       6                                8
  10P LOSS WILD-TYPE                     3                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10P LOSS MUTATED                    1              6
  10P LOSS WILD-TYPE                 16             41
D60V9, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 129                641
  INFILTRATING LOBULAR CARCINOMA                 22                178
  MEDULLARY CARCINOMA                             0                  6
  METAPLASTIC CARCINOMA                           6                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  6                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0    12
  10P LOSS WILD-TYPE                                1    48
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          24   119
  10P LOSS WILD-TYPE                       157   626
D60V11, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          12                 48
  BLACK OR AFRICAN AMERICAN                      24                157
  WHITE                                         119                626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V12, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     4 139
  10P LOSS WILD-TYPE  35 736
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4  139
  10P LOSS WILD-TYPE   35  736
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              139                736
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   191  37
  10Q LOSS WILD-TYPE 726 110
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               228                836 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                110 
$`10Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SN 
      129.14       131.67         9.96        13.68        31.79        39.32 
TCGA-A1-A0SP TCGA-A2-A04T TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CW 
       19.20        73.84        77.19        75.25         5.19       107.93 
TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A0T3 TCGA-A2-A0YE 
       67.33        25.22        27.12        17.52        49.84        18.21 
TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B 
       21.90        18.61        17.36        60.72        19.20        42.44 
TCGA-A2-A3XT TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ 
       91.07         7.30        24.39        26.96        21.90        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A2KD TCGA-A7-A4SB 
       35.67        31.73        25.15        31.36        22.32        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06U 
       14.50        21.17        14.73        10.29        17.98        29.03 
TCGA-A8-A076 TCGA-A8-A07I TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08F TCGA-A8-A08I 
       53.98        14.01         8.98        15.06        33.01        12.00 
TCGA-A8-A08L TCGA-A8-A08X TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09R 
        9.99        43.00        12.00        12.00        49.05         8.98 
TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23H TCGA-AC-A2QH 
       21.04        17.03        38.04         0.95         5.72        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A5XU TCGA-AC-A62Y TCGA-AC-A6IW 
       19.33        14.66         6.48        14.96        17.42        13.58 
TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A0AK TCGA-AN-A0AT TCGA-AN-A0FV TCGA-AN-A0FW 
        0.03         1.12         7.36         0.33         0.33         0.36 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XU TCGA-AN-A0XW TCGA-AO-A03M 
        0.33         0.30         0.33         0.33         5.59        61.35 
TCGA-AO-A03N TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A124 
       66.77        58.95        29.13        21.53        72.00       115.27 
TCGA-AO-A12F TCGA-AQ-A04J TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TV 
       48.36        26.93        32.91        19.20         5.26        75.22 
TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A1AY TCGA-AR-A24L TCGA-AR-A24Q TCGA-AR-A24R 
       98.93        83.87        33.73        94.22       104.28       112.77 
TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL 
       32.58        89.00        85.64        93.83        54.21        66.15 
TCGA-AR-A2LO TCGA-AR-A2LR TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RL 
       39.39        57.27        10.59        18.77       255.68        81.17 
TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A408 
      100.70       282.90        73.51       139.17        70.16        68.12 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B3 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BJ 
       62.93        59.84        39.55        84.13        37.22        21.70 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0EB 
       45.57        49.94        77.95        49.05        44.02        24.49 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0WA TCGA-BH-A18I 
       23.08        41.00        52.96        51.32        23.05        35.93 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1F6 TCGA-BH-A1F8 
        7.36        51.16        91.99        42.28        97.48        24.62 
TCGA-BH-A1FC TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A202 TCGA-BH-A208 
      114.15        36.92        45.63        72.07        26.14        57.83 
TCGA-BH-A5IZ TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A132 TCGA-C8-A134 
       18.64        11.93        11.77        12.66         1.87        12.59 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26W 
        4.08        11.28        12.03        12.95        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A13Y TCGA-D8-A142 TCGA-D8-A1J8 
       12.36        12.95        24.56        56.81        13.97        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1X5 TCGA-D8-A1XB TCGA-D8-A1XF 
       17.49        53.00        20.12        18.58        18.15        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XQ TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A27F TCGA-D8-A27I 
       21.80        16.41        12.99        15.16        16.04        14.43 
TCGA-D8-A27T TCGA-E2-A10C TCGA-E2-A14N TCGA-E2-A14T TCGA-E2-A14Z TCGA-E2-A159 
       13.08        40.11        47.15        75.98        18.51        25.05 
TCGA-E2-A15F TCGA-E2-A15P TCGA-E2-A1IE TCGA-E2-A1IN TCGA-E2-A1L7 TCGA-E2-A1LG 
       21.63        19.56        77.65        22.19        60.36        50.07 
TCGA-E2-A1LH TCGA-E2-A1LK TCGA-E2-A56Z TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A1NF 
      106.75         8.75         8.28        38.76        41.62        35.24 
TCGA-E9-A1NI TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A226 
        9.86         2.56        40.24         6.58        21.27        34.45 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FK 
       38.37        41.72         1.94        29.72        23.84        26.70 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A2FV 
       22.82        40.41        23.11         7.86        18.90        25.91 
TCGA-EW-A6S9 TCGA-EW-A6SD TCGA-GM-A2DC TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YW 
       15.22        33.21        83.34        69.30         2.60        11.84 
TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5RW 
       11.57         7.10        22.26        12.36        19.59        36.36 
TCGA-OL-A66I TCGA-OL-A6VO TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZG TCGA-S3-A6ZH 
       23.47        28.21        86.96         0.16        18.48        21.07 

$`10Q LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
       42.81        40.14        11.44        48.56        48.36         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
        7.96        28.01        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
      121.94        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        98.99        56.81        34.55        33.76        61.58 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
      101.72        89.36        80.28       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 
       17.13         8.38        20.52        17.46        18.90        20.75 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK 
       32.55        25.28        50.47        21.67        49.48        19.33 
TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 
       48.46        31.73        23.77        23.47        22.45        20.25 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU 
      105.34        10.59        36.23        39.65        33.93        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       21.30        23.21        21.14        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G 
       35.47        37.45        33.11        29.79        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 
       11.34        10.59        10.29        11.28        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        14.93        17.92        12.10        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
        9.37        10.42         8.75        13.02        13.02         1.02 
TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 
       53.06        31.00        26.01         1.02        17.03         9.01 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        18.97        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
        9.99        10.98         7.99        24.99         9.99        45.07 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G 
       36.95        13.02         0.99        38.01        28.96        19.96 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
       37.05        31.00        31.00         0.99        33.01       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 
       40.01        33.01        30.97        17.95        41.98         9.99 
TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
        9.99         1.02        50.04        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02        25.02        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23E 
       12.00        19.04        13.02         0.99        27.02        22.95 
TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
       73.91         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A3BB 
       90.71        60.92        87.12        26.04        74.14        32.45 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       16.57        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV 
       16.80        14.53        19.33        11.44        13.71        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS 
       12.26         1.68         8.22        20.19         1.32         2.30 
TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A 
        0.33         0.33         0.23         0.33         0.62         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR 
        1.78         1.71         9.96         7.46         0.16         0.33 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        7.17         6.90         7.04         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XV TCGA-AO-A03L 
        5.36        12.33         0.33         0.33         5.33        80.28 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A0J2 TCGA-AO-A0J3 
       81.63        95.70        68.75        47.87        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.70        50.86        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        55.33        71.80        99.25       108.72       106.78 
TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G 
      108.03        90.58        98.27        64.04        57.30        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       17.79        24.79       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TX 
        2.56       140.55        98.33        84.10       109.02        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 
       55.86       107.24        65.36       133.22       134.14       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      125.16       108.36       101.00       103.86        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
       96.00        86.07        93.90        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       94.29        61.28        86.53        86.43       160.90        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T 
      120.33        99.78       118.59         2.76        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 
       77.69       105.30        98.76        98.66        99.62        93.30 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN 
       71.05       166.42        20.25        86.53        63.62        38.17 
TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        73.35        33.30        38.96        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        12.13       275.87       129.57        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      146.50       112.37       233.62       127.33        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      129.07       140.88        68.45       212.25       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV 
      263.28       162.05       102.77       140.48        89.46       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 
      206.86       129.70       245.10        28.27        68.94        58.88 
TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 
       43.59       101.52       170.17        37.87         7.07        85.35 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       18.84       103.63        71.15        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 
       81.44        40.83        39.16        70.22        81.63        51.68 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM 
       32.02        18.21        43.53        61.51        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0C0 
       72.23        75.48        74.14        76.60        53.95        41.75 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH 
       89.06        90.97        45.83        77.98        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       29.98        13.91        78.28        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       31.00        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       53.26        24.56        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX 
       13.61        36.85        12.89        27.25        50.79         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        32.91         4.90 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ES 
       55.63        37.55        66.05        51.39        67.50       113.82 
TCGA-BH-A1ET TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       31.53        89.16       120.62        33.17        74.73       122.89 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A203 
       63.35        55.00       144.59        72.07        28.14        38.60 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       83.31       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28        20.88        23.51         9.63         5.26         9.70 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       18.87        21.76         9.44        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
       12.66        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
        3.16        13.51        12.92         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26Z 
       11.34         0.16        10.42        12.33        12.33         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         9.53         0.03         9.50        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Z 
       12.95        13.02        12.49        13.41        19.46        20.88 
TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        20.58        14.17        13.48        21.14        19.20 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       16.50        55.50        15.78        18.15        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       14.01        18.97        20.09        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58        12.39        17.16        14.73 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS 
       14.50        19.92        17.69        55.30        15.85        16.31 
TCGA-D8-A1XT TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.64        43.04        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K 
       14.24        14.14        17.42        13.45        13.05        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V 
       16.41        13.48         4.80         1.61        10.09        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       25.22        43.00        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       37.51        28.44        28.87        44.68        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        63.62        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       11.05        50.79        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        87.22        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       37.25        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       59.18         3.88        60.99        11.08        54.18        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LI TCGA-E2-A1LL 
       19.66        24.59        75.81        28.90       102.61        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 
       26.99        34.55        43.56        30.61        34.92        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       17.69        34.82        32.88        36.82        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH 
       36.20        36.56        39.55        35.77        25.84        18.94 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       24.82        28.27        34.95         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH 
       48.23        45.01        32.09         1.12        46.65        46.59 
TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22D 
       47.64        32.05        42.25        37.74        39.09        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 
       40.73        40.50        20.12         0.69        38.99         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA 
       24.56        12.33         9.47        38.07        32.91        30.18 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       30.44        23.90         0.79        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        28.77        25.94        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        29.82        18.48        30.08 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 
       10.16        23.51        16.77        24.99        31.30         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
      109.87        59.57       216.76        79.10        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 
       13.55        18.12        62.47        21.24        13.22        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
       15.32        14.70        14.47        14.79         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.68         7.46        14.50        19.53        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 
       40.08        34.92        28.87        24.72        22.32        20.38 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       26.70        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       14.07        19.73        40.11         8.91        47.01        64.21 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        0.26         9.93        18.81        20.68        19.27        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       18.87        17.39        17.26        13.94        17.03         3.81 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A 
       66.84        11.41        52.96        29.03        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.03               0.03 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            282.90             281.29 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             24.44              28.93 
[1] "0.0 - 282.9 (24.4)" "0.0 - 281.3 (28.9)"
[1] "hr=" "1.5"
D61V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  10Q LOSS MUTATED        17        9        1        1        74        54
  10Q LOSS WILD-TYPE      72       76        5        5       279       198
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           1         38          7         20        4
  10Q LOSS WILD-TYPE         1        116         22         45       16
                    vv
clus                 STAGE TIS STAGE X
  10Q LOSS MUTATED           0       2
  10Q LOSS WILD-TYPE         1      11
D61V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  17                 72
  STAGE IA                  9                 76
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                74                279
  STAGE IIB                54                198
  STAGE III                 1                  1
  STAGE IIIA               38                116
  STAGE IIIB                7                 22
  STAGE IIIC               20                 45
  STAGE IV                  4                 16
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    41 146  27  13
  10Q LOSS WILD-TYPE 235 478 109  27
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               41                235
  T2              146                478
  T3               27                109
  T4               13                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  10Q LOSS MUTATED    97  75  32  21
  10Q LOSS WILD-TYPE 410 283  87  56
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               97                410
  N1               75                283
  N2               32                 87
  N3               21                 56
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   199   4
  10Q LOSS WILD-TYPE 690  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    199    4
  10Q LOSS WILD-TYPE  690   18
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              199                690
  1                4                 18
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   228   1
  10Q LOSS WILD-TYPE 840  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    228    1
  10Q LOSS WILD-TYPE  840   11
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE              228                840
  MALE                  1                 11
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    90 109
  10Q LOSS WILD-TYPE 339 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     90  109
  10Q LOSS WILD-TYPE  339  409
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                90                339
  YES              109                409
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  10Q LOSS MUTATED                            0                           178
  10Q LOSS WILD-TYPE                          1                           592
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  10Q LOSS MUTATED                               25                   1
  10Q LOSS WILD-TYPE                            175                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  10Q LOSS MUTATED                       6                                8
  10Q LOSS WILD-TYPE                     3                               21
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  10Q LOSS MUTATED                    1              9
  10Q LOSS WILD-TYPE                 16             38
D61V9, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 178                592
  INFILTRATING LOBULAR CARCINOMA                 25                175
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           6                  3
  MIXED HISTOLOGY (PLEASE SPECIFY)                8                 21
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  9                 38
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0    18
  10Q LOSS WILD-TYPE                                1    42
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          46   144
  10Q LOSS WILD-TYPE                       135   601
D61V11, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          18                 42
  BLACK OR AFRICAN AMERICAN                      46                135
  WHITE                                         144                601
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V12, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     4 189
  10Q LOSS WILD-TYPE  35 686
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4  189
  10Q LOSS WILD-TYPE   35  686
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              189                686
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED   230  40
  11P LOSS WILD-TYPE 687 107
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               270                794 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                40                107 
$`11P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SN TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A0CO 
        9.96        13.68        39.32        18.02        73.84       114.81 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0SX 
       56.81        34.55        79.76        74.40        35.05        50.43 
TCGA-A2-A0T1 TCGA-A2-A0YG TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FX TCGA-A2-A25B 
       17.13        21.90        18.61        23.77        60.72        42.44 
TCGA-A2-A25E TCGA-A2-A3XS TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A7-A0CE TCGA-A7-A0DA 
      105.34        33.93        47.31        50.83        35.31        35.67 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A4SA TCGA-A7-A4SE 
       31.73        20.19        25.15        31.36        14.93        21.17 
TCGA-A7-A56D TCGA-A7-A6VV TCGA-A8-A06O TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A079 
       14.73        10.29        13.02        53.06         1.02         9.01 
TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J 
       43.00        14.01         9.99        33.01        19.96        37.05 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A093 
        9.99        31.00         0.99        33.01        43.00        17.95 
TCGA-A8-A097 TCGA-A8-A09B TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09T TCGA-A8-A0A1 
       12.00        12.00        49.05        45.07        19.04        12.00 
TCGA-A8-A0A2 TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FG 
       19.04        17.03        22.95        73.05        99.35        60.92 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3W5 TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A6IW 
       26.04        33.04        16.57        16.80        14.96        13.58 
TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AL 
       12.26         0.03         1.12         0.23         2.96         7.46 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XS 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XT TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA 
        0.33        61.35        95.70        20.32        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JL TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KS 
       50.70        55.33        57.30        48.36        41.62         0.53 
TCGA-AO-A1KT TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TZ 
       17.79         2.56        32.91       109.02        75.22       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AU 
       65.36        83.87       134.14       107.21       103.86        94.29 
TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24Z TCGA-AR-A2LL 
       86.53       160.90       112.77       105.27        98.66        66.15 
TCGA-AR-A2LO TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IO 
       39.39        12.13        65.72       146.50        18.77       165.76 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A1KF 
      282.90        79.63        18.35        21.47       245.10       101.52 
TCGA-B6-A1KN TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A409 TCGA-B6-A40B TCGA-BH-A0AV 
      139.17         7.07        70.16        18.84       103.63        59.84 
TCGA-BH-A0AY TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL 
       25.55        70.22        81.63        37.22        18.21        74.89 
TCGA-BH-A0BP TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       75.48        49.94        41.75        44.02        89.06        90.97 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0EE TCGA-BH-A0GZ TCGA-BH-A0H0 
       29.98        13.91        78.28        31.00        10.78        15.16 
TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A18L TCGA-BH-A18P 
       23.08        52.96        27.25        50.79        26.66        30.28 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1F2 TCGA-BH-A1F8 
       55.63         7.36        67.50       113.82        31.53        24.62 
TCGA-BH-A1FC TCGA-BH-A203 TCGA-BH-A28Q TCGA-BH-A42T TCGA-C8-A12L TCGA-C8-A12M 
      114.15        38.60         6.44        10.52        11.93        11.77 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A132 TCGA-C8-A135 
       11.77        12.66        12.66        12.66         1.87        12.92 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL 
        4.08        10.92        11.34        11.28        12.03        10.42 
TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A278 TCGA-C8-A8HQ TCGA-D8-A13Z 
       12.95        12.36        12.95         9.50        12.49        20.88 
TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       13.97        13.48        14.17        15.78        18.15        18.90 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1X6 TCGA-D8-A1XJ TCGA-D8-A1XS TCGA-D8-A1XU 
       18.97        20.12        17.79        21.80        16.31        12.99 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A27G TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 
       43.04        15.32        13.45        10.09        12.26        43.00 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14R TCGA-E2-A14X TCGA-E2-A14Z TCGA-E2-A158 
       46.59        40.11        38.60        31.96        18.51        14.79 
TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH 
       25.05        20.71        18.21        37.25        70.36        33.73 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK 
       60.36        73.64        24.59       106.75       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND 
       43.04        34.92        17.69        36.20        36.56        41.62 
TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       35.24        18.94         6.58        21.27        46.59        47.64 
TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A3HO 
       42.25        38.37        41.03        41.72        40.73        38.07 
TCGA-E9-A3QA TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P8 
       30.18        25.81        26.40        40.41        29.82         7.86 
TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-GM-A2DI 
        6.15        14.43        55.00        15.22        16.77        85.15 
TCGA-GM-A2DO TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
       85.35        69.30         7.10        15.32        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5RW 
       22.26        12.36        19.59        27.91        36.30        36.36 
TCGA-OL-A5RZ TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O TCGA-PL-A8LX TCGA-S3-A6ZF 
       22.32        65.62        41.92        17.36         0.16        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-UL-AAZ6 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       18.48        21.07        17.03        16.04       108.07       107.05 

$`11P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        20.88        31.79         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
       18.21       143.15        78.41       121.94        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU 
       92.48        88.60       107.93        77.19        75.25         5.19 
TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 
       98.99       107.93        67.33        33.76        61.58        25.22 
TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES TCGA-A2-A0EU 
      101.72        89.36        80.28       118.45        72.00        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 
       27.12        44.88        44.28        17.52         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       18.21        50.47        21.67        49.48        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       31.73        23.47        17.36        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D 
       19.56        16.47        52.47       107.70        17.19        18.15 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        39.65        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        35.93        50.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG 
       23.21        26.96        21.14        21.90        38.30        34.29 
TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13G 
       35.47        30.61        37.45        33.11        29.79        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J 
       29.56        24.26        23.74        23.80        21.73        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A5ZV 
       14.70        11.97        13.74        14.50        17.92        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P 
       10.72        11.05         9.37        10.42         8.75        13.02 
TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 
        1.02        17.98        29.03        31.00        26.01        17.03 
TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L 
       53.98        19.99        18.97        18.97        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z 
        9.99        10.98         8.98         7.99        24.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       12.00        31.00       112.08        40.01        33.01        30.97 
TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09K 
       41.98         9.99         9.99         1.02        50.04        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09V TCGA-A8-A09W 
       33.07         1.02        25.02         8.98        15.02         0.99 
TCGA-A8-A09X TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD 
       14.01        13.02        21.04         0.99        27.02        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE 
        0.95        73.91         5.72         1.48        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       90.71        87.12        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       14.53        19.33        11.44        13.71        17.42        18.67 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        1.68         8.22        20.19         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.33         0.62         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         0.16         0.33         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FX 
        5.65         7.96         7.00         7.59         7.17         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         5.36         0.33        12.33         0.30         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O 
        0.33         5.33         5.59        80.28        66.77        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0JC TCGA-AO-A0JD 
       52.18        26.04        37.48        22.36        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       76.77        65.10        26.24        50.24        62.04        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A 
      115.27        99.25       108.72       106.78       108.03        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       98.27        64.04        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       70.39        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.52        19.20       140.55        98.33         5.26        84.10 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AI 
       98.93        64.83        55.86       133.22       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      101.00        97.68        98.33        96.00        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A1AY 
       99.32        17.23        37.81        61.28        86.43        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
      104.28        97.84        77.69       105.30        32.58        98.76 
TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       89.00        99.62        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        54.21        63.62        38.17 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       281.29       275.87       129.57        50.70 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ 
      112.37       233.62       127.33        84.59       129.07       140.88 
TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM 
      255.68        68.45       212.25       234.28        81.17        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68       113.79       206.86       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU 
       28.27        68.94        58.88        43.59        73.51       170.17 
TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
       37.87        85.35        68.12        71.15        62.93        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 
       63.09        81.44        40.83        39.55        39.16        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       51.68        32.02        43.53        61.51        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW 
       72.23        74.14        76.60        53.95        45.57        77.95 
TCGA-BH-A0BZ TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DO 
       49.05        45.83        77.98        23.44        38.01        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 
       46.19        32.58        24.49        24.43        30.35        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       53.26        24.56        41.00        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX 
        2.50        13.61        36.85        12.89        51.32         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F 
       23.93        24.95        42.35        44.81        23.05        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N 
        4.90        35.93        20.12        90.84        72.56        37.74 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ET 
       37.55        66.05        51.39        51.16        91.99        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        97.48       120.62        33.17        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
       36.92        63.35        55.00        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 
       72.07        28.14        26.14        83.31        57.83       130.16 
TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 
       10.65        20.12       109.28        20.88        18.64        23.51 
TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 
        9.63         5.26         9.70        18.87        21.76         9.44 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HJ 
        3.16        13.51        12.59         4.11        12.33         0.16 
TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 
       12.33        12.33        20.25        12.53         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         0.03        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 
       13.02        13.41        19.46        56.81        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       14.17        21.14        19.20        17.49        16.50        55.50 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       12.03        53.00        14.01        20.09        20.09        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 
       20.38        21.01        12.20        13.32        14.70        18.58 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       16.73        25.74        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XY 
       55.30        16.41        15.85        16.64        15.16        16.54 
TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F 
       15.52         9.93        14.24        14.14        17.42        16.04 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N 
       13.05        14.43        48.03        16.41        13.48         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
        1.61        13.08        12.53        33.37        18.51        21.67 
TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
       16.18        12.66        25.22        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       37.51        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.24        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        63.62        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H 
       23.87        23.34        22.82        17.29        21.63        12.92 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       19.56        56.94        14.07        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE 
       87.22        33.01        32.35        28.50        16.47        77.65 
TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       37.41        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       60.99        11.08        54.18        19.66        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       50.07        26.99        34.55        43.56         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       38.76        34.29        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ 
       34.16        39.55        35.77        25.84         9.86        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       28.27        34.95         2.56         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22H TCGA-E9-A243 
       34.45        32.05        37.74        39.09        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       29.72         9.47        32.91        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
       26.70         0.79        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       25.94        22.82        29.95        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB 
       52.96        23.11        18.48        30.08        18.90        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV 
       13.94        10.52        34.55        19.96        52.73        25.91 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SB 
       22.09        34.03        17.49        10.16        23.51        24.99 
TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       31.30        33.21         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK 
       79.10        83.34        75.02        70.85        72.10        86.96 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      115.69       106.06       101.62       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.47 
TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        11.57        21.24        13.22        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN 
       24.95        32.75        29.23        25.05        17.06        14.70 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        19.53 
TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       17.49        22.39         2.10        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       40.08        34.92        28.87        24.72        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ 
       23.47        42.77        26.04        14.07        28.21        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        9.93        20.68        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       17.26        13.94         3.81        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 
       29.03        15.35 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.03               0.03 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            282.90             281.29 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            25.925             28.270 
[1] "0.0 - 282.9 (25.9)" "0.0 - 281.3 (28.3)"
[1] "hr=" "1.2"
D62V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11P LOSS MUTATED        20       11        1        1        90        62
  11P LOSS WILD-TYPE      69       74        5        5       263       190
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           0         50         14         18        4
  11P LOSS WILD-TYPE         2        104         15         47       16
                    vv
clus                 STAGE TIS STAGE X
  11P LOSS MUTATED           1       2
  11P LOSS WILD-TYPE         0      11
D62V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 11                 74
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                90                263
  STAGE IIB                62                190
  STAGE III                 0                  2
  STAGE IIIA               50                104
  STAGE IIIB               14                 15
  STAGE IIIC               18                 47
  STAGE IV                  4                 16
  STAGE TIS                 1                  0
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED    58 165  33  18
  11P LOSS WILD-TYPE 218 459 103  22
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               58                218
  T2              165                459
  T3               33                103
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11P LOSS MUTATED   119  88  42  20
  11P LOSS WILD-TYPE 388 270  77  57
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0              119                388
  N1               88                270
  N2               42                 77
  N3               20                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   228   6
  11P LOSS WILD-TYPE 661  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    228    6
  11P LOSS WILD-TYPE  661   16
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0              228                661
  1                6                 16
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   272   3
  11P LOSS WILD-TYPE 796   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    272    3
  11P LOSS WILD-TYPE  796    9
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE              272                796
  MALE                  3                  9
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED   121 128
  11P LOSS WILD-TYPE 308 390
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED    121  128
  11P LOSS WILD-TYPE  308  390
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO               121                308
  YES              128                390
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11P LOSS MUTATED                            0                           209
  11P LOSS WILD-TYPE                          1                           561
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11P LOSS MUTATED                               37                   4
  11P LOSS WILD-TYPE                            163                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11P LOSS MUTATED                       2                               10
  11P LOSS WILD-TYPE                     7                               19
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11P LOSS MUTATED                    3             10
  11P LOSS WILD-TYPE                 14             37
D62V9, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 209                561
  INFILTRATING LOBULAR CARCINOMA                 37                163
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 19
  MUCINOUS CARCINOMA                              3                 14
  OTHER  SPECIFY                                 10                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  1    19
  11P LOSS WILD-TYPE                                0    41
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                          63   163
  11P LOSS WILD-TYPE                       118   582
D62V11, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          19                 41
  BLACK OR AFRICAN AMERICAN                      63                118
  WHITE                                         163                582
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V12, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     4 218
  11P LOSS WILD-TYPE  35 657
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      4  218
  11P LOSS WILD-TYPE   35  657
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              218                657
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED   317  42
  11Q LOSS WILD-TYPE 600 105
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               359                705 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                42                105 
$`11Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALK TCGA-5T-A9QA TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SJ 
      129.14        40.14         9.96        14.37        43.43        13.68 
TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04R TCGA-A2-A04T 
        7.96        39.32        18.21        18.02       121.94        73.84 
TCGA-A2-A04V TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CX 
       63.12       136.73        24.79       114.81        75.25        56.81 
TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0SU 
       25.22        79.76        74.40        35.05        61.94        54.64 
TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC 
       50.43        17.13        49.84        20.52        20.75        32.55 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX 
       50.47        49.48        19.33        23.77        17.36        60.72 
TCGA-A2-A25B TCGA-A2-A25E TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XX 
       42.44       105.34        36.23        39.65        33.93        47.31 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC 
       50.83         7.30        35.31        30.61        35.67        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A3J1 
       31.73        20.19        25.15        29.56        31.36        11.28 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A8-A06O 
       14.93        13.74        14.50        21.17        10.29        13.02 
TCGA-A8-A06T TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07I TCGA-A8-A07W 
       53.06         1.02         9.01        43.00        14.01         9.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A097 TCGA-A8-A09B 
       33.01        43.00        33.01        17.95        12.00        12.00 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09R 
       50.04        49.05        45.07        29.98        33.07         8.98 
TCGA-A8-A09T TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 
       19.04        12.00        19.04        13.02        21.04        27.02 
TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FG 
       17.03         0.95        22.95        73.05        99.35        60.92 
TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3QQ TCGA-AC-A3W5 TCGA-AC-A4ZE 
       26.04        33.04        16.31        24.13        16.57        29.26 
TCGA-AC-A5XU TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A7VC TCGA-AC-A8OQ 
       14.96        18.67        13.58        12.26         0.03         1.12 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AL TCGA-AN-A0FS TCGA-AN-A0FT 
        0.33         0.23         2.96         7.46         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33         0.36         0.33         5.36         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A0J3 
        5.59        80.28        61.35        95.70        47.87        21.40 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A12E 
       20.32        53.03        21.53        26.24        55.33        57.30 
TCGA-AO-A12F TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AQ-A54O 
       48.36         0.53        17.79        15.62         2.56        32.91 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 
      109.02        75.22       107.24        65.36       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AM TCGA-AR-A1AU 
      134.14       107.21       108.36       103.86        98.33        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24R TCGA-AR-A24Z 
       61.28        86.53       160.90        94.22       112.77        98.66 
TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LO TCGA-B6-A0I9 
       89.00        71.05        54.21        66.15        39.39        12.13 
TCGA-B6-A0IB TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0RG TCGA-B6-A0RL 
      129.57       146.50        18.77       127.33        68.45        81.17 
TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X1 TCGA-B6-A0X7 
      282.90        79.63        18.35        21.47       245.10        58.88 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A40B TCGA-BH-A0AU 
      101.52       139.17         7.07        70.16       103.63        62.93 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B5 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BL 
       25.55        63.09        70.22        37.22        18.21        74.89 
TCGA-BH-A0BP TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 
       75.48        49.94        41.75        44.02        89.06        90.97 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0E2 TCGA-BH-A0EE 
       45.83        77.98        13.91        78.28        14.30        31.00 
TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB 
       24.43        10.78        15.16        23.08        52.96        26.50 
TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18L 
       13.61        12.89        27.25        50.79        23.05        26.66 
TCGA-BH-A18P TCGA-BH-A1EN TCGA-BH-A1ES TCGA-BH-A1F2 TCGA-BH-A1F8 TCGA-BH-A28Q 
       30.28        67.50       113.82        31.53        24.62         6.44 
TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U 
       10.52        18.64        11.77        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF 
       12.66        48.53         1.87        12.92         4.08        10.92 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26W 
       11.34        11.28        12.03        10.42        12.95        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A8HQ 
       12.36        12.95         8.28         9.50        24.56        12.49 
TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD 
       20.88        13.97        13.48        14.17        15.78        18.15 
TCGA-D8-A1JE TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1X9 
       18.90        18.97        20.12        17.79        25.74        23.90 
TCGA-D8-A1XF TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A27G 
       15.22        16.31        12.99        15.32        15.52        13.45 
TCGA-D8-A27I TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A109 
       14.43        10.09        12.53        12.26        43.00        46.59 
TCGA-E2-A14O TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A155 
       44.68        38.60        33.17        34.26        31.96        21.04 
TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15K TCGA-E2-A15M 
       14.79        25.05        20.71        18.21         9.04        11.05 
TCGA-E2-A1BD TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1IU TCGA-E2-A1L7 TCGA-E2-A1L8 
       37.25        70.36        33.73        11.08        60.36        73.64 
TCGA-E2-A1LA TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A576 
       24.59         8.75        43.04         8.28        34.92        34.29 
TCGA-E2-A9RU TCGA-E9-A1N5 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NH TCGA-E9-A1QZ 
       17.69        36.82        36.20        36.56        18.94        24.82 
TCGA-E9-A1R2 TCGA-E9-A1R7 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22B 
       34.95        48.23         6.58        21.27        47.64        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A3HO 
       41.03        41.72        40.73        38.99        12.33        38.07 
TCGA-E9-A3QA TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1J2 
       30.18        25.81        26.40        12.20        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1PC 
       16.57        15.68        29.85        40.41        29.82         6.15 
TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A423 TCGA-EW-A424 
       13.94        14.43        55.00        52.73        10.16        23.51 
TCGA-EW-A6SA TCGA-GM-A2D9 TCGA-GM-A2DO TCGA-GM-A3XL TCGA-LD-A7W5 TCGA-LD-A7W6 
       16.77        59.57        85.35        69.30         7.10        13.28 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ 
       15.32        14.47        14.79        22.26        16.08        19.53 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5DA TCGA-OL-A5RW 
       12.36        19.59        27.91         2.10        58.62        36.36 
TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66O 
       24.72        22.32        20.38        65.62        41.92        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-PE-A5DC TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG 
       14.07        28.21        47.01         0.16        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA17 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       21.07        13.94        16.04       108.07       107.05 

$`11Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SB 
      131.67        42.81        11.44        48.56        48.36         8.52 
TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SO 
       48.10        14.27        47.24        20.88        31.79        28.01 
TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A04X 
       19.20       143.15        78.41        87.25       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       36.13        99.12        92.48        88.60       107.93        77.19 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 
        5.19        98.99       107.93        67.33        34.55        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ES 
       61.58       101.72        89.36        80.28       118.45        72.00 
TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV 
       34.29        31.82        24.72        63.29        99.19        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 
       44.88        44.28        17.52         8.38        17.46        18.90 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YL 
       25.28        18.21        21.90        21.67        18.61        48.46 
TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       31.73        23.47        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25F 
       16.47        52.47       107.70        17.19        18.15        10.59 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       91.07        29.98        32.75        56.28        35.93        50.37 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A13G 
       38.30        34.29        35.47        37.45        33.11        23.61 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD 
       24.26        23.74        23.80        21.73        20.61        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.59        10.29        13.41        14.70        11.97 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VW 
       17.92        14.73        12.10        10.72        11.05         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06U 
       10.42         8.75        13.02         1.02        17.98        29.03 
TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07E TCGA-A8-A07F 
       31.00        26.01        17.03        53.98        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
        7.99        24.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08R TCGA-A8-A08T 
        0.99        38.01        28.96        12.00         0.99       112.08 
TCGA-A8-A08Z TCGA-A8-A092 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C 
       40.01        30.97        41.98         9.99         9.99         1.02 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A7 
        1.02        25.02        15.02         0.99        14.01         0.99 
TCGA-A8-A0AD TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE 
       38.04        73.91         5.72         1.48        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       90.71        87.12        74.14        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 
        6.48        14.83        22.19        25.05        14.99        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       15.48        23.24        24.79        16.80        14.53        19.33 
TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP 
       11.44        13.71        17.42         1.68         8.22        20.19 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C 
        1.32         2.30         0.33         0.33         0.62         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.71         9.96         7.36         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP 
        7.17         0.33         0.33         0.33        12.33         0.30 
TCGA-AN-A0XR TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R 
        0.33         0.33         5.33        66.77        81.63        68.75 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        52.18        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF 
       22.36        50.70        50.86        72.00        76.77        65.10 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       50.24        62.04        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12G 
      106.78       108.03        90.58        98.27        64.04        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H 
       40.57        14.73        82.62        61.87        70.39        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP 
       26.93       130.09         5.65        32.52        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY 
       98.33         5.26        84.10        98.93        64.83        55.86 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AL TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      125.16       101.00        97.68        96.00        86.07        93.90 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       99.32        17.23        37.81        86.43        33.73        50.89 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24S 
      120.33        99.78       118.59         2.76       104.28        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
      105.27        77.69       105.30        32.58        98.76        99.62 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       93.30        85.64        93.83       166.42        20.25        86.53 
TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       63.62        38.17        40.54        57.27        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA 
       38.96        10.59        77.62       143.38       281.29       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IN TCGA-B6-A0IO 
       50.70        65.72       112.37       233.62        84.59       165.76 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM 
      129.07       140.88       255.68       212.25       234.28        78.02 
TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT 
      263.28       162.05       102.77       140.48       100.70        89.46 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68       113.79       206.86       129.70 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX 
       28.27        68.94        43.59        73.51       170.17        37.87 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AV TCGA-BH-A0AW 
       85.35        68.12        18.84        71.15        59.84        20.45 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0B7 
       81.44        40.83        39.55        39.16        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BM 
       51.68        32.02        43.53        61.51        21.70        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW 
       72.23        74.14        76.60        53.95        45.57        77.95 
TCGA-BH-A0BZ TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DP 
       49.05        23.44        38.01        29.98        17.26        15.65 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
        3.22         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
        4.41        15.68         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 
       24.49        30.35        37.78        53.26        24.56        41.00 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX 
       20.38         5.85         2.50        36.85        51.32         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G 
       23.93        24.95        42.35        44.81        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18Q 
       35.93        20.12        90.84        72.56        37.74        55.63 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO 
       37.55        66.05         7.36        51.39        51.16        91.99 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       25.81        89.16        97.48       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A2L8 TCGA-BH-A42U 
       83.31        57.83       130.16        10.65        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V 
       21.76         9.44        11.93        11.77        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A137 
       12.66        12.56         3.16        13.51        12.59         4.11 
TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A273 
       12.33         0.16        12.33        12.33        20.25         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.53         0.03        14.43        33.99        12.95        13.02 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 
       13.41        19.46        56.81        13.25        20.58        14.17 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF 
       21.14        19.20        17.49        16.50        55.50        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN 
       53.00        14.01        20.09        20.09        19.40        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X7 
       21.01        12.20        13.32        14.70        18.58        16.73 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XJ 
       27.58        18.15        12.39        17.16        14.73        21.80 
TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XR 
       14.50        19.92        17.69        55.30        16.41        15.85 
TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       16.64        15.16        43.04        16.54         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L 
       14.14        17.42        16.04        13.05        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       13.48         4.80         1.61        13.08        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 
       21.67        16.18        12.66        25.22        34.42        27.52 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N 
       40.41        37.51        40.11        28.44        28.87        47.15 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y 
       40.96        38.24        75.98        43.33        32.02        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 
       18.51        63.62        69.96        23.24        19.43        23.87 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I 
       23.34        22.82        17.29        21.63        12.92        55.63 
TCGA-E2-A15J TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       53.92        20.58        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1IJ 
       28.50        16.47        77.65        37.41        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L6 TCGA-E2-A1L9 
       59.18         3.88        22.19        60.99        54.18        19.66 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 
       75.81        28.90        50.07       106.75       102.61        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N3 TCGA-E9-A1N4 
       34.55        43.56        30.61        38.76        34.82        32.88 
TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       22.29        34.16        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       25.84         9.86        28.27         2.56         6.12         3.02 
TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       11.15        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       40.50        20.12         0.69         1.94         7.13        24.56 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       29.72         9.47        32.91        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.70         0.79        27.85        39.72         8.48        18.21 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 
       28.77        25.94        22.82        29.95        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA 
       52.96        23.11        18.48        30.08         7.86        18.90 
TCGA-EW-A1PB TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FV TCGA-EW-A2FW 
       19.99        10.52        34.55        19.96        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       34.03        17.49        15.22        24.99        31.30        33.21 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
        7.40       109.87       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM 
       70.85        72.10        85.15        86.96       115.69       106.06 
TCGA-GM-A2DN TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
      101.62       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX 
       13.55        18.12         2.60        62.47        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
       21.24        13.22        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       25.05        17.06        14.70         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       14.50        17.49        22.39        36.30        58.52        31.99 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66L 
       40.08        34.92        28.87        26.70        23.47        42.77 
TCGA-OL-A66N TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE 
       26.04        19.73        40.11         8.91        64.21        86.96 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
        0.26         9.93        20.68        19.27        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G 
       17.39        17.26        17.03         3.81        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 
       52.96        29.03        15.35 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.03               0.03 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            282.90             281.29 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             25.05              29.03 
[1] "0.0 - 282.9 (25.1)" "0.0 - 281.3 (29.0)"
[1] "hr=" "1.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  11Q LOSS MUTATED        22       23        2        2       115        91
  11Q LOSS WILD-TYPE      67       62        4        4       238       161
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           1         64         14         20        6
  11Q LOSS WILD-TYPE         1         90         15         45       14
                    vv
clus                 STAGE TIS STAGE X
  11Q LOSS MUTATED           0       4
  11Q LOSS WILD-TYPE         1       9
D63V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  22                 67
  STAGE IA                 23                 62
  STAGE IB                  2                  4
  STAGE II                  2                  4
  STAGE IIA               115                238
  STAGE IIB                91                161
  STAGE III                 1                  1
  STAGE IIIA               64                 90
  STAGE IIIB               14                 15
  STAGE IIIC               20                 45
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   4                  9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED    80 221  45  18
  11Q LOSS WILD-TYPE 196 403  91  22
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               80                196
  T2              221                403
  T3               45                 91
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  11Q LOSS MUTATED   160 120  53  24
  11Q LOSS WILD-TYPE 347 238  66  53
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0              160                347
  N1              120                238
  N2               53                 66
  N3               24                 53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   290   8
  11Q LOSS WILD-TYPE 599  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    290    8
  11Q LOSS WILD-TYPE  599   14
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0              290                599
  1                8                 14
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   358   7
  11Q LOSS WILD-TYPE 710   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    358    7
  11Q LOSS WILD-TYPE  710    5
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE              358                710
  MALE                  7                  5
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED   154 177
  11Q LOSS WILD-TYPE 275 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED    154  177
  11Q LOSS WILD-TYPE  275  341
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO               154                275
  YES              177                341
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  11Q LOSS MUTATED                            0                           261
  11Q LOSS WILD-TYPE                          1                           509
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  11Q LOSS MUTATED                               70                   4
  11Q LOSS WILD-TYPE                            130                   2
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  11Q LOSS MUTATED                       2                               11
  11Q LOSS WILD-TYPE                     7                               18
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  11Q LOSS MUTATED                    4             12
  11Q LOSS WILD-TYPE                 13             35
D63V9, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 261                509
  INFILTRATING LOBULAR CARCINOMA                 70                130
  MEDULLARY CARCINOMA                             4                  2
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)               11                 18
  MUCINOUS CARCINOMA                              4                 13
  OTHER  SPECIFY                                 12                 35
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  1    23
  11Q LOSS WILD-TYPE                                0    37
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                          76   226
  11Q LOSS WILD-TYPE                       105   519
D63V11, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          23                 37
  BLACK OR AFRICAN AMERICAN                      76                105
  WHITE                                         226                519
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V12, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    12 283
  11Q LOSS WILD-TYPE  27 592
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12  283
  11Q LOSS WILD-TYPE   27  592
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              283                592
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED   123  24
  12P LOSS WILD-TYPE 794 123
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
               147                917 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                24                123 
$`12P LOSS MUTATED`
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A2-A0D1 TCGA-A2-A0T0 TCGA-A2-A0T7 TCGA-A2-A0YF 
       20.88        13.68        34.55        17.52        20.75        50.47 
TCGA-A2-A259 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3Y0 
       52.47        42.44        17.19        91.07        47.31        50.83 
TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A26I 
       24.39        26.96        30.61        35.67        31.73        21.73 
TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A07G 
       14.93        17.92        10.29        17.98        53.06        18.97 
TCGA-A8-A08F TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A09I TCGA-A8-A09Q 
       33.01         0.99        43.00        40.01        45.07        25.02 
TCGA-AC-A23H TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3W7 TCGA-AC-A6IV TCGA-AC-A7VB 
        5.72        19.33        14.66        15.48        18.67         8.22 
TCGA-AC-A8OQ TCGA-AN-A0AM TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FV 
        1.12         0.16         6.44         7.00         7.59         0.33 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AO-A03O TCGA-AO-A03T TCGA-AO-A0J4 TCGA-AO-A0JL 
        0.33        12.33        81.63        47.87        52.18        55.33 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AR-A0TR TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A1AI 
      108.03        64.04         5.26       107.24        65.36       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A24M TCGA-AR-A251 TCGA-AR-A252 
      101.00        17.23        50.89       120.33        99.62        93.30 
TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LL TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
       85.64        93.83        66.15       146.50       112.37       233.62 
TCGA-B6-A0IK TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A0RV 
       18.77       255.68       234.28       102.77       282.90       157.41 
TCGA-B6-A1KF TCGA-B6-A1KN TCGA-B6-A409 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B7 
      101.52       139.17        18.84        40.83        39.55        84.13 
TCGA-BH-A0BP TCGA-BH-A0BW TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DQ 
       75.48        77.95        41.75        90.97        23.44         3.22 
TCGA-BH-A0E6 TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A1EN TCGA-BH-A1F6 TCGA-BH-A1FN 
        9.63        31.00        23.08        67.50        97.48        72.07 
TCGA-BH-A1FU TCGA-BH-A208 TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       72.07        57.83        12.66        13.51         1.87        12.59 
TCGA-C8-A1HI TCGA-C8-A26Y TCGA-C8-A27A TCGA-D8-A142 TCGA-D8-A1JE TCGA-D8-A1JG 
       11.28        12.95        24.56        13.97        18.90        53.00 
TCGA-D8-A1X5 TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A27F 
       18.58        14.50        17.69        16.41        16.64        16.04 
TCGA-E2-A10A TCGA-E2-A14Q TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 
       40.41        38.24        18.51        63.62        21.04        25.05 
TCGA-E2-A15E TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LA 
       20.71        32.35        37.25        60.99        60.36        24.59 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1NH 
      106.75       102.61         8.75        34.92        17.69        18.94 
TCGA-E9-A1R4 TCGA-E9-A22G TCGA-E9-A3X8 TCGA-E9-A5UO TCGA-E9-A5UP TCGA-EW-A1OY 
        6.12        40.73        30.44        25.81        26.40        29.85 
TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD 
        6.15        13.94        17.49        16.77        31.30        33.21 
TCGA-GM-A2DK TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FR TCGA-LL-A73Z TCGA-OL-A5D7 
       86.96        15.32        14.79        16.08         7.46        58.52 
TCGA-OL-A5RW TCGA-OL-A66K TCGA-UU-A93S 
       36.36        41.92         3.81 

$`12P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       14.27        47.24        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        67.33        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI 
       32.55        25.28        18.21        21.90        21.67        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV 
       18.61        19.33        48.46        31.73        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       17.36        60.72        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A25A TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       16.47       107.70        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       39.65        33.93        29.98        32.75        56.28        35.93 
TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
       50.37         7.30        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        23.80        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       13.74        14.50        21.17        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P 
       11.05         9.37        10.42         8.75        13.02        13.02 
TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
        1.02        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       53.98         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        0.99        38.01        28.96        19.96        12.00        37.05 
TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A091 
        9.99        31.00        31.00        33.01       112.08        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
       12.00         1.02        50.04        49.05        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
        1.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       17.03        38.04         0.95        22.95        73.91         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3EH 
       87.12        26.04        74.14        33.04        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       16.57        19.79        23.24        24.79        29.26        16.80 
TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y 
       14.53        19.33        14.96        11.44        13.71        17.42 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR 
       13.58        12.26         1.68         0.03        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         7.46 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN 
        0.33         0.33         0.33         5.65         7.96         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.90         7.04         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        5.36         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P 
        5.33         5.59        80.28        61.35        66.77        95.70 
TCGA-AO-A03R TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 
       68.75        58.95        29.13        32.78        21.40        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI 
       50.86        72.00        76.77        65.10        26.24        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       62.04        71.80       115.27        99.25       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H 
       90.58        98.27        57.30        48.36        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT 
       14.73        82.62        61.87        70.39         0.53        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 
       24.79        26.93       130.09         5.65        15.62        32.52 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
        2.56        32.91        19.20       140.55        98.33        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U1 
      109.02        75.22        98.93        64.83        55.86       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL 
       83.87       134.14       107.21       125.16       103.86        97.68 
TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS 
       98.33        96.00        86.07        93.90        99.32        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H 
       94.29        61.28        86.53        86.43        33.73       160.90 
TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
       94.22        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       98.66        89.00        71.05       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       54.21        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       73.35        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        12.13       275.87       129.57        50.70        65.72 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG 
      127.33        84.59       165.76       129.07       140.88        68.45 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      212.25        81.17        78.02       263.28       162.05       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      100.70        89.46        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       21.47       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        58.88        43.59        73.51       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C 
        7.07        85.35        70.16        68.12       103.63        71.15 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       62.93        59.84        20.45        25.55        63.09        81.44 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       39.16        70.22        81.63        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM 
       18.21        43.53        61.51        21.70        74.89        61.68 
TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       72.23        74.14        76.60        53.95        45.57        49.94 
TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DH 
       49.05        44.02        89.06        45.83        77.98        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS 
       29.98        13.91        78.28        17.26        15.65         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 
       38.47        67.86        70.88        16.27         4.41        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI 
       14.30        44.81        46.19        32.58        24.49        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       32.91         4.90        35.93        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        51.16        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        89.16        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 
      144.59        28.14        26.14        38.60        83.31       130.16 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       18.64        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
       12.56         3.16        12.92         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM 
       10.92        11.34         0.16        12.03        10.42        12.33 
TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
       12.95        12.33        20.25        12.53        12.36         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
        9.67         9.53         0.03         9.50        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       12.95        13.02        12.49        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 
       20.88        13.25        20.58        14.17        13.48        21.14 
TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       19.20        14.17        17.49        16.50        55.50        15.78 
TCGA-D8-A1JD TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.15        12.03        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       20.09        19.40        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA 
       14.70        17.79        16.73        25.74        23.90        27.58 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ 
       18.15        12.39        17.16        15.22        14.73        21.80 
TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV 
       19.92        55.30        15.85        16.31        12.99        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       43.04        16.54        15.32        15.52         9.93        14.24 
TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       14.14        17.42        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         1.61        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       12.66        25.22        43.00        34.42        27.52        46.59 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       40.96        38.60        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       32.02        31.96        69.34        69.96        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F 
       23.87        14.79        23.34        22.82        17.29        21.63 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       18.21        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       11.05        50.79        19.56        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       76.57        53.62        87.22        33.01        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L8 
       59.18         3.88        22.19        11.08        54.18        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL TCGA-E2-A2P5 
       19.66        75.81        28.90        50.07        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A576 
       34.55        43.56         8.28        30.61        38.76        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 
       34.82        32.88        36.82        22.29        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
        9.86        24.82        28.27        34.95         2.56         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD 
       11.15        48.23        45.01        32.09        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 
       41.72        40.50        20.12         0.69        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       32.91        30.18        23.90        23.84        26.70         0.79 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.95        40.41        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB 
       23.11        18.48        30.08         7.86        18.90        19.99 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       25.91        22.09        34.03        10.16        23.51        15.22 
TCGA-EW-A6SB TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       24.99         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DL 
       83.34        75.02        70.85        72.10        85.15       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       17.06        14.70        14.47        22.26         2.63        15.68 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        19.53        12.36        19.59        17.49        27.91 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
       22.39         2.10        36.30        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       23.47        65.62        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD 
       28.21        19.73        40.11         8.91        47.01        64.21 
TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG 
       86.96         0.16         0.26         9.93        18.81        18.48 
TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
       21.07        20.68        19.27        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 
       17.26        13.94        17.03        66.84        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       29.03        15.35        16.04       108.07       107.05 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.16               0.03 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            282.90             281.29 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             30.44              27.58 
[1] "0.2 - 282.9 (30.4)" "0.0 - 281.3 (27.6)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12P LOSS MUTATED        11        8        0        1        52        40
  12P LOSS WILD-TYPE      78       77        6        5       301       212
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           0         19         10          6        2
  12P LOSS WILD-TYPE         2        135         19         59       18
                    vv
clus                 STAGE TIS STAGE X
  12P LOSS MUTATED           0       1
  12P LOSS WILD-TYPE         1      12
D64V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                  8                 77
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                52                301
  STAGE IIB                40                212
  STAGE III                 0                  2
  STAGE IIIA               19                135
  STAGE IIIB               10                 19
  STAGE IIIC                6                 59
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED    33  91  13  13
  12P LOSS WILD-TYPE 243 533 123  27
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1               33                243
  T2               91                533
  T3               13                123
  T4               13                 27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12P LOSS MUTATED    69  54  16   8
  12P LOSS WILD-TYPE 438 304 103  69
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               69                438
  N1               54                304
  N2               16                103
  N3                8                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED   132   3
  12P LOSS WILD-TYPE 757  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    132    3
  12P LOSS WILD-TYPE  757   19
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0              132                757
  1                3                 19
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED   149   2
  12P LOSS WILD-TYPE 919  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED    149    2
  12P LOSS WILD-TYPE  919   10
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE              149                919
  MALE                  2                 10
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    55  76
  12P LOSS WILD-TYPE 374 442
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     55   76
  12P LOSS WILD-TYPE  374  442
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                55                374
  YES               76                442
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12P LOSS MUTATED                            0                           130
  12P LOSS WILD-TYPE                          1                           640
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12P LOSS MUTATED                               10                   2
  12P LOSS WILD-TYPE                            190                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12P LOSS MUTATED                       3                                3
  12P LOSS WILD-TYPE                     6                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12P LOSS MUTATED                    1              2
  12P LOSS WILD-TYPE                 16             45
D64V9, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 130                640
  INFILTRATING LOBULAR CARCINOMA                 10                190
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  2                 45
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     8
  12P LOSS WILD-TYPE                                1    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                          36    96
  12P LOSS WILD-TYPE                       145   649
D64V11, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           8                 52
  BLACK OR AFRICAN AMERICAN                      36                145
  WHITE                                          96                649
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V12, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     4 127
  12P LOSS WILD-TYPE  35 748
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4  127
  12P LOSS WILD-TYPE   35  748
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              127                748
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED   104  24
  12Q LOSS WILD-TYPE 813 123
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               128                936 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                24                123 
$`12Q LOSS MUTATED`
TCGA-A1-A0SF TCGA-A1-A0SJ TCGA-A2-A0D1 TCGA-A2-A0T0 TCGA-A2-A0YE TCGA-A2-A3XS 
       48.10        13.68        34.55        17.52        18.21        33.93 
TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A7-A0CJ 
       91.07        47.31        50.83        24.39        26.96        30.61 
TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A26I TCGA-A7-A4SA TCGA-A7-A4SD 
       35.67        31.73        20.19        21.73        14.93        14.50 
TCGA-A7-A4SF TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A8-A07G TCGA-A8-A08F 
       17.92        10.29         9.37        10.42        18.97        33.01 
TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A09Q TCGA-AC-A2QJ TCGA-AC-A3W7 TCGA-AC-A7VB 
        0.99        43.00        25.02        14.66        15.48         8.22 
TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0XO 
        1.12         1.78         0.16         7.00         7.59        12.33 
TCGA-AO-A0J4 TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12F TCGA-AR-A0U0 
       52.18        55.33       115.27       108.03        48.36        65.36 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 
      108.36       101.00        99.32        17.23        50.89        99.62 
TCGA-AR-A252 TCGA-AR-A256 TCGA-AR-A2LL TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ 
       93.30        93.83        66.15       146.50       112.37       233.62 
TCGA-B6-A0RE TCGA-B6-A0RI TCGA-B6-A0RP TCGA-B6-A0RU TCGA-B6-A1KF TCGA-B6-A1KN 
      255.68       234.28       102.77       282.90       101.52       139.17 
TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B2 TCGA-BH-A0B7 TCGA-BH-A0BP 
       70.16        18.84        59.84        40.83        84.13        75.48 
TCGA-BH-A0C0 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0EE 
       41.75        90.97        23.44         3.22         4.41        31.00 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1F6 TCGA-BH-A1FN TCGA-BH-A1FU 
       51.16        67.50        91.99        97.48        72.07        72.07 
TCGA-BH-A208 TCGA-BH-A5IZ TCGA-C8-A12U TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A26Y 
       57.83        18.64        12.66        13.51         1.87        12.95 
TCGA-C8-A27A TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JG TCGA-D8-A1XK TCGA-D8-A1XQ 
       24.56        13.97        14.17        53.00        14.50        16.41 
TCGA-D8-A27F TCGA-E2-A10A TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A1AZ 
       16.04        40.41        63.62        25.05        20.71        76.57 
TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IO TCGA-E2-A1L7 TCGA-E2-A1LH TCGA-E2-A1LI 
       32.35        37.25        60.99        60.36       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A9RU TCGA-E9-A1NH TCGA-E9-A1RG 
        8.75        26.99        34.92        17.69        18.94        21.27 
TCGA-E9-A22G TCGA-E9-A3X8 TCGA-E9-A5UP TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A1PC 
       40.73        30.44        26.40        29.82         7.86         6.15 
TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2DK 
       17.49        16.77        31.30        33.21         7.40        86.96 
TCGA-LL-A5YP TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66K 
       14.79         7.46        58.52        36.36        20.38        41.92 
TCGA-OL-A6VO TCGA-UU-A93S 
       28.21         3.81 

$`12Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SG 
       48.36         9.96         8.52        14.37        43.43        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        31.79         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y 
       73.84        87.25        63.12       101.98        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW 
      107.93        77.19        75.25         5.19        98.99       107.93 
TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       56.81        67.33        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       20.75        32.55        25.28        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       49.48        18.61        19.33        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 
       23.47        17.36        60.72        22.45        20.25        19.20 
TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C 
       19.56        16.47        52.47       107.70        42.44        17.19 
TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XU 
       18.15       105.34        10.59        36.23        39.65        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RY 
       32.75        56.28        35.93        50.37         7.30        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG 
       23.21        21.14        21.90        38.30        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G 
       35.47        37.45        33.11        29.79        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J 
       29.56        31.36        24.26        23.74        23.80        20.61 
TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       22.32        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZV 
       14.70        11.97        13.74        21.17        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       10.72        11.05         8.75        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z 
       17.98        53.06        29.03        31.00        26.01         1.02 
TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       17.03        53.98         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       14.01        12.00        32.05         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99         9.99        45.07        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I 
       13.02         0.99        38.01        28.96        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T 
       37.05         9.99        31.00        31.00        33.01       112.08 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        33.01        30.97        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
        9.99         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98        33.07         1.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM 
       22.95        73.91         5.72         1.48        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
       40.57        86.66        90.71        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN 
       74.14        33.04        19.33        32.45         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 
       14.83        22.19        24.13        25.05        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       19.79        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       19.33        14.96        11.44        13.71        17.42        18.67 
TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR 
       13.58        12.26         1.68         0.03        20.19         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        2.96         1.71         9.96         7.36         7.46         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FN 
        0.33         0.33         6.44         5.65         7.96         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        6.90         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        0.33         5.36         0.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M 
        0.33         0.33         5.33         5.59        80.28        61.35 
TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
       66.77        81.63        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 
       29.13        32.78        21.40        26.04        37.48        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM 
       76.77        65.10        26.24        50.24        62.04        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
       99.25       108.72       106.78        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       57.30        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L 
       70.39         0.53        17.79        24.79        26.93       130.09 
TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
        5.65        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
      140.55        98.33         5.26        84.10       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 
       98.93        64.83        55.86       107.24       133.22        83.87 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      134.14       107.21       125.16       103.86        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       96.00        86.07        93.90        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      105.27        77.69       105.30        32.58        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       89.00        85.64        71.05       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       54.21        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       73.35        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        12.13       275.87       129.57        50.70        65.72 
TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ 
       18.77       127.33        84.59       165.76       129.07       140.88 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       212.25        81.17        78.02       263.28       162.05 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      140.48       100.70        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        18.35        21.47       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      245.10        28.27        68.94        58.88        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
      170.17        37.87         7.07        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        62.93        20.45        25.55        63.09        81.44 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA 
       39.55        39.16        70.22        81.63        51.68        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        43.53        61.51        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        72.23        74.14        76.60        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD 
       49.94        77.95        49.05        44.02        89.06        45.83 
TCGA-BH-A0DE TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       77.98        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        24.43        30.35        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       53.26        24.56        23.08        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 
       51.32        27.25        50.79         5.59        23.93        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1ES 
       55.63        37.55        66.05         7.36        51.39       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       25.81        31.53        89.16        24.62       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FM TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
       45.63       144.59        28.14        26.14        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 
       12.56         3.16        12.59        12.92         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK 
       12.33        10.92        11.34        11.28         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       10.42        12.33        12.95        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.36         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR 
       14.43        33.99        12.95        13.02        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A145 
       19.46        56.81        20.88        13.25        20.58        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        55.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       15.78        18.15        18.90        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO 
       15.22        14.73        21.80        19.92        17.69        55.30 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       17.42        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       13.48         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B 
       25.22        43.00        34.42        27.52        46.59        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A153 
       32.02        31.96        69.34        18.51        69.96        23.24 
TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C 
       19.43        21.04        23.87        14.79        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R 
        9.04        20.58        11.05        50.79        19.56        56.94 
TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B6 
       14.07        51.39        53.62        87.22        33.01        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       16.47        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18         3.88        22.19        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       73.64        19.66        24.59        75.81        28.90        50.07 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 
       43.04        34.55        43.56         8.28        30.61        38.76 
TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 
       34.29        34.82        32.88        36.82        22.29        34.16 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       36.20        36.56        39.55        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       25.84         9.86        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        6.12         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12        46.65         6.58        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       41.03        41.72        40.50        20.12         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       38.07        32.91        30.18        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        25.81        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 
       55.00        52.73        25.91        22.09        34.03        10.16 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       23.51        15.22        24.99       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DI 
       79.10        83.34        75.02        70.85        72.10        85.15 
TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
      115.69       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U 
        2.60        62.47        11.84        11.57        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 
        7.10        13.28        10.62        24.95        32.75        29.23 
TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP 
       25.05        17.06        15.32        14.70        14.47        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 
        2.63        16.08        15.68        14.50        19.53        12.36 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        40.08        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N 
       22.32        26.70        23.47        65.62        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       17.36        14.07        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       18.48        21.07        20.68        19.27        13.84        18.87 
TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G 
       17.39        17.26        13.94        17.03        66.84        11.41 
TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       52.96        29.03        15.35        16.04       108.07       107.05 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.16               0.03 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            282.90             281.29 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            31.515             26.975 
[1] "0.2 - 282.9 (31.5)" "0.0 - 281.3 (27.0)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  12Q LOSS MUTATED         9        6        0        1        46        38
  12Q LOSS WILD-TYPE      80       79        6        5       307       214
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           0         12          8          7        2
  12Q LOSS WILD-TYPE         2        142         21         58       18
                    vv
clus                 STAGE TIS STAGE X
  12Q LOSS MUTATED           0       1
  12Q LOSS WILD-TYPE         1      12
D65V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   9                 80
  STAGE IA                  6                 79
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                46                307
  STAGE IIB                38                214
  STAGE III                 0                  2
  STAGE IIIA               12                142
  STAGE IIIB                8                 21
  STAGE IIIC                7                 58
  STAGE IV                  2                 18
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED    26  83  10  11
  12Q LOSS WILD-TYPE 250 541 126  29
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1               26                250
  T2               83                541
  T3               10                126
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  12Q LOSS MUTATED    66  44  11   8
  12Q LOSS WILD-TYPE 441 314 108  69
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               66                441
  N1               44                314
  N2               11                108
  N3                8                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED   113   2
  12Q LOSS WILD-TYPE 776  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    113    2
  12Q LOSS WILD-TYPE  776   20
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0              113                776
  1                2                 20
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED   130   1
  12Q LOSS WILD-TYPE 938  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED    130    1
  12Q LOSS WILD-TYPE  938   11
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE              130                938
  MALE                  1                 11
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    39  73
  12Q LOSS WILD-TYPE 390 445
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     39   73
  12Q LOSS WILD-TYPE  390  445
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                39                390
  YES               73                445
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  12Q LOSS MUTATED                            0                           111
  12Q LOSS WILD-TYPE                          1                           659
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  12Q LOSS MUTATED                                9                   3
  12Q LOSS WILD-TYPE                            191                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  12Q LOSS MUTATED                       3                                1
  12Q LOSS WILD-TYPE                     6                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  12Q LOSS MUTATED                    0              4
  12Q LOSS WILD-TYPE                 17             43
D65V9, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 111                659
  INFILTRATING LOBULAR CARCINOMA                  9                191
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  4                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     6
  12Q LOSS WILD-TYPE                                1    54
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                          39    81
  12Q LOSS WILD-TYPE                       142   664
D65V11, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           6                 54
  BLACK OR AFRICAN AMERICAN                      39                142
  WHITE                                          81                664
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V12, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     4 112
  12Q LOSS WILD-TYPE  35 763
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4  112
  12Q LOSS WILD-TYPE   35  763
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO              112                763
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED   360  65
  13Q LOSS WILD-TYPE 557  82
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               425                639 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                65                 82 
$`13Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SI TCGA-A1-A0SJ 
      129.14       131.67        14.37        43.43        20.88        13.68 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q 
       39.32        28.01        19.20        18.21        18.02        78.41 
TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CS TCGA-A2-A0CT 
       87.25        55.43        24.79       114.81        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 
        5.19        98.99       107.93        56.81        67.33        34.55 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0ER TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0SV 
       25.22        80.28        74.40        34.29        31.82        27.12 
TCGA-A2-A0SW TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YI TCGA-A2-A0YL TCGA-A2-A0YM 
       44.88        20.75        18.21        49.48        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A3XT TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3Y0 
       23.77        23.47        91.07        56.28        47.31        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CJ 
        7.30        24.39        26.96        21.14        38.30        30.61 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A26E TCGA-A7-A26G TCGA-A7-A26I 
       29.79        31.73        25.15        31.36        23.74        21.73 
TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A4SA TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A6VV 
       22.32        10.59        14.93        14.50        17.92        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06R TCGA-A8-A06T 
        9.37        10.42         8.75        13.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       29.03        26.01         1.02        53.98         9.01        43.00 
TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A085 
       18.97        32.05         9.99        10.98         9.99        36.95 
TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       13.02        38.01        33.01        12.00         9.99        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A099 TCGA-A8-A09B 
       31.00        33.01        43.00        30.97         9.99        12.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09X 
       45.07        29.98        33.07         1.02        25.02        14.01 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A2BK 
       19.04        13.02        27.02        38.04        22.95        73.05 
TCGA-AC-A2BM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 
       99.35        33.04        14.66        32.45        16.57        19.79 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IW TCGA-AC-A7VB 
       29.26        16.80        13.71        17.42        13.58         8.22 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AN-A03X TCGA-AN-A046 TCGA-AN-A04A TCGA-AN-A04C 
        0.03        20.19         0.33         0.33         2.96         1.78 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FS TCGA-AN-A0FX 
        1.71         9.96         0.33         0.33         6.90         0.33 
TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW 
        0.33         5.36         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A0J3 TCGA-AO-A0J4 
       80.28        66.77        81.63        68.75        21.40        52.18 
TCGA-AO-A0J6 TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       37.48        76.77        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A129 TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A1KQ 
      115.27       108.03        57.30        48.36        41.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A1H2 
       70.39         0.53        17.79        24.79       130.09        15.62 
TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TV 
        2.56        32.91        19.20       140.55         5.26        75.22 
TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH 
       64.83       107.24        65.36        83.87       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AR TCGA-AR-A1AW TCGA-AR-A1AY 
      108.36       101.00       103.86        17.23        86.53        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24S TCGA-AR-A24T 
       50.89        94.22        99.78       104.28        97.84       105.27 
TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 
      105.30        32.58        98.66        99.62        93.30        71.05 
TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 
       93.83        54.21        66.15        73.35        10.59        77.62 
TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RP 
      129.57        65.72       140.88        68.45        81.17       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RU TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX 
      140.48       282.90        97.48        79.63        18.35        21.47 
TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       68.94        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY 
       37.87        85.35        68.12        18.84        59.84        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC 
       63.09        39.55        81.63        84.13        37.22        32.02 
TCGA-BH-A0BJ TCGA-BH-A0BP TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       21.70        75.48        76.60        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DH TCGA-BH-A0DK 
       41.75        44.02        90.97        45.83        38.01        13.91 
TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0E0 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0GZ 
       78.28        15.65         4.41        46.19        31.00        10.78 
TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX 
       15.16        23.08        26.50        12.89        27.25         5.59 
TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18Q TCGA-BH-A18S 
       23.93        23.05        90.84        26.66        55.63        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY 
        7.36        51.39        67.50        42.28        12.00        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FH 
       25.81        97.48       114.15        33.17        74.73        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A5J0 
       63.35        72.07        26.14       130.16         6.44        23.51 
TCGA-BH-A6R8 TCGA-BH-A8FY TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U 
        9.63         9.70        11.77        12.66        11.77        12.66 
TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI 
       48.53         3.16        12.92        10.92        11.34        11.28 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y 
       12.03        12.33        12.95        20.25        12.36        12.95 
TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z 
        9.53         9.50        12.95        13.41        56.81        20.88 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 
       13.25        13.97        14.17        13.48        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG 
       17.49        16.50        15.78        18.15        18.90        53.00 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JT TCGA-D8-A1X5 
       18.97        20.12        20.09        19.40        13.32        18.58 
TCGA-D8-A1X6 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XD TCGA-D8-A1XK TCGA-D8-A1XL 
       17.79        23.90        27.58        17.16        14.50        19.92 
TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       12.99        16.54        15.52         9.93        14.24        14.14 
TCGA-D8-A27I TCGA-D8-A27N TCGA-D8-A27T TCGA-E2-A107 TCGA-E2-A10C TCGA-E2-A14N 
       14.43         4.80        13.08        34.42        40.11        47.15 
TCGA-E2-A14O TCGA-E2-A14W TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A159 
       44.68        32.02        63.62        69.96        21.04        25.05 
TCGA-E2-A15G TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       18.21        11.05        50.79        19.56        56.94        14.07 
TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L8 TCGA-E2-A1LG 
       76.57        33.70        22.19        60.99        73.64        50.07 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A576 TCGA-E9-A1N6 
        8.75        43.04        26.99         8.28        34.29        22.29 
TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NE TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R6 
       36.20        36.56        35.77        18.94         9.86        11.15 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RG TCGA-E9-A22E TCGA-E9-A22G 
       45.01        32.09         1.12        21.27        41.72        40.73 
TCGA-E9-A22H TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A54Y 
       40.50        38.99         7.13        12.33        30.18        23.84 
TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1OV TCGA-EW-A1OW 
       25.81        26.40        27.85        12.20        25.94        22.82 
TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA 
       29.85        40.41        52.96        23.11         7.86        18.90 
TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-EW-A6S9 
        6.15        14.43        19.96        52.73        17.49        15.22 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DL 
       79.10        83.34        75.02        70.85        72.10       115.69 
TCGA-GM-A3NW TCGA-GM-A3XL TCGA-HN-A2NL TCGA-LD-A66U TCGA-LD-A74U TCGA-LL-A5YM 
      110.50        69.30         2.60        21.24        13.22        15.32 
TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A7SZ TCGA-LL-A7T0 
       14.47        14.79        22.26        16.08        19.53        12.36 
TCGA-OL-A5D7 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I 
       58.52        58.62        36.36        22.32        20.38        23.47 
TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A66O TCGA-PE-A5DD TCGA-S3-A6ZH TCGA-S3-AA10 
       41.92        26.04        17.36        64.21        21.07        19.27 
TCGA-S3-AA14 TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-XX-A89A TCGA-Z7-A8R5 
       17.39        17.03        66.84        16.04       108.07 

$`13Q LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM 
        8.52        48.10        14.27        47.24        31.79         7.96 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
      143.15       121.94        73.84        63.12       101.98        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0D2 
      136.73        99.12        92.48        88.60       107.93        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ES 
       61.58       101.72        89.36       118.45        79.76        72.00 
TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       35.05        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF 
       20.52        17.46        18.90        32.55        25.28        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A1FW TCGA-A2-A1FX 
       21.90        21.67        18.61        19.33        17.36        60.72 
TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       22.45        20.25        19.20        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XY 
       36.23        39.65        33.93        29.98        32.75        35.93 
TCGA-A2-A3XZ TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0CG 
       50.37        21.30        23.21        21.90        35.31        34.29 
TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13E TCGA-A7-A13G 
       35.47        37.45        35.67        33.11        20.19        23.61 
TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J0 
       29.56        24.26        23.80        20.61        11.34        10.29 
TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE 
       11.28        13.41        14.70        11.97        13.74        21.17 
TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A06Q 
       14.73        12.10        10.72        11.05        13.02         1.02 
TCGA-A8-A06X TCGA-A8-A075 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       31.00        17.03        19.99        18.97        14.01        12.00 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A08A 
        8.98         7.99        24.99        45.07        15.06         0.99 
TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08Z 
       28.96        19.96        37.05         0.99       112.08        40.01 
TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09C 
       33.01        17.95        41.98        12.00         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W 
       50.04        49.05         8.98        19.04        15.02         0.99 
TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-AC-A23C TCGA-AC-A23G 
       12.00        21.04         0.99        17.03         0.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        5.72         1.48        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3EH TCGA-AC-A3HN 
       87.12        26.04        74.14        19.33         6.48        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W7 
       14.83        22.19        24.13        25.05        14.99        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        14.53        19.33        14.96        11.44 
TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS 
       18.67        12.26         1.68         1.12         1.32         2.30 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         0.23         0.62         7.36         7.46         0.16 
TCGA-AN-A0AS TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL 
        0.33         6.44         5.65         7.96         7.00         7.59 
TCGA-AN-A0FN TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ TCGA-AN-A0XO 
        7.17         7.04         0.33         0.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03M TCGA-AO-A03P 
        0.30         0.33         0.33         0.33        61.35        95.70 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J7 
       47.87        58.95        29.13        32.78        26.04        20.32 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       22.36        53.03        21.53        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A 
       65.10        26.24        99.25       108.72       106.78        90.58 
TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AQ-A04J 
       98.27        64.04        40.57        14.73        82.62        26.93 
TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW 
        5.65        32.52        98.33        84.10       109.02        98.93 
TCGA-AR-A0TY TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
       55.86       133.22       134.14        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24M TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R 
       86.43       160.90       120.33       118.59         2.76       112.77 
TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       77.69        98.76        89.00        85.64       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       86.53        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       33.30        38.96       143.38       281.29        12.13       275.87 
TCGA-B6-A0IC TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM 
       50.70       146.50       112.37       233.62        18.77       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       165.76       129.07       255.68       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV 
       78.02       263.28       162.05       100.70        89.46       157.41 
TCGA-B6-A0WT TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X7 TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       58.88         7.07        70.16       103.63        71.15        62.93 
TCGA-BH-A0AW TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B9 
       20.45        81.44        40.83        39.16        70.22        51.68 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        43.53        61.51        74.89        61.68        72.23 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0C3 TCGA-BH-A0DE TCGA-BH-A0DG 
       74.14        53.95        45.57        89.06        77.98        23.44 
TCGA-BH-A0DI TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       29.98        17.26         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       70.88        16.27        15.68        14.30         9.63        44.81 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.58        24.49        24.43        30.35        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        41.00        52.96        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0W4 TCGA-BH-A0W5 
       13.61        36.85        51.32        50.79        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18M 
       44.81        32.91         4.90        35.93        20.12        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18R TCGA-BH-A18V TCGA-BH-A1EO TCGA-BH-A1ES 
       37.74        30.28        37.55        51.16        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 
       82.85        55.69        49.58        31.53        89.16        24.62 
TCGA-BH-A1FB TCGA-BH-A1FG TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
      120.62       122.89        55.00        45.63        72.07       144.59 
TCGA-BH-A201 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 
       28.14        38.60        83.31        57.83        10.65        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R9 TCGA-BH-A8FZ 
       10.52       109.28        20.88        18.64         5.26        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12Q TCGA-C8-A12V 
       21.76         9.44        11.93        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        12.66        12.56        13.51         1.87        12.59 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HO 
        4.11         4.08        12.33         0.16        10.42        12.33 
TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B 
       12.53         8.28         9.67         0.03        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A141 TCGA-D8-A147 
       33.99        13.02        12.49        19.46        20.58        19.20 
TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP 
       55.50        12.03        14.01        20.09        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC 
       12.20        14.70        16.73        25.74        18.15        12.39 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        21.80        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ 
       15.85        16.31        16.64        15.16        43.04        15.32 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27L 
       17.42        16.04        13.45        13.05        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       13.48         1.61        10.09        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F 
       27.52        46.59        40.41        37.51        28.44        28.87 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A154 
       34.26        31.96        69.34        18.51        23.24        19.43 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        12.92        55.63        53.92         9.04        20.58 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       28.44        59.18         3.88        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        28.90       106.75       102.61 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU 
       34.55        43.56        30.61        34.92        38.76        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NC TCGA-E9-A1ND 
       34.82        32.88        36.82        34.16        39.55        41.62 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 
       35.24        25.84        24.82        28.27        34.95         2.56 
TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RE TCGA-E9-A1RF 
        6.12         3.02        48.23        40.24        46.65         6.58 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       39.09        38.37        41.03        20.12         0.69         1.94 
TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3X8 
       24.56        29.72         9.47        38.07        32.91        30.44 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5FL TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       23.90        26.70         0.79        39.72         8.48        18.21 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OX 
       18.90        13.25        16.57        15.68        28.77        29.95 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB 
       41.13        39.78        29.82        18.48        30.08        19.99 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A2FW 
       13.94        10.52        34.55        55.00        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC 
       34.03        10.16        23.51        16.77        24.99        31.30 
TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DI 
       33.21         7.40       109.87        59.57       216.76        85.15 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NY TCGA-GM-A3XG 
       86.96       106.06       101.62        85.35        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW 
       66.38        72.03        13.55        18.12        62.47        11.84 
TCGA-JL-A3YX TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       11.57         7.10        13.28        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FQ TCGA-LL-A73Y 
       29.23        25.05        17.06        14.70         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
        7.46        14.50        19.59        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
        2.10        36.30        31.99        40.08        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66P TCGA-OL-A6VO 
       24.72        26.70        65.62        42.77        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DE TCGA-PL-A8LX 
       19.73        40.11         8.91        47.01        86.96         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 
        0.26         9.93        18.81        18.48        20.68        13.84 
TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 
       18.87        17.26        13.94         3.81        11.41        52.96 
TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R6 
       29.03        15.35       107.05 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.03               0.03 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            282.90             281.29 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             26.96              28.44 
[1] "0.0 - 282.9 (27.0)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.3"
D66V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  13Q LOSS MUTATED        33       29        1        1       155       102
  13Q LOSS WILD-TYPE      56       56        5        5       198       150
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           1         62         11         22        8
  13Q LOSS WILD-TYPE         1         92         18         43       12
                    vv
clus                 STAGE TIS STAGE X
  13Q LOSS MUTATED           1       4
  13Q LOSS WILD-TYPE         0       9
D66V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  33                 56
  STAGE IA                 29                 56
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA               155                198
  STAGE IIB               102                150
  STAGE III                 1                  1
  STAGE IIIA               62                 92
  STAGE IIIB               11                 18
  STAGE IIIC               22                 43
  STAGE IV                  8                 12
  STAGE TIS                 1                  0
  STAGE X                   4                  9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED    97 260  58  16
  13Q LOSS WILD-TYPE 179 364  78  24
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               97                179
  T2              260                364
  T3               58                 78
  T4               16                 24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  13Q LOSS MUTATED   209 138  51  27
  13Q LOSS WILD-TYPE 298 220  68  50
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0              209                298
  N1              138                220
  N2               51                 68
  N3               27                 50
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   357   9
  13Q LOSS WILD-TYPE 532  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    357    9
  13Q LOSS WILD-TYPE  532   13
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0              357                532
  1                9                 13
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   428   5
  13Q LOSS WILD-TYPE 640   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    428    5
  13Q LOSS WILD-TYPE  640    7
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE              428                640
  MALE                  5                  7
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED   164 212
  13Q LOSS WILD-TYPE 265 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED    164  212
  13Q LOSS WILD-TYPE  265  306
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO               164                265
  YES              212                306
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  13Q LOSS MUTATED                            0                           340
  13Q LOSS WILD-TYPE                          1                           430
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  13Q LOSS MUTATED                               58                   5
  13Q LOSS WILD-TYPE                            142                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  13Q LOSS MUTATED                       5                               11
  13Q LOSS WILD-TYPE                     4                               18
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  13Q LOSS MUTATED                    2             11
  13Q LOSS WILD-TYPE                 15             36
D66V9, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 340                430
  INFILTRATING LOBULAR CARCINOMA                 58                142
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               11                 18
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 11                 36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0    24
  13Q LOSS WILD-TYPE                                1    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          85   277
  13Q LOSS WILD-TYPE                        96   468
D66V11, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          24                 36
  BLACK OR AFRICAN AMERICAN                      85                 96
  WHITE                                         277                468
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V12, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11 340
  13Q LOSS WILD-TYPE  28 535
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11  340
  13Q LOSS WILD-TYPE   28  535
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   11                 28
  NOT HISPANIC OR LATINO              340                535
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   216  45
  14Q LOSS WILD-TYPE 701 102
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               261                803 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                45                102 
$`14Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-A1-A0SK TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04T 
      129.14        42.81        31.79        19.20        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EQ 
       87.25       101.98         5.19       107.93        67.33        79.76 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0YE TCGA-A2-A0YJ 
       35.05        34.29        27.12        50.43        18.21        18.61 
TCGA-A2-A0YT TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XX 
       23.77        19.20        33.93        91.07        29.98        47.31 
TCGA-A2-A3Y0 TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A13D TCGA-A7-A13E 
       50.83        26.96        21.90        35.31        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A26G TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SB 
       25.15        23.74        21.73        22.32        11.28        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       14.50        21.17        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A07F TCGA-A8-A07L TCGA-A8-A07O 
       13.02        31.00         1.02        18.97        32.05         9.99 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08L TCGA-A8-A097 
        8.98         9.99        33.01        19.96         9.99        12.00 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A0A6 TCGA-A8-A0AB TCGA-AC-A23C 
       45.07        29.98         1.02        21.04        17.03         0.95 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A62X 
       73.05        99.35        33.04        14.66         6.48        13.71 
TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ TCGA-AN-A04C TCGA-AN-A0AK TCGA-AN-A0FJ 
       13.58         0.03         1.12         1.78         7.36         7.96 
TCGA-AN-A0FX TCGA-AN-A0XN TCGA-AO-A0J4 TCGA-AO-A0J6 TCGA-AO-A0JL TCGA-AO-A124 
        0.33         0.33        52.18        37.48        55.33       115.27 
TCGA-AO-A129 TCGA-AO-A12F TCGA-AO-A1KR TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A54N 
      108.03        48.36        70.39       130.09         5.65         2.56 
TCGA-AQ-A54O TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0U0 TCGA-AR-A1AH 
       32.91         5.26       109.02        75.22        65.36       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AX 
      108.36       101.00        98.33        93.90        99.32        86.43 
TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24Q TCGA-AR-A24V TCGA-AR-A251 TCGA-AR-A255 
       33.73       160.90       104.28       105.30        99.62        71.05 
TCGA-AR-A256 TCGA-B6-A0I9 TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ 
       93.83        12.13       112.37       233.62       165.76       140.88 
TCGA-B6-A0RE TCGA-B6-A0RL TCGA-B6-A0WS TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A1KC 
      255.68        81.17        97.48        18.35        21.47        43.59 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A409 TCGA-BH-A0AU TCGA-BH-A0AV 
      101.52        73.51        37.87        18.84        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BF 
       20.45        39.55        70.22        84.13        51.68        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C7 
       61.51        21.70        77.95        49.05        44.02        90.97 
TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0H7 TCGA-BH-A0RX TCGA-BH-A0WA TCGA-BH-A18F 
        4.41         9.63        23.08         5.59        23.05        32.91 
TCGA-BH-A18Q TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F6 
       55.63         7.36        51.39        55.69        17.69        97.48 
TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A202 TCGA-BH-A42T TCGA-BH-A5IZ 
       24.62       114.15        74.73        26.14        10.52        18.64 
TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12X TCGA-C8-A134 TCGA-C8-A1HF TCGA-C8-A1HK 
       11.93        11.77        12.66        12.59        10.92        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A27B TCGA-C8-A8HP TCGA-C8-A9FZ 
       12.33        12.95        12.95        14.43        13.02        19.46 
TCGA-D8-A142 TCGA-D8-A1JC TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM 
       13.97        15.78        53.00        20.09        20.09        19.40 
TCGA-D8-A1JP TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XO 
       21.01        27.58        18.15        14.73        14.50        55.30 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y3 TCGA-D8-A27I 
       16.64        12.99        16.54        15.52        14.14        14.43 
TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A27T TCGA-E2-A108 TCGA-E2-A14R TCGA-E2-A14T 
       13.48        10.09        13.08        27.52        38.60        75.98 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A155 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15F 
       18.51        63.62        21.04        25.05        23.34        21.63 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1AZ TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1LE 
       11.05        19.56        76.57        33.73        33.70        28.90 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 
      106.75       102.61         8.28        34.92        38.76        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1QZ TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       34.16        36.20        24.82         6.12         3.02        11.15 
TCGA-E9-A1RB TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22G TCGA-E9-A2JS TCGA-E9-A3HO 
       32.09        39.09        38.37        40.73        29.72        38.07 
TCGA-E9-A3QA TCGA-EW-A1IZ TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1P4 
       30.18        18.21        28.77        25.94        22.82        29.82 
TCGA-EW-A1P8 TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3U0 
        7.86        14.43        19.96        55.00        25.91        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DH 
       10.16        23.51        24.99        33.21       109.87        72.10 
TCGA-GM-A2DK TCGA-GM-A3XL TCGA-GM-A5PX TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LD-A7W5 
       86.96        69.30        18.12         2.60        11.57         7.10 
TCGA-LL-A441 TCGA-LL-A5YP TCGA-LL-A7T0 TCGA-OL-A5D7 TCGA-OL-A5RZ TCGA-OL-A5S0 
       32.75        14.79        12.36        58.52        22.32        20.38 
TCGA-OL-A66I TCGA-OL-A66K TCGA-OL-A66N TCGA-OL-A6VO TCGA-PE-A5DC TCGA-PL-A8LX 
       23.47        41.92        26.04        28.21        47.01         0.16 
TCGA-S3-A6ZF TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       18.81        20.68        19.27        13.94        17.03         3.81 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       52.96        15.35        16.04 

$`14Q LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      131.67        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SQ 
       20.88        13.68         7.96        39.32        28.01        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y 
      143.15        78.41       121.94        63.12        55.43        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 
      107.93        77.19        75.25        98.99        56.81        34.55 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO 
       33.76        61.58        25.22       101.72        89.36        80.28 
TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
      118.45        74.40        72.00        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 
       63.29        99.19        54.64        44.88        44.28        17.52 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH 
       20.75        32.55        25.28        50.47        21.90        21.67 
TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FW 
       49.48        19.33        48.46        31.73        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
      107.70        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3XZ 
       36.23        39.65        32.75        56.28        35.93        50.37 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD 
        7.30        24.39        21.30        23.21        21.14        38.30 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26H 
       29.79        23.61        29.56        31.36        24.26        23.80 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       20.61        11.34        10.59        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        14.93        17.92        14.73        12.10        10.72 
TCGA-A7-A5ZX TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U 
       11.05        13.02         1.02        17.98        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01        17.03        53.98         9.01        43.00        19.99 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       18.97        14.01        12.00        10.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R 
       28.96        12.00        37.05        31.00        31.00         0.99 
TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
       33.01       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       17.95        41.98         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       50.04        49.05        33.07        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
        0.99        27.02        38.04        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        74.14        19.33        32.45        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       15.48        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX 
       19.33        14.96        11.44        17.42        18.67        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        1.68         8.22        20.19         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         2.96         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT 
        9.96         7.46         0.16         0.33         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        6.44         5.65         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        7.04         0.33         0.36         0.33         0.33         5.36 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        5.33         5.59        80.28        61.35        66.77        81.63 
TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 
       95.70        68.75        47.87        58.95        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       21.40        26.04        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 
       50.24        62.04        71.80        99.25       108.72       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H 
       90.58        98.27        64.04        57.30        41.62        40.57 
TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       14.73        82.62        61.87         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       26.93        15.62        32.52        19.20       140.55        98.33 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       84.10        98.93        64.83        55.86       107.24       133.22 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AN 
       83.87       134.14       107.21       103.86        97.68        96.00 
TCGA-AR-A1AO TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       86.07        17.23        37.81        94.29        61.28        86.53 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24W TCGA-AR-A24X 
      112.77        97.84       105.27        77.69        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH 
       98.66        89.00        93.30        85.64       166.42        20.25 
TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       86.53        54.21        66.15        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
       77.62       143.38       281.29       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
       65.72       146.50        18.77       127.33        84.59       129.07 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
       68.45       212.25       234.28        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
      188.68        79.63       113.79       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 
       28.27        68.94        58.88       139.17       170.17         7.07 
TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AY 
       85.35        70.16        68.12       103.63        71.15        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BA 
       63.09        81.44        40.83        39.16        81.63        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       32.02        18.21        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0C0 
       74.14        76.60        53.95        45.57        49.94        41.75 
TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       89.06        45.83        77.98        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        78.28        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 
       38.47        67.86        70.88        16.27        15.68        14.30 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.58        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18I 
       23.93        24.95        42.35        44.81         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       37.55        66.05        51.16        67.50        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 
       82.85        42.28        12.00        49.58        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FD TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ 
       89.16       120.62        33.17       122.89        36.92        63.35 
TCGA-BH-A1FL TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       55.00        45.63        72.07       144.59        72.07        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       38.60        83.31        57.83       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       20.12       109.28        20.88        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12O 
        9.70        18.87        21.76         9.44        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y 
       11.77        12.66        12.66        12.66        12.66        48.53 
TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A137 
       12.56         3.16        13.51         1.87        12.92         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL 
        4.08        12.33        11.34        11.28         0.16        10.42 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 
       12.33        20.25        12.53        12.36         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.53         0.03         9.50        24.56        33.99        12.95 
TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 
       12.49        13.41        56.81        20.88        13.25        20.58 
TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 
       14.17        13.48        21.14        19.20        14.17        17.49 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JH 
       16.50        55.50        18.15        18.90        12.03        14.01 
TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       18.97        20.12        20.38        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC 
       18.58        17.79        16.73        25.74        23.90        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ 
       17.16        15.22        21.80        19.92        17.69        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y1 
       15.85        16.31        15.16        43.04        15.32         9.93 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27K 
       14.24        17.42        16.04        13.45        13.05        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       16.41         4.80         1.61        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14S 
       28.87        47.15        44.68        40.96        38.24        33.17 
TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 
       43.33        34.26        32.02        31.96        69.34        69.96 
TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C TCGA-E2-A15D 
       23.24        19.43        23.87        14.79        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 
       20.58        50.79        56.94        14.07        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL 
       77.65        37.41        70.36        28.44        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       22.19        60.99        11.08        54.18        60.36        73.64 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A1LL 
       19.66        24.59        75.81        50.07         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU 
       26.99        34.55        43.56        30.61        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       34.82        32.88        36.82        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1R0 
       35.77        35.24        25.84        18.94         9.86        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RC TCGA-E9-A1RD 
       34.95         2.56        48.23        45.01        40.24         1.12 
TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 
       46.65         6.58        21.27        46.59        47.64        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H 
       32.05        42.25        37.74        41.03        41.72        40.50 
TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A 
       20.12         0.69        38.99         1.94         7.13        24.56 
TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       12.33         9.47        32.91        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       26.70         0.79        25.81        26.40        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
       39.72         8.48        18.90        13.25        16.57        15.68 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48        30.08        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 
       13.94        10.52        34.55        52.73        22.09        34.03 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 TCGA-GM-A2DA 
       15.22        16.77        31.30         7.40        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DL 
       79.10        83.34        75.02        70.85        85.15       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U 
       66.38        72.03        13.55        62.47        11.84        21.24 
TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       13.22        13.28        10.62        24.95        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ 
       17.06        15.32        14.70        14.47        22.26         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 
       16.08        15.68         7.46        14.50        19.53        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 
       17.49        27.91        22.39         2.10        36.30        31.99 
TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY 
       58.62        40.08        34.92        36.36        28.87        24.72 
TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ 
       26.70        65.62        42.77        17.36        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ 
       40.11         8.91        64.21        86.96         0.26         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       18.48        21.07        13.84        18.87        17.39        17.26 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB44 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       66.84        11.41        29.03       108.07       107.05 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.03               0.03 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            255.68             282.90 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             24.82              29.03 
[1] "0.0 - 255.7 (24.8)" "0.0 - 282.9 (29.0)"
[1] "hr=" "1.4"
D67V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  14Q LOSS MUTATED        19       20        0        2        93        64
  14Q LOSS WILD-TYPE      70       65        6        4       260       188
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           0         35          5         16        7
  14Q LOSS WILD-TYPE         2        119         24         49       13
                    vv
clus                 STAGE TIS STAGE X
  14Q LOSS MUTATED           0       4
  14Q LOSS WILD-TYPE         1       9
D67V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  19                 70
  STAGE IA                 20                 65
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA                93                260
  STAGE IIB                64                188
  STAGE III                 0                  2
  STAGE IIIA               35                119
  STAGE IIIB                5                 24
  STAGE IIIC               16                 49
  STAGE IV                  7                 13
  STAGE TIS                 0                  1
  STAGE X                   4                  9
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED    53 174  29   8
  14Q LOSS WILD-TYPE 223 450 107  32
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1               53                223
  T2              174                450
  T3               29                107
  T4                8                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  14Q LOSS MUTATED   139  76  30  17
  14Q LOSS WILD-TYPE 368 282  89  60
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              139                368
  N1               76                282
  N2               30                 89
  N3               17                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   216   7
  14Q LOSS WILD-TYPE 673  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    216    7
  14Q LOSS WILD-TYPE  673   15
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              216                673
  1                7                 15
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   265   1
  14Q LOSS WILD-TYPE 803  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    265    1
  14Q LOSS WILD-TYPE  803   11
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE              265                803
  MALE                  1                 11
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   101 136
  14Q LOSS WILD-TYPE 328 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    101  136
  14Q LOSS WILD-TYPE  328  382
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               101                328
  YES              136                382
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  14Q LOSS MUTATED                            0                           215
  14Q LOSS WILD-TYPE                          1                           555
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  14Q LOSS MUTATED                               29                   5
  14Q LOSS WILD-TYPE                            171                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  14Q LOSS MUTATED                       5                                4
  14Q LOSS WILD-TYPE                     4                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  14Q LOSS MUTATED                    1              6
  14Q LOSS WILD-TYPE                 16             41
D67V9, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 215                555
  INFILTRATING LOBULAR CARCINOMA                 29                171
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  6                 41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0    14
  14Q LOSS WILD-TYPE                                1    46
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          69   161
  14Q LOSS WILD-TYPE                       112   584
D67V11, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          14                 46
  BLACK OR AFRICAN AMERICAN                      69                112
  WHITE                                         161                584
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V12, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    12 213
  14Q LOSS WILD-TYPE  27 662
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     12  213
  14Q LOSS WILD-TYPE   27  662
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              213                662
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   269  49
  15Q LOSS WILD-TYPE 648  98
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               318                746 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                49                 98 
$`15Q LOSS MUTATED`
TCGA-3C-AALJ TCGA-A1-A0SI TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04P TCGA-A2-A04Q 
       42.81        20.88        28.01        19.20        18.02        78.41 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CS 
       73.84        87.25       101.98        99.12        24.79        77.19 
TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0EN TCGA-A2-A0EO 
       75.25       107.93        56.81        67.33        89.36        80.28 
TCGA-A2-A0EQ TCGA-A2-A0ET TCGA-A2-A0EY TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       79.76        35.05        63.29        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YJ TCGA-A2-A0YM 
       50.43        17.52        20.75        18.21        18.61        31.73 
TCGA-A2-A1G1 TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3Y0 TCGA-A2-A4RW 
       19.20        33.93        29.98        47.31        50.83         7.30 
TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13D 
       26.96        21.90        30.61        35.67        29.79        31.73 
TCGA-A7-A13E TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3J1 
       20.19        31.36        24.26        21.73        22.32        11.28 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX 
       14.50        17.92        14.73        10.29         9.37        10.42 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07B 
       17.98        29.03        26.01         1.02        53.98        43.00 
TCGA-A8-A07F TCGA-A8-A07R TCGA-A8-A084 TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O 
       18.97         8.98        15.06        12.00         9.99        31.00 
TCGA-A8-A08X TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09N 
       43.00        30.97        17.95         9.99         1.02         1.02 
TCGA-A8-A09W TCGA-A8-A0AB TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2FM TCGA-AC-A2QJ 
        0.99        17.03        22.95        73.05        26.04        14.66 
TCGA-AC-A3OD TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A8OP TCGA-AN-A04A 
       14.83        14.96        13.71        13.58        20.19         2.96 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FT 
        9.96         7.36         0.33         6.44         7.00         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN 
        0.33         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XS TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03V TCGA-AO-A0J6 
       12.33         0.33        80.28        61.35        29.13        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J9 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12F 
       20.32        53.03        72.00        55.33       108.03        48.36 
TCGA-AO-A1KQ TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A54N TCGA-AQ-A54O 
       61.87         0.53        17.79        24.79         2.56        32.91 
TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 
        5.26       109.02        75.22        64.83        55.86        65.36 
TCGA-AR-A0U1 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AQ TCGA-AR-A1AR 
      133.22       125.16       108.36       101.00        99.32        17.23 
TCGA-AR-A1AW TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V 
       86.53        33.73       104.28       112.77        97.84       105.30 
TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A256 TCGA-AR-A2LK TCGA-AR-A2LR 
       32.58        98.66        89.00        93.83        54.21        57.27 
TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0RE 
       77.62       129.57       112.37       233.62       165.76       255.68 
TCGA-B6-A0RG TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WV TCGA-B6-A0WX 
       68.45       102.77       100.70       282.90        79.63        21.47 
TCGA-B6-A0WY TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A402 
      113.79        43.59       101.52        73.51        37.87        70.16 
TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0B2 TCGA-BH-A0B5 
       68.12        18.84        71.15        62.93        40.83        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BL TCGA-BH-A0BT TCGA-BH-A0BZ 
       81.63        51.68        37.22        74.89        45.57        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C7 TCGA-BH-A0DP TCGA-BH-A0DX TCGA-BH-A0E0 
       41.75        44.02        90.97        15.65        70.88         4.41 
TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HP TCGA-BH-A0HU 
        9.63        24.49        23.08        41.00        13.61        12.89 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W7 TCGA-BH-A18F TCGA-BH-A18J 
       27.25        50.79         5.59        44.81        32.91        20.12 
TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       90.84        26.66         7.36        51.39        67.50        91.99 
TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1F6 TCGA-BH-A1FC TCGA-BH-A1FM TCGA-BH-A1FN 
      113.82        12.00        97.48       114.15        45.63        72.07 
TCGA-BH-A208 TCGA-BH-A5IZ TCGA-C8-A12P TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A135 
       57.83        18.64        11.77        12.66        48.53        12.92 
TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A278 
        4.08        10.92        12.03        12.95        12.95         9.50 
TCGA-C8-A27A TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A142 TCGA-D8-A146 TCGA-D8-A1J8 
       24.56        13.02        20.88        13.97        21.14        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1XB TCGA-D8-A1XF 
       17.49        18.90        12.03        53.00        18.15        15.22 
TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XU 
       21.80        19.92        55.30        16.41        16.31        12.99 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M TCGA-D8-A73U TCGA-D8-A73X 
       16.54        15.32         9.93        13.48        16.18        25.22 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A14O TCGA-E2-A14V TCGA-E2-A150 TCGA-E2-A152 
       46.59        40.11        44.68        34.26        63.62        69.96 
TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A1AZ TCGA-E2-A1BD 
       19.43        25.05        18.21        12.92        76.57        37.25 
TCGA-E2-A1IF TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LK 
       37.41        33.70        60.36        73.64        24.59         8.75 
TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1N9 
       26.99        34.92        38.76        34.29        22.29        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1R4 TCGA-E9-A1RC TCGA-E9-A1RE 
       36.56        39.55        41.62         6.12        40.24        46.65 
TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22D TCGA-E9-A22E 
        6.58        21.27        46.59        34.45        41.03        41.72 
TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A295 
       40.73         0.69        38.99         1.94         7.13        12.33 
TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       38.07        30.18        30.44         0.79        25.81        26.40 
TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P8 TCGA-EW-A1PC 
       25.94        29.85        40.41        41.13         7.86         6.15 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A6SA 
       19.96        55.00        52.73        25.91        34.03        16.77 
TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL TCGA-JL-A3YX 
       24.99        33.21        72.10        69.30         2.60        11.57 
TCGA-LL-A441 TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A8F5 
       32.75        14.70        14.79        22.26        16.08        19.59 
TCGA-OL-A5D7 TCGA-OL-A66I TCGA-OL-A66K TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZF 
       58.52        23.47        41.92        64.21        86.96        18.81 
TCGA-S3-A6ZG TCGA-S3-AA10 TCGA-S3-AA17 TCGA-WT-AB41 TCGA-WT-AB44 TCGA-Z7-A8R5 
       18.48        19.27        13.94        52.96        29.03       108.07 

$`15Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SQ 
       47.24        13.68        31.79         7.96        39.32        18.21 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
      143.15       121.94        63.12        55.43        36.13       136.73 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV 
      114.81        92.48        88.60       107.93         5.19        98.99 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EP 
       34.55        33.76        61.58        25.22       101.72       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       74.40        72.00        34.29        31.82        61.94        24.72 
TCGA-A2-A0ST TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       99.19        44.28        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        32.55        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FV 
       21.67        49.48        19.33        48.46        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       17.36        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW 
       10.59        36.23        39.65        91.07        32.75        56.28 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 
       35.93        50.37        24.39        21.30        23.21        21.14 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        34.29        35.47        37.45        33.11 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J 
       25.15        23.61        29.56        23.74        23.80        20.61 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       11.34        10.59        10.29        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       14.93        13.74        21.17        12.10        10.72        11.05 
TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X 
        8.75        13.02        13.02         1.02        53.06        31.00 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J 
       17.03         9.01        19.99        18.97        14.01        12.00 
TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
       32.05         9.99        10.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       45.07        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       33.01        19.96        37.05        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 
      112.08        40.01        33.01        41.98        12.00         9.99 
TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       12.00        50.04        49.05        45.07        29.98        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 
       25.02         8.98        19.04        15.02        14.01        12.00 
TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD 
       19.04        13.02        21.04         0.99        27.02        38.04 
TCGA-AC-A23C TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB 
        0.95        73.91         5.72         1.48        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH 
       86.66        90.71        60.92        87.12        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3QP TCGA-AC-A3QQ 
       19.33        32.45         6.48        16.31        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62V 
       24.79        29.26        16.80        14.53        19.33        11.44 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       17.42        18.67        12.26         1.68         8.22         0.03 
TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 
        1.12         1.32         2.30         0.33         0.33         0.23 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         0.62         1.78         1.71         7.46         0.16 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         0.33         5.65         7.96         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0XL TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU 
        6.90         5.36         0.30         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.33         5.59        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0J5 
       47.87        58.95        32.78        21.40        52.18        26.04 
TCGA-AO-A0J8 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       22.36        21.53        50.70        50.86        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        62.04        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      108.72       106.78        90.58        98.27        64.04        57.30 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AQ-A04J 
       41.62        40.57        14.73        82.62        70.39        26.93 
TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A7U7 TCGA-AR-A0TP 
      130.09         5.65        15.62        32.52        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0TZ TCGA-AR-A0U2 TCGA-AR-A0U3 
       98.33        84.10        98.93       107.24        83.87       134.14 
TCGA-AR-A0U4 TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      107.21       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AX TCGA-AR-A24H 
       93.90        37.81        94.29        61.28        86.43       160.90 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 
      105.27        77.69        98.76        99.62        93.30        85.64 
TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM 
       71.05       166.42        20.25        86.53        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       38.17        39.39        40.54        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       10.59       143.38       281.29        12.13       275.87        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IP 
       65.72       146.50        18.77       127.33        84.59       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN 
      140.88       212.25       234.28        81.17        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      162.05       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WW TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
       18.35       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A40B 
       58.88       139.17       170.17         7.07        85.35       103.63 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B3 
       59.84        20.45        25.55        63.09        81.44        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       39.16        84.13        32.02        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       21.70        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       53.95        49.94        77.95        89.06        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E1 
        3.22         2.56        38.47        67.86        16.27        15.68 
TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI 
       14.30        44.81        46.19        32.58        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HQ 
       52.96        26.50        20.38         5.85         2.50        36.85 
TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0WA TCGA-BH-A18G 
       51.32        23.93        24.95        42.35        23.05         4.90 
TCGA-BH-A18I TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       35.93        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18V TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX 
       66.05        51.16        82.85        42.28        55.69        49.58 
TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB 
       17.69        25.81        31.53        89.16        24.62       120.62 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U 
      130.16        10.65         6.44        20.12        10.52       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG 
       13.51         1.87        12.59         4.11        12.33        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V 
       11.28         0.16        10.42        12.33        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.53        12.36         8.28         9.67         9.53         0.03 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       14.43        33.99        12.95        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 
       56.81        13.25        20.58        14.17        13.48        19.20 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JH TCGA-D8-A1JI 
       16.50        55.50        15.78        18.15        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       20.09        20.12        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG 
       25.74        23.90        27.58        12.39        17.16        14.73 
TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       14.50        17.69        15.85        16.64        15.16        43.04 
TCGA-D8-A1Y0 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       15.52        14.24        14.14        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P 
       13.05        14.43        48.03        16.41         4.80         1.61 
TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
       10.09        13.08        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A 
       21.67        12.66        43.00        34.42        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       37.51        28.44        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14X 
       38.60        33.17        75.98        43.33        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       69.34        18.51        23.24        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15I 
       23.34        22.82        17.29        20.71        21.63        55.63 
TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P 
       53.92         9.04        20.58        11.05        50.79        19.56 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        14.07        51.39        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH 
       32.35        28.50        16.47        77.65        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH 
       54.18        19.66        75.81        28.90        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
      102.61        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1NE 
       17.69        34.82        32.88        36.82        34.16        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.24        25.84        18.94         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         2.56         3.02        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       32.09         1.12        47.64        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A24A TCGA-E9-A2JS 
       39.09        38.37        40.50        20.12        24.56        29.72 
TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A6HE 
        9.47        32.91        23.90        23.84        26.70        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P1 
       16.57        15.68        28.77        22.82        29.95        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       52.96        29.82        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A2FW 
       19.99        13.94        10.52        14.43        34.55        22.09 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SC TCGA-GI-A2C8 
       17.49        10.16        23.51        15.22        31.30         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 
       85.35       110.50        38.20        43.73        66.38        72.03 
TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U 
       13.55        18.12        62.47        11.84        21.24        13.22 
TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
        7.10        13.28        10.62        24.95        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z 
       17.06        15.32        14.47         2.63        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U 
       14.50        19.53        12.36        17.49        27.91        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        36.30        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       36.36        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        42.77        26.04        17.36        14.07        28.21 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LX TCGA-PL-A8LY 
       19.73        40.11         8.91        47.01         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 
        9.93        21.07        20.68        13.84        18.87        17.39 
TCGA-S3-AA15 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-XX-A899 
       17.26        17.03         3.81        66.84        11.41        15.35 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.33               0.03 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            282.90             281.29 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             30.08              26.60 
[1] "0.3 - 282.9 (30.1)" "0.0 - 281.3 (26.6)"
[1] "hr=" "1.2"
D68V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  15Q LOSS MUTATED        20       22        0        2       118        74
  15Q LOSS WILD-TYPE      69       63        6        4       235       178
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           1         50          5         16        7
  15Q LOSS WILD-TYPE         1        104         24         49       13
                    vv
clus                 STAGE TIS STAGE X
  15Q LOSS MUTATED           0       3
  15Q LOSS WILD-TYPE         1      10
D68V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 22                 63
  STAGE IB                  0                  6
  STAGE II                  2                  4
  STAGE IIA               118                235
  STAGE IIB                74                178
  STAGE III                 1                  1
  STAGE IIIA               50                104
  STAGE IIIB                5                 24
  STAGE IIIC               16                 49
  STAGE IV                  7                 13
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    62 212  36   9
  15Q LOSS WILD-TYPE 214 412 100  31
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               62                214
  T2              212                412
  T3               36                100
  T4                9                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  15Q LOSS MUTATED   164  89  44  20
  15Q LOSS WILD-TYPE 343 269  75  57
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              164                343
  N1               89                269
  N2               44                 75
  N3               20                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   271   7
  15Q LOSS WILD-TYPE 618  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    271    7
  15Q LOSS WILD-TYPE  618   15
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              271                618
  1                7                 15
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   316   4
  15Q LOSS WILD-TYPE 752   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    316    4
  15Q LOSS WILD-TYPE  752    8
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              316                752
  MALE                  4                  8
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   125 158
  15Q LOSS WILD-TYPE 304 360
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    125  158
  15Q LOSS WILD-TYPE  304  360
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               125                304
  YES              158                360
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  15Q LOSS MUTATED                            0                           254
  15Q LOSS WILD-TYPE                          1                           516
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  15Q LOSS MUTATED                               34                   3
  15Q LOSS WILD-TYPE                            166                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  15Q LOSS MUTATED                       5                               10
  15Q LOSS WILD-TYPE                     4                               19
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  15Q LOSS MUTATED                    2             12
  15Q LOSS WILD-TYPE                 15             35
D68V9, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 254                516
  INFILTRATING LOBULAR CARCINOMA                 34                166
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               10                 19
  MUCINOUS CARCINOMA                              2                 15
  OTHER  SPECIFY                                 12                 35
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0    15
  15Q LOSS WILD-TYPE                                1    45
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                          63   215
  15Q LOSS WILD-TYPE                       118   530
D68V11, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          15                 45
  BLACK OR AFRICAN AMERICAN                      63                118
  WHITE                                         215                530
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V12, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     9 261
  15Q LOSS WILD-TYPE  30 614
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      9  261
  15Q LOSS WILD-TYPE   30  614
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              261                614
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED   149  23
  16P LOSS WILD-TYPE 768 124
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               172                892 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                23                124 
$`16P LOSS MUTATED`
TCGA-A1-A0SE TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CR 
       43.43        31.79        39.32        73.84        87.25       107.93 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EQ TCGA-A2-A0EY 
       75.25        98.99        67.33        25.22        79.76        63.29 
TCGA-A2-A0SX TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A1FX TCGA-A2-A3XT TCGA-A2-A4RY 
       50.43        20.75        32.55        60.72        91.07        21.30 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A13D 
       38.30        34.29        35.47        30.61        35.67        31.73 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A4SD TCGA-A7-A56D TCGA-A7-A5ZW 
       25.15        23.61        20.61        14.50        14.73        10.72 
TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A075 TCGA-A8-A07B TCGA-A8-A07L TCGA-A8-A08J 
        9.37        13.02        17.03        43.00        32.05        37.05 
TCGA-A8-A08X TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09W TCGA-AC-A2BK 
       43.00        33.07         1.02        25.02         0.99        73.05 
TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FF TCGA-AC-A3TM TCGA-AC-A5EI TCGA-AC-A6IW 
       99.35        40.57        90.71        25.05        14.53        13.58 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AN-A046 TCGA-AN-A0AL TCGA-AN-A0AR 
        0.03        20.19         1.12         0.33         7.46         0.33 
TCGA-AN-A0FN TCGA-AN-A0XN TCGA-AN-A0XR TCGA-AO-A0JD TCGA-AO-A129 TCGA-AO-A12B 
        7.17         0.33         0.33        72.00       108.03        98.27 
TCGA-AO-A12G TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0U3 TCGA-AR-A1AH 
       41.62        17.79        32.52         2.56       134.14       125.16 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24O TCGA-AR-A24U 
       99.32        17.23       160.90        50.89       118.59        77.69 
TCGA-AR-A24V TCGA-AR-A251 TCGA-AR-A2LR TCGA-B6-A0I5 TCGA-B6-A0IJ TCGA-B6-A0RE 
      105.30        99.62        57.27       281.29       233.62       255.68 
TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0X0 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 
      212.25        81.17       129.70        43.59       170.17        70.16 
TCGA-BH-A0B4 TCGA-BH-A0B6 TCGA-BH-A0BO TCGA-BH-A0C0 TCGA-BH-A0DE TCGA-BH-A0E0 
       39.16        81.63        72.23        41.75        77.98         4.41 
TCGA-BH-A0E2 TCGA-BH-A0H5 TCGA-BH-A0HP TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A18K 
       14.30        53.26        13.61        51.32        50.79        90.84 
TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1FC 
       51.39        67.50        82.85        42.28        55.69       114.15 
TCGA-BH-A1FD TCGA-BH-A1FL TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A5IZ 
       33.17        55.00        38.60       130.16         6.44        18.64 
TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-C8-A130 TCGA-C8-A1HG TCGA-C8-A26X TCGA-C8-A278 
       18.87        21.76         3.16        11.34        12.36         9.50 
TCGA-C8-A27B TCGA-C8-A3M7 TCGA-D8-A1JC TCGA-D8-A1JN TCGA-D8-A1JT TCGA-D8-A1JU 
       14.43        33.99        15.78        20.38        13.32        14.70 
TCGA-D8-A27V TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-E2-A14W TCGA-E2-A14Y 
       12.53        18.51        21.67        16.18        32.02        69.34 
TCGA-E2-A150 TCGA-E2-A159 TCGA-E2-A15J TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T 
       63.62        25.05        53.92        56.94        14.07        51.39 
TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1L7 TCGA-E2-A1LK TCGA-E2-A573 
       76.57        33.70         3.88        60.36         8.75        34.92 
TCGA-E2-A574 TCGA-E9-A1ND TCGA-E9-A1NH TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 
       38.76        41.62        18.94        41.03        40.73         0.69 
TCGA-E9-A248 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A3U0 
        1.94        15.68        28.77         7.86         6.15        17.49 
TCGA-EW-A423 TCGA-GM-A2D9 TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DO TCGA-GM-A3NY 
       10.16        59.57        83.34        72.10        85.35        38.20 
TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-HN-A2OB TCGA-LL-A50Y TCGA-LL-A5YN 
       69.30        72.03         2.60        62.47        25.05        14.70 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A5D7 TCGA-OL-A5RW TCGA-OL-A66L TCGA-OL-A6VO 
       12.36        19.59        58.52        36.36        42.77        28.21 
TCGA-PE-A5DC TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 
       47.01        20.68        19.27        18.87 

$`16P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         9.96         8.52        14.37        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP 
       47.24        20.88        13.68         7.96        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V 
       18.21       143.15        18.02        78.41       121.94        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW 
      114.81        92.48        88.60        77.19         5.19       107.93 
TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN 
       56.81        34.55        33.76        61.58       101.72        89.36 
TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
       80.28       118.45        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       31.82        61.94        24.72        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       44.88        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       20.52        17.46        18.90        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G0 
       31.73        23.77        23.47        17.36        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         7.30        24.39        23.21        26.96 
TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DB TCGA-A7-A0DC 
       21.14        21.90        35.31        37.45        33.11        29.79 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       20.19        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       21.73        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       13.41        14.70        11.97        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY 
       17.92        12.10        11.05        10.29        10.42         8.75 
TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02         1.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02        53.98         9.01        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R 
       18.97        14.01        12.00         9.99        10.98         8.98 
TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 
        7.99        24.99         9.99        45.07        15.06        36.95 
TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F TCGA-A8-A08G 
       13.02         0.99        38.01        28.96        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       12.00         9.99        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
      112.08        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       12.00         9.99         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       49.05        45.07        29.98         8.98        19.04        15.02 
TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       14.01        12.00        19.04        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM 
        5.72         1.48        86.66        60.92        87.12        26.04 
TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       74.14        33.04        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TN TCGA-AC-A3W5 
       16.31        14.83        22.19        24.13        14.99        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH 
       19.79        15.48        23.24        24.79        29.26        16.80 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV 
       19.33        14.96        11.44        13.71        17.42        18.67 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
       12.26         1.68         8.22         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.62         2.96         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD 
        9.96         7.36         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FS TCGA-AN-A0FT 
        5.65         7.96         7.00         7.59         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         5.36 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
       12.33         0.30         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.59        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 
       52.18        26.04        37.48        20.32        22.36        53.03 
TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       21.53        50.70        50.86        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F 
      108.72       106.78        90.58        64.04        57.30        48.36 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        14.73        82.62        61.87        70.39         0.53 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O 
       24.79        26.93       130.09         5.65        15.62        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT 
       19.20       140.55        98.33         5.26        84.10       109.02 
TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 
       75.22        98.93        64.83        55.86       107.24        65.36 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK 
      133.22        83.87       107.21       108.36       101.00       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
       97.68        98.33        96.00        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24L 
       94.29        61.28        86.53        86.43        33.73        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
      120.33        99.78         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 
      105.27        32.58        98.76        98.66        89.00        93.30 
TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ 
       85.64        71.05        93.83       166.42        20.25        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ 
       54.21        66.15        63.62        38.17        39.39        40.54 
TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       73.35        33.30        38.96        10.59        77.62       143.38 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG 
       12.13       275.87       129.57        50.70        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      112.37        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      140.88        68.45       234.28        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
      102.77       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY 
       97.48       188.68        79.63        18.35        21.47       113.79 
TCGA-B6-A0WZ TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KF 
      206.86       245.10        28.27        68.94        58.88       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 
       73.51       139.17        37.87         7.07        85.35        68.12 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW 
       18.84       103.63        71.15        62.93        59.84        20.45 
TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 
       25.55        63.09        81.44        40.83        39.55        70.22 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ 
       61.51        21.70        74.89        61.68        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH 
       44.02        89.06        90.97        45.83        23.44        38.01 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ 
       29.98        13.91        78.28        17.26        15.65         3.22 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 
        2.56        38.47        67.86        70.88        16.27        15.68 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H6 
       24.43        30.35        10.78        15.16        37.78        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 
        2.50        36.85        12.89        27.25         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G 
       24.95        42.35        44.81        23.05        32.91         4.90 
TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       35.93        20.12        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1EO 
       55.63        37.55        66.05         7.36        51.16        91.99 
TCGA-BH-A1ES TCGA-BH-A1EV TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
      113.82        12.00        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FE TCGA-BH-A1FG 
       89.16        97.48        24.62       120.62        74.73       122.89 
TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU 
       36.92        63.35        45.63        72.07       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A2L8 
       28.14        26.14        83.31        57.83        10.65        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       109.28        20.88        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
        9.70         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 
       48.53        12.56        13.51         1.87        12.59        12.92 
TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
        4.11         4.08        12.33        10.92        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
       12.03        10.42        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.53        12.95         8.28         9.67         9.53         0.03 
TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ 
       24.56        12.95        13.02        12.49        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       56.81        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       55.50        18.15        18.90        12.03        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP 
       18.97        20.09        20.12        20.09        19.40        21.01 
TCGA-D8-A1JS TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       12.20        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG 
       27.58        18.15        12.39        17.16        15.22        14.73 
TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       21.80        14.50        19.92        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         1.61        10.09        13.08 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       12.26        33.37        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Z 
       33.17        75.98        43.33        34.26        31.96        18.51 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       69.96        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       12.92        55.63         9.04        20.58        11.05        50.79 
TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       19.56        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       28.44        59.18        22.19        60.99        11.08        54.18 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       73.64        19.66        24.59        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61        43.04        26.99        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       36.82        22.29        34.16        36.20        36.56        39.55 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02        11.15        48.23 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       45.01        32.09        40.24         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 
       21.27        46.59        47.64        34.45        32.05        42.25 
TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       37.74        39.09        38.37        41.72        40.50        20.12 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
       38.99         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       38.07        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       26.70         0.79        25.81        26.40        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 
       25.94        22.82        29.95        29.85        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       39.78        52.96        29.82        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       18.90        19.99        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 
       19.96        55.00        52.73        25.91        22.09        34.03 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       23.51        15.22        16.77        24.99        31.30        33.21 
TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF 
        7.40       109.87       216.76        79.10        75.02        70.85 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A3NW 
       85.15        86.96       115.69       106.06       101.62       110.50 
TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX TCGA-JL-A3YW TCGA-JL-A3YX 
       43.73        66.38        13.55        18.12        11.84        11.57 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP 
       32.75        29.23        17.06        15.32        14.47        14.79 
TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 
       22.26         2.63        16.08        15.68         7.46        14.50 
TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.53        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY 
       31.99        58.62        40.08        34.92        28.87        24.72 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       26.04        17.36        14.07        19.73        40.11         8.91 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF 
       64.21        86.96         0.16         0.26         9.93        18.81 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       18.48        21.07        13.84        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       17.03         3.81        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.03               0.03 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            281.29             282.90 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             35.57              26.09 
[1] "0.0 - 281.3 (35.6)" "0.0 - 282.9 (26.1)"
[1] "hr=" "1.3"
D69V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16P LOSS MUTATED        20       11        1        0        68        33
  16P LOSS WILD-TYPE      69       74        5        6       285       219
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0         22          5         11        1
  16P LOSS WILD-TYPE         2        132         24         54       19
                    vv
clus                 STAGE TIS STAGE X
  16P LOSS MUTATED           0       1
  16P LOSS WILD-TYPE         1      12
D69V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  20                 69
  STAGE IA                 11                 74
  STAGE IB                  1                  5
  STAGE II                  0                  6
  STAGE IIA                68                285
  STAGE IIB                33                219
  STAGE III                 0                  2
  STAGE IIIA               22                132
  STAGE IIIB                5                 24
  STAGE IIIC               11                 54
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED    44 100  21   7
  16P LOSS WILD-TYPE 232 524 115  33
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1               44                232
  T2              100                524
  T3               21                115
  T4                7                 33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16P LOSS MUTATED    95  47  17  13
  16P LOSS WILD-TYPE 412 311 102  64
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               95                412
  N1               47                311
  N2               17                102
  N3               13                 64
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   149   1
  16P LOSS WILD-TYPE 740  21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    149    1
  16P LOSS WILD-TYPE  740   21
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0              149                740
  1                1                 21
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED   171   2
  16P LOSS WILD-TYPE 897  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED    171    2
  16P LOSS WILD-TYPE  897   10
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE              171                897
  MALE                  2                 10
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    72  78
  16P LOSS WILD-TYPE 357 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     72   78
  16P LOSS WILD-TYPE  357  440
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                72                357
  YES               78                440
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16P LOSS MUTATED                            0                           131
  16P LOSS WILD-TYPE                          1                           639
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16P LOSS MUTATED                               29                   3
  16P LOSS WILD-TYPE                            171                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16P LOSS MUTATED                       2                                3
  16P LOSS WILD-TYPE                     7                               26
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16P LOSS MUTATED                    0              5
  16P LOSS WILD-TYPE                 17             42
D69V9, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 131                639
  INFILTRATING LOBULAR CARCINOMA                 29                171
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                3                 26
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  5                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0    11
  16P LOSS WILD-TYPE                                1    49
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                          42   108
  16P LOSS WILD-TYPE                       139   637
D69V11, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          11                 49
  BLACK OR AFRICAN AMERICAN                      42                139
  WHITE                                         108                637
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V12, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7 143
  16P LOSS WILD-TYPE  32 732
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7  143
  16P LOSS WILD-TYPE   32  732
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    7                 32
  NOT HISPANIC OR LATINO              143                732
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED   510  75
  16Q LOSS WILD-TYPE 407  72
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               585                479 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                75                 72 
$`16Q LOSS MUTATED`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-A1-A0SD TCGA-A1-A0SE 
       40.14        11.44        48.56        48.36        14.37        43.43 
TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       48.10        47.24        31.79         7.96        39.32        28.01 
TCGA-A2-A04N TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A0CK 
      143.15       121.94        73.84        87.25        63.12       136.73 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        77.19        75.25 
TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       98.99        67.33        34.55        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EQ TCGA-A2-A0EU TCGA-A2-A0EX TCGA-A2-A0EY 
       89.36        80.28        79.76        34.29        24.72        63.29 
TCGA-A2-A0SU TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       54.64        44.28        17.13        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YH 
       20.75        32.55        25.28        18.21        50.47        21.67 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1G0 
       19.33        48.46        31.73        23.47        60.72        20.25 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A4RY 
       52.47       107.70        36.23        39.65        91.07        21.30 
TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DB 
       21.90        38.30        34.29        35.47        30.61        33.11 
TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26I 
       31.73        25.15        23.61        29.56        31.36        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB 
       20.61        22.32        10.59        11.28        14.93        13.74 
TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       14.50        21.17        14.73        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06U TCGA-A8-A06X 
        9.37        13.02        13.02         1.02        29.03        31.00 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07J 
       17.03         9.01        43.00        19.99        18.97        12.00 
TCGA-A8-A07L TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A084 TCGA-A8-A086 
       32.05        10.98         8.98         7.99        15.06        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08O 
        0.99        38.01        28.96        19.96        37.05        31.00 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09K 
       30.97        17.95        41.98         9.99        12.00        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 
       27.02        17.03        38.04        22.95        73.91         1.48 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.05        99.35        40.57        86.66        90.71        60.92 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       26.04        74.14        19.33         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU 
       15.48        29.26        16.80        14.53        19.33        14.96 
TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC 
       13.71        13.58        12.26         1.68         8.22         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 
       20.19         1.12         2.30         0.33         0.33         0.33 
TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0XL 
        7.36         0.33         7.00         7.17         6.90         5.36 
TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A0J3 
       80.28        66.77        81.63        95.70        68.75        21.40 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JD TCGA-AO-A0JF 
       20.32        22.36        53.03        21.53        72.00        65.10 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A129 TCGA-AO-A12A 
       50.24        62.04        99.25       108.72       108.03        90.58 
TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A1KP TCGA-AO-A1KS TCGA-AO-A1KT 
       98.27        57.30        41.62        82.62         0.53        17.79 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AR-A0TV TCGA-AR-A0TZ TCGA-AR-A0U2 
       15.62        32.52         2.56        75.22       107.24        83.87 
TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      134.14       125.16       103.86        97.68        98.33        96.00 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       93.90        99.32        17.23       160.90        50.89        94.22 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U 
       99.78       118.59         2.76        97.84       105.27        77.69 
TCGA-AR-A24V TCGA-AR-A24X TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LJ 
      105.30        98.76        99.62        85.64       166.42        86.53 
TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A5QN 
       54.21        66.15        63.62        38.17        39.39        33.30 
TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IM 
      281.29       275.87       129.57        50.70       112.37       127.33 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RN TCGA-B6-A0RP TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WW 
       81.17       263.28       102.77       157.41        97.48        18.35 
TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A2IU TCGA-B6-A402 
      206.86       129.70        58.88        43.59       170.17        70.16 
TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AY 
       68.12       103.63        71.15        62.93        59.84        25.55 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       81.44        40.83        39.16        70.22        81.63        84.13 
TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       37.22        43.53        61.68        72.23        75.48        74.14 
TCGA-BH-A0BS TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DE 
       53.95        41.75        44.02        89.06        90.97        77.98 
TCGA-BH-A0DH TCGA-BH-A0DK TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT 
       38.01        13.91        17.26        15.65         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY 
       44.81        46.19        32.58        24.49        31.00        30.35 
TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       15.16        37.78        53.26        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18J 
       23.93        24.95        44.81        23.05        32.91        20.12 
TCGA-BH-A18K TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN 
       90.84        37.74        30.28         7.36        51.39        67.50 
TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY 
       91.99        82.85        42.28        12.00        55.69        17.69 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG 
       31.53        89.16       114.15        33.17        74.73       122.89 
TCGA-BH-A1FL TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A209 TCGA-BH-A28Q TCGA-BH-A2L8 
       55.00        26.14        38.60       130.16         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       10.52        20.88        18.64         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A137 
        9.44        11.77        48.53        12.56         3.16         4.11 
TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HM 
        4.08        12.33        10.92        11.34        11.28        12.33 
TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A27B 
       12.95        12.53        12.36         9.53         9.50        14.43 
TCGA-C8-A3M7 TCGA-C8-A8HQ TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A141 TCGA-D8-A1J8 
       33.99        12.49        56.81        20.88        20.58        14.17 
TCGA-D8-A1J9 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JI 
       17.49        15.78        18.15        18.90        53.00        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X8 TCGA-D8-A1XK TCGA-D8-A1XO TCGA-D8-A1XQ 
       18.58        17.79        25.74        14.50        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y3 
       15.85        16.31        16.54        15.52         9.93        14.14 
TCGA-D8-A27G TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V 
       13.45        48.03        16.41         1.61        13.08        12.53 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A107 TCGA-E2-A10A TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Q 
       34.42        40.41        40.11        28.44        44.68        38.24 
TCGA-E2-A14S TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       33.17        43.33        32.02        69.34        18.51        63.62 
TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       23.24        21.04        23.87        25.05        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       20.58        50.79        56.94        14.07        51.39        76.57 
TCGA-E2-A1B4 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IH 
       33.01        16.47        37.25        77.65        37.41        33.73 
TCGA-E2-A1II TCGA-E2-A1IL TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 
       33.70         3.88        11.08        54.18        60.36        73.64 
TCGA-E2-A1LA TCGA-E2-A1LG TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
       24.59        50.07         8.75        26.99        34.55        43.56 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N5 
       30.61        34.92        38.76        34.29        32.88        36.82 
TCGA-E9-A1N8 TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1QZ 
       34.16        41.62        35.24        25.84        18.94        24.82 
TCGA-E9-A1R0 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       28.27         2.56         6.12         3.02        11.15        48.23 
TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RG TCGA-E9-A1RI 
       45.01        32.09         1.12        46.65        21.27        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H 
       34.45        32.05        41.03        41.72        40.73        40.50 
TCGA-E9-A244 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A3HO 
        0.69         1.94         7.13        24.56        12.33        38.07 
TCGA-E9-A3X8 TCGA-E9-A54Y TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IY 
       30.44        23.84        26.40        27.85        12.20         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.21        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PE 
       40.41        52.96        18.48         7.86         6.15        10.52 
TCGA-EW-A1PG TCGA-EW-A2FS TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       34.55        52.73        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GM-A2D9 
       15.22        16.77        31.30        33.21         7.40        59.57 
TCGA-GM-A2DC TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       83.34        72.10        85.15       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XL TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       38.20        69.30        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W6 TCGA-LL-A50Y 
       62.47        11.57        21.24        13.22        13.28        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LQ-A4E4 
       17.06        14.70        22.26        12.36        19.59        27.91 
TCGA-MS-A51U TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RV 
       22.39        36.30        58.52        31.99        58.62        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5S0 TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L 
       36.36        28.87        20.38        65.62        41.92        42.77 
TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-S3-A6ZF 
       26.04        28.21        19.73        47.01        64.21        18.81 
TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA12 TCGA-W8-A86G TCGA-WT-AB44 
       18.48        20.68        19.27        18.87        11.41        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R6 
       15.35        16.04       107.05 

$`16Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SG 
      129.14       131.67        42.81         9.96         8.52        14.27 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04Q 
       20.88        13.68        19.20        18.21        18.02        78.41 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CU 
      101.98        55.43        36.13        99.12        24.79         5.19 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0EP TCGA-A2-A0ER TCGA-A2-A0ES 
      107.93        56.81        33.76       118.45        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW 
       35.05        31.82        61.94        99.19        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0YG TCGA-A2-A0YI 
       50.43        17.52         8.38        49.84        21.90        49.48 
TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 
       18.61        23.77        17.36        22.45        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       16.47        42.44        17.19        18.15       105.34        10.59 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S0 TCGA-A2-A4S1 
       50.37        50.83         7.30        24.39        23.21        26.96 
TCGA-A2-A4S2 TCGA-A7-A0CE TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DC TCGA-A7-A13E 
       21.14        35.31        37.45        35.67        29.79        20.19 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF 
       24.26        23.74        23.80        11.34        10.29        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A6VX TCGA-A7-A6VY 
       14.70        11.97        17.92        12.10        10.42         8.75 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A07G 
       17.98        53.06        26.01         1.02        53.98        18.97 
TCGA-A8-A07I TCGA-A8-A07O TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 
       14.01         9.99        24.99         9.99        45.07        36.95 
TCGA-A8-A08F TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08R TCGA-A8-A097 TCGA-A8-A09A 
       33.01        12.00         9.99         0.99        12.00         9.99 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A0A7 TCGA-AC-A23C 
        1.02        50.04        49.05        45.07         0.99         0.95 
TCGA-AC-A23H TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3YI 
        5.72        87.12        33.04        14.66        32.45        23.24 
TCGA-AC-A3YJ TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A8OR TCGA-AN-A041 
       24.79        11.44        17.42        18.67         1.32         0.23 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL 
        0.62         2.96         1.78         1.71         9.96         7.46 
TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.16         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.59         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03T 
        0.33        12.33         5.33         5.59        61.35        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        52.18        26.04        37.48 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM 
       50.70        50.86        76.77        26.24        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A128 TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO 
      115.27       106.78        64.04        48.36        40.57        14.73 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
       61.87        70.39        24.79        26.93       130.09         5.65 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       140.55        98.33         5.26        84.10 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 
      109.02        98.93        64.83        55.86        65.36       133.22 
TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AO TCGA-AR-A1AS TCGA-AR-A1AU 
      107.21       108.36       101.00        86.07        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24M TCGA-AR-A24Q 
       61.28        86.53        86.43        33.73       120.33       104.28 
TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 
      112.77        32.58        98.66        89.00        93.30        71.05 
TCGA-AR-A256 TCGA-AR-A2LH TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QP 
       93.83        20.25        40.54        57.27        73.35        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I9 TCGA-B6-A0IE TCGA-B6-A0IG 
       10.59        77.62       143.38        12.13        65.72       146.50 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0RM TCGA-B6-A0RO 
      233.62        18.77        84.59       165.76        78.02       162.05 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0WT TCGA-B6-A0WV 
      140.48       100.70        89.46       282.90       188.68        79.63 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A1KF 
       21.47       113.79       245.10        28.27        68.94       101.52 
TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A409 
       73.51       139.17        37.87         7.07        85.35        18.84 
TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BD 
       20.45        63.09        39.55        51.68        32.02        18.21 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV 
       61.51        21.70        74.89        76.60        45.57        49.94 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DL 
       77.95        49.05        45.83        23.44        29.98        78.28 
TCGA-BH-A0DQ TCGA-BH-A0DX TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H6 TCGA-BH-A0H7 
        3.22        70.88        24.43        10.78        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0RX TCGA-BH-A0W5 TCGA-BH-A18G 
       41.00        52.96        26.50         5.59        42.35         4.90 
TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       35.93        26.66        72.56        55.63        37.55        66.05 
TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F6 TCGA-BH-A1F8 
       51.16       113.82        49.58        25.81        97.48        24.62 
TCGA-BH-A1FB TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A1FR 
      120.62        36.92        63.35        45.63        72.07       144.59 
TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A42U 
       72.07        28.14        83.31        57.83        10.65       109.28 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O 
       23.51         9.63         5.26        11.93        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       11.77        12.66        12.66        12.66        12.66        12.66 
TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HJ TCGA-C8-A1HK 
       13.51         1.87        12.59        12.92         0.16        12.03 
TCGA-C8-A1HL TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       10.42        12.33        20.25        12.95         8.28         9.67 
TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ 
        0.03        24.56        12.95        13.02        13.41        19.46 
TCGA-D8-A140 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       13.25        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL 
       16.50        55.50        12.03        14.01        20.12        20.09 
TCGA-D8-A1JM TCGA-D8-A1X7 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC 
       19.40        16.73        23.90        27.58        18.15        12.39 
TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XM 
       17.16        15.22        14.73        21.80        19.92        17.69 
TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y2 
       16.64        12.99        15.16        43.04        15.32        14.24 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27M TCGA-D8-A27N 
       17.42        16.04        13.05        14.43        13.48         4.80 
TCGA-D8-A27R TCGA-D8-A27W TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10B 
       10.09        12.26        43.00        27.52        46.59        37.51 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14R TCGA-E2-A14T TCGA-E2-A14V 
       28.87        47.15        40.96        38.60        75.98        34.26 
TCGA-E2-A14X TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15F 
       31.96        69.96        19.43        14.79        23.34        21.63 
TCGA-E2-A15M TCGA-E2-A15P TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1B6 
       11.05        19.56        53.62        87.22        32.35        28.50 
TCGA-E2-A1IG TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L9 
       70.36        28.44        59.18        22.19        60.99        19.66 
TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LL TCGA-E2-A56Z 
       75.81        28.90       106.75       102.61        43.04         8.28 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       17.69        34.82        22.29        36.20        36.56        39.55 
TCGA-E9-A1NE TCGA-E9-A1NI TCGA-E9-A1R2 TCGA-E9-A1RC TCGA-E9-A1RF TCGA-E9-A1RH 
       35.77         9.86        34.95        40.24         6.58        46.59 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A243 TCGA-E9-A247 
       42.25        37.74        39.09        38.37        20.12        38.99 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A54X TCGA-E9-A5FK 
       29.72         9.47        32.91        30.18        23.90        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-EW-A1IX TCGA-EW-A1J1 TCGA-EW-A1OW TCGA-EW-A1OX 
        0.79        25.81        39.72        18.90        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P7 
       29.85        41.13        39.78        29.82        23.11        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PF TCGA-EW-A1PH TCGA-EW-A2FR 
       18.90        19.99        13.94        14.43        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A6SB TCGA-GI-A2C9 TCGA-GM-A2DA TCGA-GM-A2DB 
       25.91        22.09        24.99       109.87       216.76        79.10 
TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A3XG 
       75.02        70.85        86.96       115.69       106.06        43.73 
TCGA-GM-A3XN TCGA-JL-A3YW TCGA-LD-A7W5 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 
       66.38        11.84         7.10        10.62        24.95        32.75 
TCGA-LL-A442 TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
       29.23        15.32        14.47        14.79         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A9Q3 TCGA-OK-A5Q2 
       15.68         7.46        14.50        19.53        17.49         2.10 
TCGA-OL-A5RU TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66O 
       40.08        24.72        22.32        26.70        23.47        17.36 
TCGA-OL-A66P TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LX TCGA-PL-A8LY 
       14.07        40.11         8.91        86.96         0.16         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZH TCGA-S3-AA11 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
        9.93        21.07        13.84        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB41 TCGA-Z7-A8R5 
       17.03         3.81        66.84        52.96       108.07 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.03               0.03 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            281.29             282.90 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             29.03              26.24 
[1] "0.0 - 281.3 (29.0)" "0.0 - 282.9 (26.2)"
[1] "hr=" "1.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  16Q LOSS MUTATED        55       45        3        4       203       134
  16Q LOSS WILD-TYPE      34       40        3        2       150       118
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           1         81         13         37        7
  16Q LOSS WILD-TYPE         1         73         16         28       13
                    vv
clus                 STAGE TIS STAGE X
  16Q LOSS MUTATED           0       8
  16Q LOSS WILD-TYPE         1       5
D70V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  55                 34
  STAGE IA                 45                 40
  STAGE IB                  3                  3
  STAGE II                  4                  2
  STAGE IIA               203                150
  STAGE IIB               134                118
  STAGE III                 1                  1
  STAGE IIIA               81                 73
  STAGE IIIB               13                 16
  STAGE IIIC               37                 28
  STAGE IV                  7                 13
  STAGE TIS                 0                  1
  STAGE X                   8                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED   154 340  80  18
  16Q LOSS WILD-TYPE 122 284  56  22
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1              154                122
  T2              340                284
  T3               80                 56
  T4               18                 22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  16Q LOSS MUTATED   295 185  60  46
  16Q LOSS WILD-TYPE 212 173  59  31
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0              295                212
  N1              185                173
  N2               60                 59
  N3               46                 31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   486   8
  16Q LOSS WILD-TYPE 403  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    486    8
  16Q LOSS WILD-TYPE  403   14
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0              486                403
  1                8                 14
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   588   5
  16Q LOSS WILD-TYPE 480   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    588    5
  16Q LOSS WILD-TYPE  480    7
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE              588                480
  MALE                  5                  7
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED   242 279
  16Q LOSS WILD-TYPE 187 239
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED    242  279
  16Q LOSS WILD-TYPE  187  239
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO               242                187
  YES              279                239
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  16Q LOSS MUTATED                            0                           390
  16Q LOSS WILD-TYPE                          1                           380
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  16Q LOSS MUTATED                              158                   3
  16Q LOSS WILD-TYPE                             42                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  16Q LOSS MUTATED                       1                               18
  16Q LOSS WILD-TYPE                     8                               11
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  16Q LOSS MUTATED                    3             19
  16Q LOSS WILD-TYPE                 14             28
D70V9, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 390                380
  INFILTRATING LOBULAR CARCINOMA                158                 42
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           1                  8
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 11
  MUCINOUS CARCINOMA                              3                 14
  OTHER  SPECIFY                                 19                 28
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  1    29
  16Q LOSS WILD-TYPE                                0    31
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                          91   410
  16Q LOSS WILD-TYPE                        90   335
D70V11, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          29                 31
  BLACK OR AFRICAN AMERICAN                      91                 90
  WHITE                                         410                335
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V12, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    21 466
  16Q LOSS WILD-TYPE  18 409
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21  466
  16Q LOSS WILD-TYPE   18  409
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   21                 18
  NOT HISPANIC OR LATINO              466                409
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   484  88
  17P LOSS WILD-TYPE 433  59
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               572                492 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                88                 59 
$`17P LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK 
       14.37        43.43        48.10        47.24        20.88        31.79 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04R 
       39.32        28.01        19.20        18.21        18.02       121.94 
TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK 
       73.84        87.25        63.12       101.98        36.13       136.73 
TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CR TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       24.79       114.81       107.93        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 TCGA-A2-A0EN TCGA-A2-A0EO 
      107.93        67.33        34.55        25.22        89.36        80.28 
TCGA-A2-A0EQ TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX 
       79.76        24.72        63.29        27.12        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YC 
       44.28        17.13        49.84        20.52        20.75        32.55 
TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A1FV 
       18.21        21.90        21.67        19.33        48.46        23.47 
TCGA-A2-A1FW TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A25A TCGA-A2-A25B 
       17.36        20.25        19.20        19.56       107.70        42.44 
TCGA-A2-A25D TCGA-A2-A3KD TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY 
       18.15        39.65        91.07        32.75        56.28        35.93 
TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG 
       50.83         7.30        24.39        26.96        21.90        34.29 
TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13H 
       30.61        37.45        35.67        31.73        25.15        29.56 
TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A2KD 
       31.36        24.26        23.74        23.80        21.73        22.32 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZX TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06Q 
       11.05         9.37        10.42         8.75        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       17.98        29.03        31.00         1.02        17.03        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07L 
        9.01        43.00        19.99        18.97        14.01        32.05 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08B 
        8.98         9.99        15.06        36.95        13.02        38.01 
TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08R TCGA-A8-A08X TCGA-A8-A092 
       33.01         9.99        31.00         0.99        43.00        30.97 
TCGA-A8-A093 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M 
       17.95         9.99         1.02        45.07        29.98        33.07 
TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09X TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A7 
        1.02         8.98        14.01        19.04        13.02         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A2BK TCGA-AC-A2BM 
       17.03        38.04         0.95        22.95        73.05        99.35 
TCGA-AC-A2FB TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3OD 
       40.57        19.33        14.66        32.45         6.48        14.83 
TCGA-AC-A3QQ TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A4ZE 
       24.13        14.99        16.57        19.79        15.48        29.26 
TCGA-AC-A5EH TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A7VB TCGA-AC-A8OS TCGA-AN-A041 
       16.80        13.71        17.42         8.22         2.30         0.23 
TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AM 
        0.33         1.78         1.71         9.96         7.46         0.16 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FT 
        0.33         0.33         6.44         7.96         7.59         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        61.35        66.77        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JA 
       47.87        29.13        32.78        21.40        52.18        21.53 
TCGA-AO-A0JB TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A126 
       50.70        72.00        76.77        62.04        71.80       108.72 
TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12G TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H 
      108.03        64.04        41.62        70.39         0.53        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O 
       26.93       130.09         5.65        32.52         2.56        32.91 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
      140.55         5.26       109.02        98.93        55.86       107.24 
TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      133.22        83.87       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS 
      101.00        98.33        96.00        99.32        17.23        37.81 
TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24O 
       94.29        86.43        33.73       160.90        94.22       118.59 
TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24Z 
        2.76        97.84       105.27        77.69       105.30        98.66 
TCGA-AR-A250 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE TCGA-AR-A2LJ 
       89.00        85.64        71.05        93.83       166.42        86.53 
TCGA-AR-A2LM TCGA-AR-A5QM TCGA-B6-A0I9 TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0IG 
       63.62        73.35        12.13       129.57        65.72       146.50 
TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO 
      112.37       233.62        18.77       127.33        84.59       165.76 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RS 
      140.88       255.68        68.45       212.25       234.28       100.70 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WV TCGA-B6-A0WY TCGA-B6-A0WZ 
      282.90       157.41        97.48        79.63       113.79       206.86 
TCGA-B6-A0X7 TCGA-B6-A1KN TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AV 
       58.88       139.17        70.16        68.12        18.84        59.84 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B9 
       25.55        81.44        40.83        70.22        81.63        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BM TCGA-BH-A0BP TCGA-BH-A0BQ 
       37.22        32.02        43.53        61.68        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE 
       76.60        77.95        49.05        44.02        45.83        77.98 
TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DP TCGA-BH-A0DX TCGA-BH-A0DZ 
       29.98        13.91        78.28        15.65        70.88        16.27 
TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 TCGA-BH-A0EE TCGA-BH-A0EI 
        4.41        14.30         9.63        46.19        31.00        24.43 
TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HP 
       15.16        23.08        52.96        26.50         5.85        13.61 
TCGA-BH-A0HU TCGA-BH-A0W4 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       12.89        24.95        23.05        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18L TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18S TCGA-BH-A18T 
       20.12        26.66        30.28        55.63        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1EU 
       51.39        51.16        67.50        91.99       113.82        42.28 
TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FE 
       12.00        17.69        97.48        24.62        33.17        74.73 
TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A201 
      122.89        36.92        63.35        45.63        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5IZ 
       26.14        38.60        57.83       130.16        10.52        18.64 
TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P 
       23.51        18.87        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A131 TCGA-C8-A134 
       12.66        12.66        48.53        12.56        13.51        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ 
       12.92         4.11         4.08        10.92        11.34         0.16 
TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W 
       12.03        10.42        12.33        12.33        20.25        12.53 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
       12.36        12.95         8.28         9.50        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A13Z 
       33.99        13.02        12.49        19.46        56.81        20.88 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JK TCGA-D8-A1JM 
       15.78        18.15        18.90        53.00        20.12        19.40 
TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JT TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X9 
       20.38        21.01        13.32        18.58        16.73        23.90 
TCGA-D8-A1XA TCGA-D8-A1XF TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       27.58        15.22        21.80        14.50        19.92        17.69 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 
       16.41        16.64        12.99        16.54        15.32        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27M 
        9.93        14.24        14.14        13.45        13.05        13.48 
TCGA-D8-A27N TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A73U TCGA-D8-A73W TCGA-E2-A105 
        4.80        10.09        13.08        16.18        12.66        43.00 
TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14V 
       40.11        28.87        38.24        38.60        33.17        34.26 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 
       31.96        69.34        18.51        63.62        69.96        23.24 
TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15G 
       21.04        14.79        25.05        23.34        20.71        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       12.92        55.63        11.05        14.07        51.39        76.57 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IO 
       77.65        70.36        33.73        33.70        28.44        60.99 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LL 
       60.36        73.64        24.59        28.90        50.07        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU 
       26.99        34.55         8.28        34.92        34.29        17.69 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC 
       36.82        22.29        34.16        36.20        36.56        39.55 
TCGA-E9-A1ND TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1R4 TCGA-E9-A1R7 TCGA-E9-A1RA 
       41.62        35.24        18.94         6.12        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A226 
       32.09        46.65         6.58        21.27        47.64        34.45 
TCGA-E9-A228 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 
       42.25        39.09        38.37        41.03        40.73         0.69 
TCGA-E9-A247 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A3HO TCGA-E9-A3QA TCGA-E9-A3X8 
       38.99        12.33        29.72        38.07        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       23.90         0.79        25.81        26.40        27.85        12.20 
TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV 
       18.90        13.25        16.57        15.68        28.77        25.94 
TCGA-EW-A1OZ TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P8 TCGA-EW-A1PA 
       40.41        52.96        29.82        23.11         7.86        18.90 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A3E8 
       13.94        10.52        14.43        55.00        25.91        34.03 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       15.22        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DL TCGA-GM-A3XL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 
       85.15       115.69        69.30        11.84        13.22         7.10 
TCGA-LD-A9QF TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z TCGA-LL-A740 
       10.62        15.32        14.70        14.47         7.46        14.50 
TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OL-A5D6 TCGA-OL-A5D7 
       12.36        19.59        17.49        27.91        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66I 
       31.99        58.62        36.36        22.32        20.38        23.47 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA10 
       47.01        64.21        86.96        18.81        21.07        19.27 
TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       13.94        17.03         3.81        11.41        52.96        29.03 
TCGA-XX-A89A TCGA-Z7-A8R6 
       16.04       107.05 

$`17P LOSS WILD-TYPE`
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SG TCGA-A1-A0SJ TCGA-A1-A0SM 
       48.36         9.96         8.52        14.27        13.68         7.96 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04X TCGA-A2-A0CL TCGA-A2-A0CP TCGA-A2-A0CQ 
      143.15        78.41        55.43        99.12        92.48        88.60 
TCGA-A2-A0CS TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP 
       77.19        56.81        33.76        61.58       101.72       118.45 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0T6 
       99.19        54.64        17.52         8.38        17.46        18.90 
TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A0YT 
       25.28        50.47        49.48        18.61        31.73        23.77 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25E 
       60.72        22.45        16.47        52.47        17.19       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XX TCGA-A2-A3XZ 
       10.59        36.23        33.93        29.98        47.31        50.37 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CH 
       21.30        23.21        21.14        38.30        35.31        35.47 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A26J TCGA-A7-A3IY 
       33.11        29.79        20.19        23.61        20.61        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A6VV TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06Y 
       12.10        10.72        10.29        13.02        53.06        26.01 
TCGA-A8-A07F TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
       18.97        12.00         9.99        10.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
       45.07         0.99        28.96        19.96        12.00        37.05 
TCGA-A8-A08P TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A095 
       31.00        33.01       112.08        40.01        33.01        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09Q 
       12.00         9.99        12.00        50.04        49.05        25.02 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A9 
       19.04        15.02         0.99        12.00        21.04        27.02 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
       73.91         5.72         1.48        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A3HN TCGA-AC-A3QP 
       87.12        26.04        74.14        33.04        16.31        22.19 
TCGA-AC-A3TM TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU 
       25.05        23.24        24.79        14.53        19.33        14.96 
TCGA-AC-A62V TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC 
       11.44        18.67        13.58        12.26         1.68         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A049 
       20.19         1.12         1.32         0.33         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AR TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN 
        2.96         7.36         0.33         5.65         7.00         7.17 
TCGA-AN-A0FS TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03U TCGA-AO-A0J5 
        6.90         0.33         5.33        80.28        58.95        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JC TCGA-AO-A0JF 
       37.48        20.32        22.36        53.03        50.86        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A128 
       26.24        50.24        55.33       115.27        99.25       106.78 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12H TCGA-AO-A1KO 
       90.58        98.27        57.30        48.36        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A1H2 TCGA-AQ-A7U7 TCGA-AR-A0TQ 
       82.62        61.87        17.79        15.62        19.20        98.33 
TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A1AK TCGA-AR-A1AL 
       84.10        75.22        64.83        65.36       103.86        97.68 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24K TCGA-AR-A24M 
       86.07        93.90        61.28        86.53        50.89       120.33 
TCGA-AR-A24N TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A251 
       99.78       104.28       112.77        32.58        98.76        99.62 
TCGA-AR-A252 TCGA-AR-A2LH TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LN TCGA-AR-A2LO 
       93.30        20.25        54.21        66.15        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 
       40.54        57.27        33.30        38.96        10.59        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IP TCGA-B6-A0RL 
      143.38       281.29       275.87        50.70       129.07        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       263.28       162.05       102.77       140.48        89.46 
TCGA-B6-A0WT TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68        18.35        21.47       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX 
       68.94        43.59       101.52        73.51       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW 
        7.07        85.35       103.63        71.15        62.93        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD TCGA-BH-A0BG 
       63.09        39.55        39.16        84.13        18.21        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BO TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV 
       21.70        74.89        72.23        53.95        45.57        49.94 
TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DO 
       41.75        89.06        90.97        23.44        38.01        17.26 
TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0E1 TCGA-BH-A0E7 
        3.22         2.56        38.47        67.86        15.68        44.81 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.58        24.49        30.35        10.78        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HI TCGA-BH-A0HO TCGA-BH-A0HQ TCGA-BH-A0HW 
       24.56        41.00        20.38         2.50        36.85        51.32 
TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 
       27.25        50.79         5.59        23.93        42.35        44.81 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A1ET TCGA-BH-A1EW 
       90.84        72.56        37.74        37.55        82.85        55.69 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1FB TCGA-BH-A1FC 
       49.58        25.81        31.53        89.16       120.62       114.15 
TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A28O TCGA-BH-A28Q 
       55.00       144.59        72.07        83.31        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
       20.12       109.28        20.88         9.63         5.26         9.70 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X 
       21.76         9.44        11.77        12.66        12.66        12.66 
TCGA-C8-A130 TCGA-C8-A132 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HN TCGA-C8-A273 
        3.16         1.87        12.33        11.28        12.95         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A3M8 TCGA-C8-A8HR TCGA-D8-A140 TCGA-D8-A141 
        9.53         0.03        12.95        13.41        13.25        20.58 
TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A1JB TCGA-D8-A1JF TCGA-D8-A1JH TCGA-D8-A1JI 
       13.97        14.17        55.50        12.03        14.01        18.97 
TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X8 
       20.09        20.09        12.20        14.70        17.79        25.74 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XG TCGA-D8-A1XO TCGA-D8-A1XR 
       18.15        12.39        17.16        14.73        55.30        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27I 
       16.31        15.16        43.04        17.42        16.04        14.43 
TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
       48.03        16.41         1.61        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       18.51        21.67        25.22        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.41        37.51        28.44        47.15        44.68        40.96 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14W TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A15C 
       75.98        43.33        32.02        19.43        23.87        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       17.29        21.63        53.92         9.04        20.58        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       19.56        56.94        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IK TCGA-E2-A1IL 
       28.50        16.47        37.25        37.41        59.18         3.88 
TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LH 
       22.19        11.08        54.18        19.66        75.81       106.75 
TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A3DX TCGA-E2-A570 TCGA-E2-A574 TCGA-E9-A1N3 
      102.61         8.75        43.56        30.61        38.76        34.82 
TCGA-E9-A1N4 TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       32.88        35.77        25.84         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RC TCGA-E9-A1RD 
       34.95         2.56         3.02        11.15        40.24         1.12 
TCGA-E9-A1RH TCGA-E9-A227 TCGA-E9-A229 TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       46.59        32.05        37.74        41.72        40.50        20.12 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A54Y 
        1.94         7.13        24.56         9.47        32.91        23.84 
TCGA-E9-A5FK TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1OW TCGA-EW-A1OX 
       26.70        39.72         8.48        18.21        22.82        29.95 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB 
       29.85        41.13        39.78        18.48        30.08        19.99 
TCGA-EW-A1PC TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3U0 
        6.15        34.55        19.96        52.73        22.09        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-GM-A2D9 TCGA-GM-A2DK TCGA-GM-A2DM 
       10.16        23.51        16.77        59.57        86.96       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN 
      101.62        85.35       110.50        38.20        43.73        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX 
       72.03        13.55        18.12         2.60        62.47        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       21.24        13.28        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y 
       17.06        14.79        22.26         2.63        16.08        15.68 
TCGA-LL-A7SZ TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX 
       19.53        22.39         2.10        40.08        34.92        28.87 
TCGA-OL-A5RY TCGA-OL-A66H TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       24.72        26.70        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C 
       17.36        14.07        28.21        19.73        40.11         8.91 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA11 
        0.16         0.26         9.93        18.48        20.68        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-V7-A7HQ TCGA-XX-A899 TCGA-Z7-A8R5 
       18.87        17.39        17.26        66.84        15.35       108.07 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.16               0.03 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            282.90             281.29 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            27.055             28.355 
[1] "0.2 - 282.9 (27.1)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.2"
D71V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17P LOSS MUTATED        43       41        1        4       186       145
  17P LOSS WILD-TYPE      46       44        5        2       167       107
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED           0         86         11         38       11
  17P LOSS WILD-TYPE         2         68         18         27        9
                    vv
clus                 STAGE TIS STAGE X
  17P LOSS MUTATED           1       8
  17P LOSS WILD-TYPE         0       5
D71V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  43                 46
  STAGE IA                 41                 44
  STAGE IB                  1                  5
  STAGE II                  4                  2
  STAGE IIA               186                167
  STAGE IIB               145                107
  STAGE III                 0                  2
  STAGE IIIA               86                 68
  STAGE IIIB               11                 18
  STAGE IIIC               38                 27
  STAGE IV                 11                  9
  STAGE TIS                 1                  0
  STAGE X                   8                  5
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED   126 359  74  17
  17P LOSS WILD-TYPE 150 265  62  23
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1              126                150
  T2              359                265
  T3               74                 62
  T4               17                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17P LOSS MUTATED   272 185  67  43
  17P LOSS WILD-TYPE 235 173  52  34
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              272                235
  N1              185                173
  N2               67                 52
  N3               43                 34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   483  12
  17P LOSS WILD-TYPE 406  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    483   12
  17P LOSS WILD-TYPE  406   10
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              483                406
  1               12                 10
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   575   4
  17P LOSS WILD-TYPE 493   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    575    4
  17P LOSS WILD-TYPE  493    8
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              575                493
  MALE                  4                  8
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   236 270
  17P LOSS WILD-TYPE 193 248
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    236  270
  17P LOSS WILD-TYPE  193  248
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               236                193
  YES              270                248
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17P LOSS MUTATED                            0                           433
  17P LOSS WILD-TYPE                          1                           337
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17P LOSS MUTATED                               92                   5
  17P LOSS WILD-TYPE                            108                   1
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17P LOSS MUTATED                       5                               18
  17P LOSS WILD-TYPE                     4                               11
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17P LOSS MUTATED                    6             19
  17P LOSS WILD-TYPE                 11             28
D71V9, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 433                337
  INFILTRATING LOBULAR CARCINOMA                 92                108
  MEDULLARY CARCINOMA                             5                  1
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)               18                 11
  MUCINOUS CARCINOMA                              6                 11
  OTHER  SPECIFY                                 19                 28
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  1    39
  17P LOSS WILD-TYPE                                0    21
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                         103   388
  17P LOSS WILD-TYPE                        78   357
D71V11, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          39                 21
  BLACK OR AFRICAN AMERICAN                     103                 78
  WHITE                                         388                357
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V12, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    21 476
  17P LOSS WILD-TYPE  18 399
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     21  476
  17P LOSS WILD-TYPE   18  399
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                   21                 18
  NOT HISPANIC OR LATINO              476                399
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED   231  41
  17Q LOSS WILD-TYPE 686 106
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               272                792 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                41                106 
$`17Q LOSS MUTATED`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-A1-A0SK TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       42.81        40.14        31.79        39.32        28.01        19.20 
TCGA-A2-A04P TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A0CK TCGA-A2-A0CM TCGA-A2-A0CR 
       18.02        73.84        87.25       136.73        24.79       107.93 
TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0EN TCGA-A2-A0SW 
       75.25        98.99        67.33        34.55        89.36        44.88 
TCGA-A2-A0SX TCGA-A2-A0T1 TCGA-A2-A0YC TCGA-A2-A0YE TCGA-A2-A0YK TCGA-A2-A1FW 
       50.43        17.13        32.55        18.21        19.33        17.36 
TCGA-A2-A1G1 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XY 
       19.20       107.70        42.44        91.07        32.75        35.93 
TCGA-A2-A3Y0 TCGA-A2-A4RX TCGA-A2-A4S1 TCGA-A2-A4S3 TCGA-A7-A0CG TCGA-A7-A0CJ 
       50.83        24.39        26.96        21.90        34.29        30.61 
TCGA-A7-A0D9 TCGA-A7-A13D TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26I 
       37.45        31.73        31.36        24.26        23.74        21.73 
TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A56D TCGA-A7-A6VV TCGA-A7-A6VW 
       13.74        14.50        21.17        14.73        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A076 
       10.42         8.75         1.02        17.98        31.00        53.98 
TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07I TCGA-A8-A07L TCGA-A8-A07R 
        9.01        43.00        19.99        14.01        32.05         8.98 
TCGA-A8-A084 TCGA-A8-A086 TCGA-A8-A08B TCGA-A8-A08I TCGA-A8-A08X TCGA-A8-A093 
       15.06        13.02        38.01        12.00        43.00        17.95 
TCGA-A8-A09K TCGA-A8-A09N TCGA-A8-A0A7 TCGA-A8-A0AB TCGA-AC-A2BK TCGA-AC-A2BM 
       29.98         1.02         0.99        17.03        73.05        99.35 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A62Y 
       14.66        32.45        16.57        19.79        15.48        17.42 
TCGA-AC-A8OS TCGA-AN-A046 TCGA-AN-A04C TCGA-AN-A0AL TCGA-AN-A0AS TCGA-AN-A0FJ 
        2.30         0.33         1.78         7.46         0.33         7.96 
TCGA-AN-A0FL TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.59         7.04         0.33         0.36         0.33         0.33 
TCGA-AN-A0XR TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03N TCGA-AO-A03V TCGA-AO-A0J2 
        0.33         0.33         0.33        66.77        29.13        32.78 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A129 TCGA-AO-A12D 
       21.40        52.18        72.00        55.33       108.03        64.04 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TP TCGA-AR-A0TY 
       70.39         0.53         5.65         2.56       140.55        55.86 
TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AN 
      133.22       134.14       125.16       108.36       101.00        96.00 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AY TCGA-AR-A24S TCGA-AR-A24U TCGA-AR-A250 
       99.32        17.23        33.73        97.84        77.69        89.00 
TCGA-B6-A0IB TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE 
      129.57       112.37       233.62       165.76       140.88       255.68 
TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RS TCGA-B6-A0RU TCGA-B6-A0WY TCGA-B6-A1KN 
       68.45       212.25       100.70       282.90       113.79       139.17 
TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B5 
       68.12        18.84        59.84        25.55        81.44        70.22 
TCGA-BH-A0B6 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BP TCGA-BH-A0BR 
       81.63        51.68        37.22        32.02        75.48        76.60 
TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E9 
       77.95        44.02         4.41        14.30         9.63        46.19 
TCGA-BH-A0EE TCGA-BH-A0H7 TCGA-BH-A0HB TCGA-BH-A0HP TCGA-BH-A0HU TCGA-BH-A18F 
       31.00        23.08        26.50        13.61        12.89        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18V TCGA-BH-A1EN 
        4.90        35.93        30.28        55.63        51.16        67.50 
TCGA-BH-A1ES TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F6 TCGA-BH-A1FD 
      113.82        42.28        12.00        17.69        97.48        33.17 
TCGA-BH-A1FH TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A208 TCGA-BH-A5J0 TCGA-C8-A12L 
       36.92        45.63        72.07        57.83        23.51        11.93 
TCGA-C8-A12M TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12Z 
       11.77        12.66        11.77        12.66        12.66        12.56 
TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HK TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Z 
       13.51         4.11        12.03        12.53        12.36         8.28 
TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A8HP TCGA-C8-A9FZ TCGA-D8-A13Y 
        9.50        14.43        33.99        13.02        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       20.88        13.48        19.20        14.17        17.49        16.50 
TCGA-D8-A1JC TCGA-D8-A1JK TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1XJ TCGA-D8-A1XK 
       15.78        20.12        19.40        20.38        21.80        14.50 
TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XZ TCGA-D8-A27M TCGA-D8-A73U 
       16.41        16.64        12.99        15.32        13.48        16.18 
TCGA-E2-A105 TCGA-E2-A14V TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       43.00        34.26        31.96        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15G TCGA-E2-A15M 
       69.96        23.24        14.79        25.05        18.21        11.05 
TCGA-E2-A1AZ TCGA-E2-A1II TCGA-E2-A1L7 TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A573 
       76.57        33.70        60.36        43.04        26.99        34.92 
TCGA-E2-A576 TCGA-E9-A1N6 TCGA-E9-A1NH TCGA-E9-A1RA TCGA-E9-A1RF TCGA-E9-A1RG 
       34.29        22.29        18.94        45.01         6.58        21.27 
TCGA-E9-A22D TCGA-E9-A244 TCGA-E9-A295 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A5FL 
       41.03         0.69        12.33        30.18        30.44         0.79 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OZ TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FV 
       28.77        25.94        40.41        29.82         7.86        25.91 
TCGA-EW-A6S9 TCGA-EW-A6SB TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DA 
       15.22        24.99        33.21         7.40       109.87       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 
       79.10        75.02        85.15        11.84        13.22         7.10 
TCGA-LD-A9QF TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A73Z TCGA-OL-A5D7 TCGA-OL-A5RW 
       10.62        14.70        14.47         7.46        58.52        36.36 
TCGA-OL-A5S0 TCGA-OL-A66I TCGA-PE-A5DD TCGA-PE-A5DE TCGA-UL-AAZ6 TCGA-UU-A93S 
       20.38        23.47        64.21        86.96        17.03         3.81 
TCGA-WT-AB44 TCGA-XX-A89A 
       29.03        16.04 

$`17Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
      129.14       131.67        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04Q 
       20.88        13.68         7.96        18.21       143.15        78.41 
TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CL 
      121.94        63.12       101.98        55.43        36.13        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CS TCGA-A2-A0CU TCGA-A2-A0CW 
      114.81        92.48        88.60        77.19         5.19       107.93 
TCGA-A2-A0CX TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       56.81        33.76        61.58        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU 
      118.45        79.76        74.40        72.00        35.05        34.29 
TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU 
       31.82        61.94        24.72        63.29        99.19        54.64 
TCGA-A2-A0SV TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       27.12        44.28        17.52         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       17.46        18.90        20.75        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT 
       21.67        49.48        18.61        48.46        31.73        23.77 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       52.47        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ 
       39.65        33.93        29.98        56.28        47.31        50.37 
TCGA-A2-A4RW TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CE 
        7.30        21.30        23.21        21.14        38.30        35.31 
TCGA-A7-A0CH TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13F 
       35.47        35.67        33.11        29.79        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       23.61        29.56        23.80        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A8-A06O 
       14.93        17.92        12.10        10.72        11.05        13.02 
TCGA-A8-A06P TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       13.02        53.06        29.03        26.01         1.02        17.03 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S 
       18.97        18.97        12.00         9.99        10.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A08A TCGA-A8-A08C 
       24.99         9.99        45.07        36.95         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08P 
       33.01        19.96        37.05         9.99        31.00        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
        0.99        33.01       112.08        40.01        33.01        30.97 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C 
       41.98        12.00         9.99         9.99        12.00         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
       50.04        49.05        45.07        33.07        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 
       19.04        15.02         0.99        14.01        12.00        19.04 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E 
       13.02        21.04        27.02        38.04         0.95        22.95 
TCGA-AC-A23G TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
       73.91         5.72         1.48        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       14.99        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IV TCGA-AC-A6IW 
       19.33        14.96        11.44        13.71        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A04A 
        1.32         0.33         0.33         0.23         0.62         2.96 
TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT 
        1.71         9.96         7.36         0.16         0.33         0.33 
TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FZ 
        6.44         5.65         7.00         7.17         6.90         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XS TCGA-AN-A0XV 
        5.36         0.33        12.33         0.30         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.59        80.28        61.35        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       47.87        58.95        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       26.24        50.24        62.04        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12E TCGA-AO-A12F 
      108.72       106.78        90.58        98.27        57.30        48.36 
TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KT 
       41.62        40.57        14.73        82.62        61.87        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O 
       24.79        26.93       130.09        15.62        32.52        32.91 
TCGA-AQ-A7U7 TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV 
       19.20        98.33         5.26        84.10       109.02        75.22 
TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U4 
       98.93        64.83       107.24        65.36        83.87       107.21 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AS 
      103.86        97.68        98.33        86.07        93.90        37.81 
TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K 
       94.29        61.28        86.53        86.43       160.90        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24R TCGA-AR-A24T TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      112.77       105.27       105.30        32.58        98.76        98.66 
TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       99.62        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       10.59        77.62       143.38       281.29        12.13       275.87 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO 
      129.07       234.28        81.17        78.02       263.28       162.05 
TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      102.77       140.48        89.46       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       79.63        18.35        21.47       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A40B 
      170.17        37.87         7.07        85.35        70.16       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 
       71.15        62.93        20.45        63.09        40.83        39.55 
TCGA-BH-A0B4 TCGA-BH-A0B7 TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       39.16        84.13        18.21        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       74.89        61.68        72.23        74.14        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD 
       49.94        49.05        41.75        89.06        90.97        45.83 
TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       77.98        23.44        38.01        29.98        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB 
       70.88        16.27        15.68        44.81        32.58        24.49 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       24.43        30.35        10.78        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       24.56        41.00        52.96        20.38         5.85         2.50 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 
       36.85        51.32        27.25        50.79         5.59        23.93 
TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18J TCGA-BH-A18K 
       24.95        42.35        44.81        23.05        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       26.66        72.56        37.74        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 
       51.39        91.99        82.85        55.69        49.58        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE 
       31.53        89.16        24.62       120.62       114.15        74.73 
TCGA-BH-A1FG TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
      122.89        63.35        55.00       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q 
       26.14        38.60        83.31       130.16        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 
       20.12        10.52       109.28        20.88        18.64         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12N 
        5.26         9.70        18.87        21.76         9.44        11.77 
TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A132 
       12.66        12.66        12.66        48.53         3.16         1.87 
TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.59        12.92         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO 
       11.28         0.16        10.42        12.33        12.95        12.33 
TCGA-C8-A26V TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27A 
       20.25        12.95         9.67         9.53         0.03        24.56 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       12.95        12.49        13.41        13.25        20.58        13.97 
TCGA-D8-A143 TCGA-D8-A146 TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       14.17        21.14        55.50        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JP 
       53.00        14.01        18.97        20.09        20.09        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR 
       15.22        14.73        19.92        17.69        55.30        15.85 
TCGA-D8-A1XS TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       16.31        15.16        43.04        16.54        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43        48.03        16.41         4.80         1.61        10.09 
TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 
       13.08        12.53        12.26        33.37        18.51        21.67 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A 
       12.66        25.22        34.42        27.52        46.59        40.41 
TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O 
       37.51        40.11        28.44        28.87        47.15        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14W TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C 
       32.02        19.43        21.04        23.87        23.34        22.82 
TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        20.71        21.63        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH 
       16.47        37.25        77.65        37.41        70.36        33.73 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       54.18        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P6 TCGA-E2-A3DX 
       50.07       106.75       102.61         8.75        34.55        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
        8.28        30.61        38.76        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND 
       36.82        34.16        36.20        36.56        39.55        41.62 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 
       34.95         2.56         6.12         3.02        11.15        48.23 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A1RI 
       32.09        40.24         1.12        46.65        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22E TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 
       41.72        40.73        40.50        20.12        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
        7.13        24.56        29.72         9.47        38.07        32.91 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE 
       23.90        23.84        26.70        25.81        26.40        27.85 
TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       12.20        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 
       16.57        15.68        22.82        29.95        29.85        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        52.96        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG 
       19.99         6.15        13.94        10.52        14.43        34.55 
TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       19.96        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6SA TCGA-EW-A6SC TCGA-GM-A2D9 TCGA-GM-A2DC 
       10.16        23.51        16.77        31.30        59.57        83.34 
TCGA-GM-A2DF TCGA-GM-A2DH TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       70.85        72.10        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YX 
       72.03        13.55        18.12         2.60        62.47        11.57 
TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       21.24        13.28        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        15.32        14.79        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
       15.68        14.50        19.53        12.36        19.59        17.49 
TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       27.91        22.39         2.10        36.30        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H 
       40.08        34.92        28.87        24.72        22.32        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LX 
       28.21        19.73        40.11         8.91        47.01         0.16 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z 
        0.26         9.93        18.81        18.48        21.07        20.68 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       19.27        13.84        18.87        17.39        17.26        13.94 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       66.84        11.41        52.96        15.35       108.07       107.05 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.33               0.03 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            282.90             281.29 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            25.925             28.270 
[1] "0.3 - 282.9 (25.9)" "0.0 - 281.3 (28.3)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  17Q LOSS MUTATED        19       24        0        1        95        61
  17Q LOSS WILD-TYPE      70       61        6        5       258       191
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           0         41          6         16        6
  17Q LOSS WILD-TYPE         2        113         23         49       14
                    vv
clus                 STAGE TIS STAGE X
  17Q LOSS MUTATED           0       2
  17Q LOSS WILD-TYPE         1      11
D72V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  19                 70
  STAGE IA                 24                 61
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                95                258
  STAGE IIB                61                191
  STAGE III                 0                  2
  STAGE IIIA               41                113
  STAGE IIIB                6                 23
  STAGE IIIC               16                 49
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    63 166  34  11
  17Q LOSS WILD-TYPE 213 458 102  29
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               63                213
  T2              166                458
  T3               34                102
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  17Q LOSS MUTATED   140  77  35  20
  17Q LOSS WILD-TYPE 367 281  84  57
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0              140                367
  N1               77                281
  N2               35                 84
  N3               20                 57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   237   6
  17Q LOSS WILD-TYPE 652  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    237    6
  17Q LOSS WILD-TYPE  652   16
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0              237                652
  1                6                 16
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   275   0
  17Q LOSS WILD-TYPE 793  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    275    0
  17Q LOSS WILD-TYPE  793   12
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE              275                793
  MALE                  0                 12
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED   107 134
  17Q LOSS WILD-TYPE 322 384
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED    107  134
  17Q LOSS WILD-TYPE  322  384
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO               107                322
  YES              134                384
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  17Q LOSS MUTATED                            0                           220
  17Q LOSS WILD-TYPE                          1                           550
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  17Q LOSS MUTATED                               34                   3
  17Q LOSS WILD-TYPE                            166                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  17Q LOSS MUTATED                       5                                5
  17Q LOSS WILD-TYPE                     4                               24
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  17Q LOSS MUTATED                    0              8
  17Q LOSS WILD-TYPE                 17             39
D72V9, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 220                550
  INFILTRATING LOBULAR CARCINOMA                 34                166
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                5                 24
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  8                 39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  1    22
  17Q LOSS WILD-TYPE                                0    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                          58   171
  17Q LOSS WILD-TYPE                       123   574
D72V11, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                          22                 38
  BLACK OR AFRICAN AMERICAN                      58                123
  WHITE                                         171                574
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    10 220
  17Q LOSS WILD-TYPE  29 655
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10  220
  17Q LOSS WILD-TYPE   29  655
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 29
  NOT HISPANIC OR LATINO              220                655
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   254  59
  18P LOSS WILD-TYPE 663  88
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               313                751 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                59                 88 
$`18P LOSS MUTATED`
TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SO TCGA-A2-A04P 
      131.67        14.37        20.88        13.68        28.01        18.02 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A0CU TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 
      101.98        55.43         5.19        67.33        34.55        25.22 
TCGA-A2-A0EN TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EY TCGA-A2-A0SX TCGA-A2-A0T4 
       89.36        34.29        31.82        63.29        50.43        20.52 
TCGA-A2-A0T7 TCGA-A2-A0YE TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL 
       20.75        18.21        21.90        49.48        19.33        48.46 
TCGA-A2-A0YT TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25C TCGA-A2-A25D 
       23.77        17.36        60.72        19.20        17.19        18.15 
TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A13F TCGA-A7-A26F 
       91.07        29.98        26.96        34.29        25.15        24.26 
TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SF TCGA-A7-A56D 
       22.32        11.28        14.93        13.74        17.92        14.73 
TCGA-A7-A6VX TCGA-A8-A06R TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A076 TCGA-A8-A07G 
       10.42        17.98        29.03        26.01        53.98        18.97 
TCGA-A8-A07P TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08L 
       10.98         9.99        15.06        38.01        37.05         9.99 
TCGA-A8-A092 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M TCGA-A8-A09N 
       30.97        12.00        50.04        49.05        33.07         1.02 
TCGA-A8-A09Q TCGA-A8-A09X TCGA-A8-A0A2 TCGA-AC-A23H TCGA-AC-A2FF TCGA-AC-A2FM 
       25.02        14.01        19.04         5.72        90.71        26.04 
TCGA-AC-A2FO TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3W5 TCGA-AC-A3W6 
       74.14        14.66        32.45         6.48        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A5EH TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A7VC TCGA-AC-A8OP 
       15.48        16.80        14.96        11.44         0.03        20.19 
TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AJ TCGA-AN-A0AK 
        1.12         2.30         0.33         2.96         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ 
        7.46         0.16         0.33         0.33         0.36         0.33 
TCGA-AN-A0XP TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        0.30         0.33        80.28        61.35        66.77        81.63 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A0JG TCGA-AO-A129 
       52.18        26.04        20.32        21.53        26.24       108.03 
TCGA-AO-A12E TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       57.30        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A54O TCGA-AR-A0TT TCGA-AR-A0TX TCGA-AR-A0U2 TCGA-AR-A1AI TCGA-AR-A1AP 
       32.91       109.02        64.83        83.87       108.36        93.90 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24V TCGA-AR-A24W 
       61.28        86.53       160.90       112.77       105.30        32.58 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QQ 
       93.30        71.05        93.83        73.35        33.30        10.59 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RH TCGA-B6-A0RL TCGA-B6-A0RP 
      233.62        18.77       165.76       212.25        81.17       102.77 
TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A1KI TCGA-B6-A1KN 
      100.70        79.63        18.35       113.79        73.51       139.17 
TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0AY TCGA-BH-A0B3 TCGA-BH-A0B6 
       70.16        18.84        59.84        25.55        39.55        81.63 
TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BP TCGA-BH-A0BT TCGA-BH-A0BZ TCGA-BH-A0C0 
       37.22        18.21        75.48        45.57        49.05        41.75 
TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DX TCGA-BH-A0E6 TCGA-BH-A0GY TCGA-BH-A0H6 
       90.97        38.01        70.88         9.63        30.35        24.56 
TCGA-BH-A0H7 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0W3 
       23.08        52.96        20.38        27.25        50.79        23.93 
TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       32.91        90.84        26.66        51.39        51.16        67.50 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EY TCGA-BH-A1F0 
       91.99        42.28        12.00        55.69        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A201 
       31.53        97.48        24.62        33.17        45.63        28.14 
TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-C8-A12O 
       38.60        83.31       130.16        18.64        23.51        12.66 
TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A132 TCGA-C8-A134 
       11.77        12.66        12.66        12.56         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HI TCGA-C8-A1HJ 
       12.92         4.08        12.33        10.92        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.03        12.33        12.95        12.36        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Y TCGA-D8-A142 
        9.67         9.53         9.50        33.99        56.81        13.97 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JD TCGA-D8-A1JE 
       21.14        14.17        17.49        16.50        18.15        18.90 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN 
       53.00        14.01        18.97        20.09        19.40        20.38 
TCGA-D8-A1X5 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XU 
       18.58        27.58        21.80        19.92        15.85        12.99 
TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 TCGA-D8-A73U 
       16.54        14.14        13.48        10.09        18.51        16.18 
TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Q 
       34.42        46.59        40.11        28.44        44.68        38.24 
TCGA-E2-A14R TCGA-E2-A14V TCGA-E2-A14Z TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A158 
       38.60        34.26        18.51        69.96        19.43        14.79 
TCGA-E2-A159 TCGA-E2-A15E TCGA-E2-A15M TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH 
       25.05        20.71        11.05        76.57        37.25        33.73 
TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 
       60.99        28.90         8.75        43.04        34.55        34.92 
TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NG 
       38.76        17.69        32.88        36.56        41.62        25.84 
TCGA-E9-A1NH TCGA-E9-A1R6 TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A22E 
       18.94        11.15         6.58        21.27        47.64        41.72 
TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y TCGA-E9-A5FL TCGA-EW-A1IW 
        1.94        12.33        29.72        23.84         0.79        12.20 
TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PC 
       18.90        25.94        29.85        52.96         7.86         6.15 
TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV TCGA-EW-A423 TCGA-EW-A6SD TCGA-GI-A2C8 
       14.43        55.00        25.91        10.16        33.21         7.40 
TCGA-GM-A2DH TCGA-GM-A2DL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A9QF 
       72.10       115.69        11.84        13.22         7.10        10.62 
TCGA-LL-A441 TCGA-LL-A5YM TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       32.75        15.32        22.26        12.36        17.49        27.91 
TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A6VQ TCGA-PE-A5DD TCGA-PE-A5DE 
       36.30        20.38        26.04        19.73        64.21        86.96 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-UU-A93S TCGA-WT-AB44 
        0.16        18.81        21.07        19.27         3.81        29.03 
TCGA-XX-A89A 
       16.04 

$`18P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        43.43        48.10        14.27        47.24 
TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N 
       31.79         7.96        39.32        19.20        18.21       143.15 
TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04Y 
       78.41       121.94        73.84        87.25        63.12        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ 
      136.73        99.12        24.79       114.81        92.48        88.60 
TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
      107.93        77.19        75.25        98.99       107.93        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       33.76        61.58       101.72        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0ST 
       74.40        72.00        35.05        61.94        24.72        99.19 
TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 
       54.64        27.12        44.88        44.28        17.52        17.13 
TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD 
        8.38        49.84        17.46        18.90        32.55        25.28 
TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM TCGA-A2-A1FV TCGA-A2-A1FZ 
       50.47        21.67        18.61        31.73        23.47        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       20.25        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XV 
      105.34        10.59        36.23        39.65        33.93        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD 
       24.39        21.30        23.21        21.14        21.90        38.30 
TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       35.31        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       29.79        31.73        20.19        23.61        29.56        31.36 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        21.73        20.61        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD TCGA-A7-A4SE 
       10.29        13.41        14.70        11.97        14.50        21.17 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29         9.37         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Z 
       13.02        13.02         1.02        53.06        31.00         1.02 
TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       17.03         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       12.00        32.05         9.99         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C TCGA-A8-A08F 
       45.07        36.95        13.02         0.99        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       19.96        12.00        31.00        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
      112.08        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K 
       12.00         9.99         9.99         1.02        45.07        29.98 
TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A0A1 TCGA-A8-A0A4 
        8.98        19.04        15.02         0.99        12.00        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C 
       21.04         0.99        27.02        17.03        38.04         0.95 
TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB 
       22.95        73.91         1.48        73.05        99.35        40.57 
TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN 
       86.66        60.92        87.12        33.04        19.33        16.31 
TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3YI 
       14.83        22.19        24.13        25.05        14.99        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A62X TCGA-AC-A62Y 
       24.79        29.26        14.53        19.33        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR 
       18.67        13.58        12.26         1.68         8.22         1.32 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY 
        7.59         7.17         6.90         7.04         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        5.36         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.33         5.59        95.70        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J6 TCGA-AO-A0J8 TCGA-AO-A0J9 
       29.13        32.78        21.40        37.48        22.36        53.03 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI 
       50.70        50.86        72.00        76.77        65.10        50.24 
TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       62.04        55.33        71.80       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G 
      106.78        90.58        98.27        64.04        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS 
       40.57        14.73        82.62        61.87        70.39         0.53 
TCGA-AO-A1KT TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       17.79        32.52         2.56        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ 
        5.26        84.10        75.22        98.93        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AJ 
       65.36       133.22       134.14       107.21       125.16       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
      103.86        97.68        98.33        96.00        86.07        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       17.23        37.81        94.29        86.43        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       97.84       105.27        77.69        98.76        98.66        89.00 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       99.62        85.64       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR 
       66.15        63.62        38.17        39.39        40.54        57.27 
TCGA-AR-A5QP TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA 
       38.96        77.62       143.38       281.29        12.13       275.87 
TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM 
      129.57        50.70        65.72       146.50       112.37       127.33 
TCGA-B6-A0IN TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RI 
       84.59       129.07       140.88       255.68        68.45       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU 
       78.02       263.28       162.05       140.48        89.46       282.90 
TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 
      157.41        97.48       188.68        21.47       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF 
      245.10        28.27        68.94        58.88        43.59       101.52 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B 
      170.17        37.87         7.07        85.35        68.12       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       71.15        62.93        20.45        63.09        81.44        40.83 
TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF 
       39.16        70.22        84.13        51.68        32.02        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ 
       61.51        21.70        74.89        61.68        72.23        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0C1 TCGA-BH-A0C3 
       76.60        53.95        49.94        77.95        44.02        89.06 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL 
       45.83        77.98        23.44        29.98        13.91        78.28 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 
       32.58        24.49        31.00        24.43        10.78        15.16 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO 
       37.78        53.26        41.00        26.50         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W4 
       13.61        36.85        12.89        51.32         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       42.35        44.81        23.05         4.90        35.93        20.12 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EX TCGA-BH-A1F5 TCGA-BH-A1FB 
        7.36       113.82        82.85        49.58        89.16       120.62 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 TCGA-BH-A208 TCGA-BH-A28O 
       72.07       144.59        72.07        26.14        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R8 
        6.44        20.12        10.52       109.28        20.88         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y 
       11.77        11.77        12.66        12.66        12.66        48.53 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A137 TCGA-C8-A1HG TCGA-C8-A1HL TCGA-C8-A1HO 
        3.16        13.51         4.11        11.34        10.42        12.33 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 
       20.25        12.53         0.03        24.56        14.43        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Z TCGA-D8-A140 
       13.02        12.49        13.41        19.46        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JC 
       20.58        14.17        13.48        19.20        55.50        15.78 
TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       12.03        20.12        20.09        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       14.70        17.79        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XM 
       12.39        17.16        15.22        14.73        14.50        17.69 
TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV TCGA-D8-A1XW 
       55.30        16.41        16.31        16.64        15.16        43.04 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         9.93        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43        48.03        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A4Z1 
        1.61        13.08        12.53        12.26        33.37        21.67 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       12.66        25.22        43.00        27.52        40.41        37.51 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       28.87        47.15        40.96        33.17        75.98        43.33 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A155 
       32.02        31.96        69.34        63.62        23.24        21.04 
TCGA-E2-A156 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       23.87        23.34        22.82        17.29        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O 
       12.92        55.63        53.92         9.04        20.58        50.79 
TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 
       19.56        56.94        14.07        51.39        53.62        87.22 
TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF 
       33.01        32.35        28.50        16.47        77.65        37.41 
TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       70.36        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA 
       11.08        54.18        60.36        73.64        19.66        24.59 
TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A3DX 
       75.81        50.07       106.75       102.61        26.99        43.56 
TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 
        8.28        30.61        34.29        34.82        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NI 
       34.16        36.20        39.55        35.77        35.24         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 
       24.82        28.27        34.95         2.56         6.12         3.02 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE 
       48.23        45.01        32.09        40.24         1.12        46.65 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.03        40.73        40.50        20.12         0.69 
TCGA-E9-A247 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       38.99         7.13        24.56         9.47        38.07        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       30.18        30.44        23.90        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 
       27.85        39.72         8.48        18.21        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 
       15.68        28.77        22.82        29.95        40.41        41.13 
TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA 
       39.78        29.82        23.11        18.48        30.08        18.90 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS 
       19.99        13.94        10.52        34.55        19.96        52.73 
TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA 
       22.09        34.03        17.49        23.51        15.22        16.77 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       24.99        31.30       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM 
       83.34        75.02        70.85        85.15        86.96       106.06 
TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL 
      101.62        85.35       110.50        38.20        43.73        69.30 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB 
       66.38        72.03        13.55        18.12         2.60        62.47 
TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W6 TCGA-LL-A440 TCGA-LL-A442 TCGA-LL-A50Y 
       11.57        21.24        13.28        24.95        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR 
       17.06        14.70        14.47        14.79         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-MS-A51U 
       15.68         7.46        14.50        19.53        19.59        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO 
       65.62        41.92        42.77        17.36        14.07        28.21 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG 
       40.11         8.91        47.01         0.26         9.93        18.48 
TCGA-S3-AA0Z TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       20.68        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R5 
       17.03        66.84        11.41        52.96        15.35       108.07 
TCGA-Z7-A8R6 
      107.05 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.03               0.03 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            233.62             282.90 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             23.93              30.61 
[1] "0.0 - 233.6 (23.9)" "0.0 - 282.9 (30.6)"
[1] "hr=" "2.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18P LOSS MUTATED        25       23        0        0       100        73
  18P LOSS WILD-TYPE      64       62        6        6       253       179
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED           0         48         16         26        6
  18P LOSS WILD-TYPE         2        106         13         39       14
                    vv
clus                 STAGE TIS STAGE X
  18P LOSS MUTATED           0       1
  18P LOSS WILD-TYPE         1      12
D73V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  25                 64
  STAGE IA                 23                 62
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA               100                253
  STAGE IIB                73                179
  STAGE III                 0                  2
  STAGE IIIA               48                106
  STAGE IIIB               16                 13
  STAGE IIIC               26                 39
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   1                 12
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    69 189  40  22
  18P LOSS WILD-TYPE 207 435  96  18
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               69                207
  T2              189                435
  T3               40                 96
  T4               22                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18P LOSS MUTATED   142 103  40  28
  18P LOSS WILD-TYPE 365 255  79  49
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              142                365
  N1              103                255
  N2               40                 79
  N3               28                 49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   263   6
  18P LOSS WILD-TYPE 626  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    263    6
  18P LOSS WILD-TYPE  626   16
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              263                626
  1                6                 16
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   317   3
  18P LOSS WILD-TYPE 751   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    317    3
  18P LOSS WILD-TYPE  751    9
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              317                751
  MALE                  3                  9
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   129 149
  18P LOSS WILD-TYPE 300 369
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    129  149
  18P LOSS WILD-TYPE  300  369
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               129                300
  YES              149                369
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18P LOSS MUTATED                            0                           250
  18P LOSS WILD-TYPE                          1                           520
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18P LOSS MUTATED                               47                   3
  18P LOSS WILD-TYPE                            153                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18P LOSS MUTATED                       4                                6
  18P LOSS WILD-TYPE                     5                               23
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18P LOSS MUTATED                    0             10
  18P LOSS WILD-TYPE                 17             37
D73V9, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 250                520
  INFILTRATING LOBULAR CARCINOMA                 47                153
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           4                  5
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                 10                 37
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0    27
  18P LOSS WILD-TYPE                                1    33
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          54   212
  18P LOSS WILD-TYPE                       127   533
D73V11, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          27                 33
  BLACK OR AFRICAN AMERICAN                      54                127
  WHITE                                         212                533
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V12, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    12 262
  18P LOSS WILD-TYPE  27 613
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     12  262
  18P LOSS WILD-TYPE   27  613
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                   12                 27
  NOT HISPANIC OR LATINO              262                613
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   262  52
  18Q LOSS WILD-TYPE 655  95
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               314                750 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                52                 95 
$`18Q LOSS MUTATED`
TCGA-3C-AALI TCGA-A1-A0SD TCGA-A1-A0SI TCGA-A1-A0SO TCGA-A2-A04P TCGA-A2-A04W 
      131.67        14.37        20.88        28.01        18.02       101.98 
TCGA-A2-A04X TCGA-A2-A0CU TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0EN TCGA-A2-A0EU 
       55.43         5.19       107.93        67.33        89.36        34.29 
TCGA-A2-A0EV TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T4 TCGA-A2-A0T7 TCGA-A2-A0YE 
       31.82        27.12        50.43        20.52        20.75        18.21 
TCGA-A2-A0YG TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YT TCGA-A2-A1FW 
       21.90        49.48        19.33        48.46        23.77        17.36 
TCGA-A2-A1FX TCGA-A2-A1G1 TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A3XT 
       60.72        19.20        42.44        17.19        18.15        91.07 
TCGA-A2-A3XU TCGA-A2-A4S1 TCGA-A7-A0CG TCGA-A7-A0DA TCGA-A7-A13D TCGA-A7-A13F 
       29.98        26.96        34.29        35.67        31.73        25.15 
TCGA-A7-A26F TCGA-A7-A2KD TCGA-A7-A3J1 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE 
       24.26        22.32        11.28        14.93        13.74        21.17 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06R 
       17.92        14.73        12.10        10.29        10.42        17.98 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07G 
       29.03        26.01         1.02        17.03        53.98        18.97 
TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A08B TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R 
        9.99        15.06        38.01        37.05        31.00         0.99 
TCGA-A8-A092 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09M 
       30.97         9.99        12.00        50.04        49.05        33.07 
TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A2 TCGA-AC-A23H 
        1.02        25.02         0.99        14.01        19.04         5.72 
TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3W5 
       90.71        26.04        14.66        32.45         6.48        16.57 
TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A5EH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A7VC 
       19.79        15.48        16.80        11.44        12.26         0.03 
TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A04A TCGA-AN-A0AK 
       20.19         1.12         2.30         0.33         2.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0FL TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FZ 
        7.46         0.16         7.59         0.33         0.36         0.33 
TCGA-AN-A0XP TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A0J2 TCGA-AO-A0J4 
        0.30         0.33        80.28        66.77        32.78        52.18 
TCGA-AO-A0J7 TCGA-AO-A0JA TCGA-AO-A129 TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A1KT 
       20.32        21.53       108.03        64.04        57.30        17.79 
TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 TCGA-AQ-A54O 
       24.79        26.93       130.09         5.65        15.62        32.91 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP 
       84.10       109.02        98.93       133.22        83.87        93.90 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24V 
       61.28        86.53       160.90       112.77        97.84       105.30 
TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LR 
       32.58        89.00        99.62        93.30        71.05        57.27 
TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0IK TCGA-B6-A0IO TCGA-B6-A0RE TCGA-B6-A0RH 
       73.35        10.59        18.77       165.76       255.68       212.25 
TCGA-B6-A0RL TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY 
       81.17       102.77       100.70        79.63        18.35       113.79 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A402 TCGA-B6-A409 TCGA-BH-A0AZ 
      101.52        73.51       170.17        70.16        18.84        63.09 
TCGA-BH-A0B6 TCGA-BH-A0BA TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0BT 
       81.63        37.22        18.21        61.51        75.48        45.57 
TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C7 TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0GY 
       77.95        49.05        90.97        38.01         3.22        30.35 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HI TCGA-BH-A0HU TCGA-BH-A0HX 
       23.08        41.00        52.96        20.38        12.89        27.25 
TCGA-BH-A0W3 TCGA-BH-A18F TCGA-BH-A18K TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN 
       23.93        32.91        90.84        51.39        51.16        67.50 
TCGA-BH-A1EO TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       91.99        42.28        12.00        17.69        25.81        31.53 
TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FM TCGA-BH-A201 TCGA-BH-A204 TCGA-BH-A209 
       97.48        24.62        45.63        28.14        83.31       130.16 
TCGA-BH-A5J0 TCGA-BH-A8FZ TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12W TCGA-C8-A12Z 
       23.51        18.87        11.77        12.66        12.66        12.56 
TCGA-C8-A132 TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HJ 
        1.87        12.92         4.08        12.33        11.28         0.16 
TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 
       12.03        12.33        12.36        12.95         8.28         9.67 
TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-D8-A13Z TCGA-D8-A142 
        9.53         0.03         9.50        33.99        20.88        13.97 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE 
       21.14        14.17        17.49        16.50        15.78        18.90 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1X5 
       53.00        14.01        18.97        20.09        20.38        18.58 
TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XR TCGA-D8-A1XU TCGA-D8-A1XY 
       27.58        21.80        19.92        15.85        12.99        16.54 
TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-D8-A27R TCGA-D8-A3Z6 TCGA-D8-A73U TCGA-E2-A107 
       14.14        13.48        10.09        18.51        16.18        34.42 
TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A14O TCGA-E2-A14Z TCGA-E2-A150 
       46.59        40.11        28.44        44.68        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15E TCGA-E2-A15M 
       69.96        19.43        25.05        23.34        20.71        11.05 
TCGA-E2-A1AZ TCGA-E2-A1BD TCGA-E2-A1IH TCGA-E2-A1IO TCGA-E2-A1LE TCGA-E2-A1LK 
       76.57        37.25        33.73        60.99        28.90         8.75 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N4 
       43.04        34.55        34.92        38.76        17.69        32.88 
TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NH TCGA-E9-A1R6 TCGA-E9-A1RF TCGA-E9-A1RG 
       36.56        41.62        18.94        11.15         6.58        21.27 
TCGA-E9-A1RI TCGA-E9-A22E TCGA-E9-A248 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A54Y 
       47.64        41.72         1.94        12.33        29.72        23.84 
TCGA-E9-A5FL TCGA-EW-A1IW TCGA-EW-A1J1 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1OZ 
        0.79        12.20        18.90        25.94        29.85        40.41 
TCGA-EW-A1P3 TCGA-EW-A1P8 TCGA-EW-A1PC TCGA-EW-A1PF TCGA-EW-A2FR TCGA-EW-A2FV 
       52.96         7.86         6.15        14.43        55.00        25.91 
TCGA-EW-A423 TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2DH TCGA-GM-A2DL 
       10.16        33.21         7.40       109.87        72.10       115.69 
TCGA-HN-A2NL TCGA-JL-A3YW TCGA-LD-A74U TCGA-LD-A9QF TCGA-LL-A441 TCGA-LL-A5YL 
        2.60        11.84        13.22        10.62        32.75        17.06 
TCGA-LL-A5YM TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FR TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       15.32        14.47        22.26        16.08        17.49        27.91 
TCGA-OL-A5D6 TCGA-OL-A5S0 TCGA-OL-A66N TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC 
       36.30        20.38        26.04        28.21        19.73        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZH TCGA-UU-A93S 
       64.21        86.96         0.16        18.81        21.07         3.81 
TCGA-WT-AB44 TCGA-XX-A89A 
       29.03        16.04 

$`18Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        9.96         8.52        43.43        48.10        14.27        47.24 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68        31.79         7.96        39.32        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V 
      143.15        78.41       121.94        73.84        87.25        63.12 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CV TCGA-A2-A0CX 
       88.60       107.93        77.19        75.25        98.99        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EO 
       34.55        33.76        61.58        25.22       101.72        80.28 
TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EW 
      118.45        79.76        74.40        72.00        35.05        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SY 
       24.72        63.29        99.19        54.64        44.88        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.52        17.13         8.38        49.84        17.46        18.90 
TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YH TCGA-A2-A0YJ TCGA-A2-A0YM 
       32.55        25.28        50.47        21.67        18.61        31.73 
TCGA-A2-A1FV TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       23.47        22.45        20.25        19.56        16.47        52.47 
TCGA-A2-A25A TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS 
      107.70       105.34        10.59        36.23        39.65        33.93 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 
       32.75        56.28        47.31        35.93        50.37        50.83 
TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 
        7.30        24.39        21.30        23.21        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        35.31        35.47        30.61        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13E TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26G 
       29.79        20.19        23.61        29.56        31.36        23.74 
TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 
       23.80        21.73        20.61        11.34        10.59        10.29 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SD TCGA-A7-A5ZW TCGA-A7-A5ZX 
       13.41        14.70        11.97        14.50        10.72        11.05 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06T 
        9.37         8.75        13.02        13.02         1.02        53.06 
TCGA-A8-A06X TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I 
       31.00         9.01        43.00        19.99        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       12.00        32.05         9.99        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07Z TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08C 
       24.99        45.07        36.95        13.02         0.99        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A08S 
       33.01        19.96        12.00         9.99        31.00        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A093 TCGA-A8-A095 
      112.08        43.00        40.01        33.01        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09R 
       12.00         9.99         1.02        45.07        29.98         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A0A1 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 
       19.04        15.02        12.00        13.02        21.04         0.99 
TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       27.02        17.03        38.04         0.95        22.95        73.91 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG 
        1.48        73.05        99.35        40.57        86.66        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A3HN TCGA-AC-A3OD 
       87.12        74.14        33.04        19.33        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3YI TCGA-AC-A3YJ 
       22.19        24.13        25.05        14.99        23.24        24.79 
TCGA-AC-A4ZE TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y 
       29.26        14.53        19.33        14.96        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OR TCGA-AN-A03Y 
       18.67        13.58         1.68         8.22         1.32         0.33 
TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.23         0.33         0.62         1.78         1.71         9.96 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FX TCGA-AN-A0FY 
        7.00         7.17         6.90         7.04         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        5.36         0.33        12.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03R 
        5.33         5.59        61.35        81.63        95.70        68.75 
TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J3 TCGA-AO-A0J5 TCGA-AO-A0J6 
       47.87        58.95        29.13        21.40        26.04        37.48 
TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE 
       22.36        53.03        50.70        50.86        72.00        76.77 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       65.10        26.24        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A12A TCGA-AO-A12B 
      115.27        99.25       108.72       106.78        90.58        98.27 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KQ 
       48.36        41.62        40.57        14.73        82.62        61.87 
TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A7U7 TCGA-AR-A0TP 
       70.39         0.53        32.52         2.56        19.20       140.55 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
       98.33         5.26        75.22        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ 
       65.36       134.14       107.21       125.16       108.36       101.00 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AQ 
      103.86        97.68        98.33        96.00        86.07        99.32 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24K 
       17.23        37.81        94.29        86.43        33.73        50.89 
TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q 
       94.22       120.33        99.78       118.59         2.76       104.28 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A254 TCGA-AR-A256 
      105.27        77.69        98.76        98.66        85.64        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0I1 
       38.17        39.39        40.54        33.30        38.96        77.62 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC 
      143.38       281.29        12.13       275.87       129.57        50.70 
TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM TCGA-B6-A0IN 
       65.72       146.50       112.37       233.62       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN 
      129.07       140.88        68.45       234.28        78.02       263.28 
TCGA-B6-A0RO TCGA-B6-A0RQ TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      162.05       140.48        89.46       282.90       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WX TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
      188.68        21.47       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A3ZX TCGA-B6-A400 
       68.94        58.88        43.59       139.17        37.87         7.07 
TCGA-B6-A401 TCGA-B6-A408 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV 
       85.35        68.12       103.63        71.15        62.93        59.84 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 
       20.45        25.55        81.44        40.83        39.55        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BC TCGA-BH-A0BF TCGA-BH-A0BJ 
       70.22        84.13        51.68        32.02        43.53        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       74.89        61.68        72.23        74.14        76.60        53.95 
TCGA-BH-A0BV TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0DD TCGA-BH-A0DE 
       49.94        41.75        44.02        89.06        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP 
       23.44        29.98        13.91        78.28        17.26        15.65 
TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 
        2.56        38.47        67.86        70.88        16.27         4.41 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 
       24.49        31.00        24.43        10.78        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0HB TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP 
       53.26        24.56        26.50         5.85         2.50        13.61 
TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       36.85        51.32        50.79         5.59        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18L 
       44.81        23.05         4.90        35.93        20.12        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F5 
        7.36       113.82        82.85        55.69        49.58        89.16 
TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
      120.62       114.15        33.17        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A202 
       63.35        55.00        72.07       144.59        72.07        26.14 
TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       38.60        57.83        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY 
      109.28        20.88        18.64         9.63         5.26         9.70 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        12.66        48.53         3.16        13.51 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HL TCGA-C8-A1HN 
       12.59         4.11        10.92        11.34        10.42        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M8 
       12.33        20.25        12.53        24.56        14.43        12.95 
TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A140 
       13.02        12.49        13.41        19.46        56.81        13.25 
TCGA-D8-A141 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A147 TCGA-D8-A1JB TCGA-D8-A1JD 
       20.58        14.17        13.48        19.20        55.50        18.15 
TCGA-D8-A1JF TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1JS 
       12.03        20.12        20.09        19.40        21.01        12.20 
TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       13.32        14.70        17.79        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK 
       18.15        12.39        17.16        15.22        14.73        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XV 
       17.69        55.30        16.41        16.31        16.64        15.16 
TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E 
       43.04        15.32        15.52         9.93        14.24        17.42 
TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       16.04        13.45        13.05        14.43        48.03        16.41 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        4.80         1.61        13.08        12.53        12.26        33.37 
TCGA-D8-A4Z1 TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A 
       21.67        12.66        25.22        43.00        27.52        40.41 
TCGA-E2-A10B TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       37.51        28.87        47.15        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A153 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15C 
       69.34        23.24        21.04        23.87        14.79        22.82 
TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J 
       17.29        21.63        18.21        12.92        55.63        53.92 
TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
        9.04        20.58        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 
       51.39        53.62        87.22        33.01        32.35        28.50 
TCGA-E2-A1BC TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       16.47        77.65        37.41        70.36        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       59.18         3.88        22.19        11.08        54.18        60.36 
TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH 
       73.64        19.66        24.59        75.81        50.07       106.75 
TCGA-E2-A1LI TCGA-E2-A2P5 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
      102.61        26.99        43.56         8.28        30.61        34.29 
TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NC 
       34.82        36.82        22.29        34.16        36.20        39.55 
TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       35.77        35.24        25.84         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         2.56         6.12         3.02        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RH TCGA-E9-A226 
       32.09        40.24         1.12        46.65        46.59        34.45 
TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D 
       32.05        42.25        37.74        39.09        38.37        41.03 
TCGA-E9-A22G TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A249 
       40.73        40.50        20.12         0.69        38.99         7.13 
TCGA-E9-A24A TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       24.56         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IX 
       23.90        26.70        25.81        26.40        27.85        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
        8.48        18.21        13.25        16.57        15.68        28.77 
TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P4 TCGA-EW-A1P5 
       22.82        29.95        41.13        39.78        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE 
       18.48        30.08        18.90        19.99        13.94        10.52 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        19.96        52.73        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GM-A2D9 
       23.51        15.22        16.77        24.99        31.30        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI 
      216.76        79.10        83.34        75.02        70.85        85.15 
TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY 
       86.96       106.06       101.62        85.35       110.50        38.20 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX 
       43.73        69.30        66.38        72.03        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A440 
       62.47        11.57        21.24         7.10        13.28        24.95 
TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YN TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A73Y 
       29.23        25.05        14.70        14.79         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-MS-A51U 
        7.46        14.50        19.53        12.36        19.59        22.39 
TCGA-OK-A5Q2 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV 
        2.10        58.52        31.99        58.62        40.08        34.92 
TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       36.36        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VR 
       65.62        41.92        42.77        17.36        14.07        40.11 
TCGA-OL-A97C TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        8.91         0.26         9.93        18.48        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 
       13.84        18.87        17.39        17.26        13.94        17.03 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       66.84        11.41        52.96        15.35       108.07       107.05 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.03               0.23 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            255.68             282.90 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            23.425             30.525 
[1] "0.0 - 255.7 (23.4)" "0.2 - 282.9 (30.5)"
[1] "hr=" "1.6"
D74V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  18Q LOSS MUTATED        23       26        0        0        98        70
  18Q LOSS WILD-TYPE      66       59        6        6       255       182
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED           0         50         16         26        6
  18Q LOSS WILD-TYPE         2        104         13         39       14
                    vv
clus                 STAGE TIS STAGE X
  18Q LOSS MUTATED           0       3
  18Q LOSS WILD-TYPE         1      10
D74V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  23                 66
  STAGE IA                 26                 59
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                98                255
  STAGE IIB                70                182
  STAGE III                 0                  2
  STAGE IIIA               50                104
  STAGE IIIB               16                 13
  STAGE IIIC               26                 39
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    70 192  38  20
  18Q LOSS WILD-TYPE 206 432  98  20
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               70                206
  T2              192                432
  T3               38                 98
  T4               20                 20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  18Q LOSS MUTATED   144  97  44  29
  18Q LOSS WILD-TYPE 363 261  75  48
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              144                363
  N1               97                261
  N2               44                 75
  N3               29                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   260   6
  18Q LOSS WILD-TYPE 629  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    260    6
  18Q LOSS WILD-TYPE  629   16
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              260                629
  1                6                 16
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   318   3
  18Q LOSS WILD-TYPE 750   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    318    3
  18Q LOSS WILD-TYPE  750    9
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              318                750
  MALE                  3                  9
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   118 161
  18Q LOSS WILD-TYPE 311 357
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    118  161
  18Q LOSS WILD-TYPE  311  357
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               118                311
  YES              161                357
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  18Q LOSS MUTATED                            1                           247
  18Q LOSS WILD-TYPE                          0                           523
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  18Q LOSS MUTATED                               52                   2
  18Q LOSS WILD-TYPE                            148                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  18Q LOSS MUTATED                       5                                6
  18Q LOSS WILD-TYPE                     4                               23
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  18Q LOSS MUTATED                    0              8
  18Q LOSS WILD-TYPE                 17             39
D74V9, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      1                  0
  INFILTRATING DUCTAL CARCINOMA                 247                523
  INFILTRATING LOBULAR CARCINOMA                 52                148
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           5                  4
  MIXED HISTOLOGY (PLEASE SPECIFY)                6                 23
  MUCINOUS CARCINOMA                              0                 17
  OTHER  SPECIFY                                  8                 39
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0    24
  18Q LOSS WILD-TYPE                                1    36
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          56   210
  18Q LOSS WILD-TYPE                       125   535
D74V11, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          24                 36
  BLACK OR AFRICAN AMERICAN                      56                125
  WHITE                                         210                535
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V12, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    13 262
  18Q LOSS WILD-TYPE  26 613
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     13  262
  18Q LOSS WILD-TYPE   26  613
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 26
  NOT HISPANIC OR LATINO              262                613
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED   164  28
  19P LOSS WILD-TYPE 753 119
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               192                872 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                28                119 
$`19P LOSS MUTATED`
TCGA-3C-AALJ TCGA-5T-A9QA TCGA-A1-A0SJ TCGA-A1-A0SQ TCGA-A2-A04P TCGA-A2-A04T 
       42.81         9.96        13.68        18.21        18.02        73.84 
TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0CW TCGA-A2-A0D4 TCGA-A2-A0EO 
       87.25        55.43        24.79       107.93        25.22        80.28 
TCGA-A2-A0T3 TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT TCGA-A2-A1FW 
       49.84        20.75        21.90        21.67        23.77        17.36 
TCGA-A2-A3XT TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4S1 TCGA-A7-A13D TCGA-A7-A13E 
       91.07        47.31        50.37        26.96        31.73        20.19 
TCGA-A7-A26I TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VX TCGA-A8-A06Q 
       21.73        14.50        17.92        14.73        10.42         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L 
       17.98        53.06        17.03        53.98        18.97        32.05 
TCGA-A8-A07O TCGA-A8-A07W TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J 
        9.99         9.99        33.01        19.96        12.00        37.05 
TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A09A TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09N 
       31.00        33.01         9.99         1.02        45.07         1.02 
TCGA-AC-A2BM TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A62V TCGA-AC-A6IX TCGA-AC-A8OQ 
       99.35        26.04        33.04        11.44        12.26         1.12 
TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AS TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ 
        0.23         2.96         0.33         7.04         0.33         0.33 
TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03P TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD 
       61.35        66.77        95.70        21.40        52.18        72.00 
TCGA-AO-A0JM TCGA-AO-A1KQ TCGA-AO-A1KT TCGA-AQ-A0Y5 TCGA-AQ-A54N TCGA-AR-A0TQ 
       71.80        61.87        17.79         5.65         2.56        98.33 
TCGA-AR-A0TS TCGA-AR-A0TW TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ TCGA-AR-A1AQ 
       84.10        98.93        83.87       134.14       101.00        99.32 
TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A2LK 
      160.90       112.77        97.84        89.00        93.30        54.21 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0IO TCGA-B6-A1KF TCGA-B6-A1KN 
       10.59        77.62       129.57       165.76       101.52       139.17 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0AV TCGA-BH-A0B3 
        7.07        70.16        68.12        18.84        59.84        39.55 
TCGA-BH-A0BG TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0EB 
       61.51        45.57        77.95         3.22         4.41        24.49 
TCGA-BH-A0H0 TCGA-BH-A0H7 TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18F 
       15.16        23.08        27.25        50.79        23.05        32.91 
TCGA-BH-A18I TCGA-BH-A18L TCGA-BH-A18S TCGA-BH-A1EV TCGA-BH-A1F8 TCGA-BH-A1FN 
       35.93        26.66        66.05        12.00        24.62        72.07 
TCGA-BH-A1FU TCGA-BH-A204 TCGA-BH-A209 TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12U 
       72.07        83.31       130.16        11.77        11.77        12.66 
TCGA-C8-A12W TCGA-C8-A12Z TCGA-C8-A135 TCGA-C8-A138 TCGA-C8-A1HF TCGA-C8-A1HK 
       12.66        12.56        12.92         4.08        10.92        12.03 
TCGA-C8-A1HL TCGA-C8-A1HN TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A27A TCGA-C8-A8HP 
       10.42        12.95        12.95         8.28        24.56        13.02 
TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A1JC TCGA-D8-A1JI TCGA-D8-A1JJ 
       12.49        19.46        56.81        15.78        18.97        20.09 
TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XT TCGA-D8-A1XY TCGA-D8-A1Y3 
       19.40        27.58        16.41        16.64        16.54        14.14 
TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A152 TCGA-E2-A159 TCGA-E2-A15H 
       13.48        46.59        44.68        69.96        25.05        12.92 
TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 TCGA-E9-A1NI 
       14.07        76.57        34.92        38.76        22.29         9.86 
TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1RC TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22D 
       24.82         2.56        40.24        46.59        34.45        41.03 
TCGA-E9-A22G TCGA-E9-A2JS TCGA-E9-A5UO TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX 
       40.73        29.72        25.81        25.94        22.82        29.95 
TCGA-EW-A1OZ TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FR 
       40.41         7.86        18.90         6.15        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SD TCGA-GM-A2DC 
       52.73        17.49        15.22        16.77        33.21        83.34 
TCGA-GM-A2DH TCGA-LL-A6FP TCGA-LL-A7T0 TCGA-MS-A51U TCGA-OL-A5D7 TCGA-OL-A5S0 
       72.10        22.26        12.36        22.39        58.52        20.38 
TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-AA14 TCGA-V7-A7HQ TCGA-WT-AB44 
       28.21         0.16        18.81        17.39        66.84        29.03 

$`19P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      129.14       131.67        40.14        11.44        48.56        48.36 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH 
        8.52        14.37        43.43        48.10        14.27        47.24 
TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        31.79         7.96        39.32        28.01        19.20 
TCGA-A2-A04N TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y 
      143.15        78.41       121.94        63.12       101.98        36.13 
TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
      136.73        99.12       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D0 
       77.19        75.25         5.19        98.99        56.81        67.33 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP 
       34.55        33.76        61.58       101.72        89.36       118.45 
TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV 
       79.76        74.40        72.00        35.05        34.29        31.82 
TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV 
       61.94        24.72        63.29        99.19        54.64        27.12 
TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 
       44.88        50.43        44.28        17.52        17.13         8.38 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE 
       20.52        17.46        18.90        32.55        25.28        18.21 
TCGA-A2-A0YF TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       50.47        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 
       23.47        60.72        22.45        20.25        19.20        19.56 
TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D 
       16.47        52.47       107.70        42.44        17.19        18.15 
TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU 
      105.34        10.59        36.23        39.65        33.93        29.98 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX 
       32.75        56.28        35.93        50.83         7.30        24.39 
TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       21.30        23.21        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB 
       34.29        35.47        30.61        37.45        35.67        33.11 
TCGA-A7-A0DC TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F 
       29.79        25.15        23.61        29.56        31.36        24.26 
TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ 
       23.74        23.80        20.61        22.32        11.34        10.59 
TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA 
       10.29        11.28        13.41        14.70        11.97        14.93 
TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       13.74        21.17        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A06X 
        9.37         8.75        13.02        13.02        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
       26.01         1.02         9.01        43.00        19.99        18.97 
TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       14.01        12.00        10.98         8.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B 
       45.07        15.06        36.95        13.02         0.99        38.01 
TCGA-A8-A08C TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X 
       28.96         9.99        31.00         0.99       112.08        43.00 
TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 
       40.01        33.01        30.97        17.95        41.98        12.00 
TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M 
        9.99        12.00        50.04        49.05        29.98        33.07 
TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X 
       25.02         8.98        19.04        15.02         0.99        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 
       12.00        19.04        13.02        21.04         0.99        27.02 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG 
        1.48        73.05        40.57        86.66        90.71        60.92 
TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH 
       87.12        74.14        19.33        14.66        32.45         6.48 
TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN 
       16.31        14.83        22.19        24.13        25.05        14.99 
TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       16.57        19.79        15.48        23.24        24.79        29.26 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62X TCGA-AC-A62Y 
       16.80        14.53        19.33        14.96        13.71        17.42 
TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP 
       18.67        13.58         1.68         8.22         0.03        20.19 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 
        1.32         2.30         0.33         0.33         0.33         0.62 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM 
        1.78         1.71         9.96         7.36         7.46         0.16 
TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK 
        0.33         0.33         6.44         5.65         7.96         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY 
        7.59         7.17         6.90         0.36         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS 
        5.36         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03O 
        0.33         0.33         5.33         5.59        80.28        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 
       68.75        47.87        58.95        29.13        32.78        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       37.48        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ 
       50.86        76.77        65.10        26.24        50.24        62.04 
TCGA-AO-A0JL TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 
       55.33       115.27        99.25       108.72       106.78       108.03 
TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G 
       90.58        98.27        64.04        57.30        48.36        41.62 
TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H 
       40.57        14.73        82.62        70.39         0.53        24.79 
TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 
       26.93       130.09        15.62        32.52        32.91        19.20 
TCGA-AR-A0TP TCGA-AR-A0TR TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TX TCGA-AR-A0TY 
      140.55         5.26       109.02        75.22        64.83        55.86 
TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
      107.24        65.36       133.22       107.21       125.16       108.36 
TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP 
      103.86        97.68        98.33        96.00        86.07        93.90 
TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX 
       17.23        37.81        94.29        61.28        86.53        86.43 
TCGA-AR-A1AY TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O 
       33.73        50.89        94.22       120.33        99.78       118.59 
TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W 
        2.76       104.28       105.27        77.69       105.30        32.58 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.76        98.66        99.62        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       281.29        12.13       275.87        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI 
      129.07       140.88       255.68        68.45       212.25       234.28 
TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
       81.17        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT 
      100.70        89.46       282.90       157.41        97.48       188.68 
TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
       79.63        18.35        21.47       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      245.10        28.27        68.94        58.88        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        37.87        85.35       103.63        71.15        62.93 
TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B4 
       20.45        25.55        63.09        81.44        40.83        39.16 
TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC 
       70.22        81.63        84.13        51.68        37.22        32.02 
TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO 
       18.21        43.53        21.70        74.89        61.68        72.23 
TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BZ 
       75.48        74.14        76.60        53.95        49.94        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ 
       15.65         2.56        38.47        67.86        70.88        16.27 
TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA 
       15.68        14.30         9.63        44.81        46.19        32.58 
TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H3 TCGA-BH-A0H5 
       31.00        24.43        30.35        10.78        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       24.56        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0RX 
        2.50        13.61        36.85        12.89        51.32         5.59 
TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J 
       23.93        24.95        42.35        44.81         4.90        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
        7.36        51.39        51.16        67.50        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       82.85        42.28        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       31.53        89.16        97.48       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O 
      144.59        28.14        26.14        38.60        57.83        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ 
        6.44        20.12        10.52       109.28        20.88        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12V 
        9.44        11.93        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53         3.16        13.51         1.87        12.59 
TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HM 
        4.11        12.33        11.34        11.28         0.16        12.33 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A273 TCGA-C8-A274 
       12.33        20.25        12.53        12.36         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HR 
        0.03         9.50        14.43        33.99        12.95        13.41 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        55.50 
TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK 
       18.15        18.90        12.03        53.00        14.01        20.12 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB 
       18.58        17.79        16.73        25.74        23.90        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK 
       12.39        17.16        15.22        14.73        21.80        14.50 
TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU 
       19.92        17.69        55.30        15.85        16.31        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 
       15.16        43.04        15.32        15.52         9.93        14.24 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V 
       16.41         4.80         1.61        10.09        13.08        12.53 
TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.26        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B 
       25.22        43.00        34.42        27.52        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        47.15        40.96        38.24 
TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W 
       38.60        33.17        75.98        43.33        34.26        32.02 
TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 
       31.96        69.34        18.51        63.62        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       20.71        21.63        18.21        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T 
       20.58        11.05        50.79        19.56        56.94        51.39 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        87.22        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        60.36        73.64        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        50.07       106.75       102.61         8.75        43.04 
TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 
       26.99        34.55        43.56         8.28        30.61        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 
       17.69        34.82        32.88        36.82        34.16        36.20 
TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG 
       36.56        39.55        41.62        35.77        35.24        25.84 
TCGA-E9-A1NH TCGA-E9-A1R0 TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 
       18.94        28.27        34.95         6.12         3.02        11.15 
TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       48.23        45.01        32.09         1.12        46.65         6.58 
TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       21.27        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A247 
       38.37        41.72        40.50        20.12         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JT TCGA-E9-A3HO 
        1.94         7.13        24.56        12.33         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY 
        0.79        26.40        27.85        12.20        39.72         8.48 
TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 
       18.21        18.90        13.25        16.57        15.68        28.77 
TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       29.85        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.48        30.08        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 
       34.55        25.91        22.09        34.03        10.16        23.51 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA 
       24.99        31.30         7.40       109.87        59.57       216.76 
TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       79.10        75.02        70.85        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FQ 
       17.06        15.32        14.70        14.47        14.79         2.63 
TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 
       16.08        15.68         7.46        14.50        19.53        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA 
       17.49        27.91         2.10        36.30        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ 
       40.08        34.92        36.36        28.87        24.72        22.32 
TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N 
       26.70        23.47        65.62        41.92        42.77        26.04 
TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC 
       17.36        14.07        19.73        40.11         8.91        47.01 
TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZG TCGA-S3-A6ZH 
       64.21        86.96         0.26         9.93        18.48        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 
       20.68        19.27        13.84        18.87        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A 
       17.03         3.81        11.41        52.96        15.35        16.04 
TCGA-Z7-A8R5 TCGA-Z7-A8R6 
      108.07       107.05 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.16               0.03 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            165.76             282.90 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            24.705             28.885 
[1] "0.2 - 165.8 (24.7)" "0.0 - 282.9 (28.9)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19P LOSS MUTATED        16       11        1        1        62        46
  19P LOSS WILD-TYPE      73       74        5        5       291       206
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           1         30          5         12        6
  19P LOSS WILD-TYPE         1        124         24         53       14
                    vv
clus                 STAGE TIS STAGE X
  19P LOSS MUTATED           0       2
  19P LOSS WILD-TYPE         1      11
D75V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  16                 73
  STAGE IA                 11                 74
  STAGE IB                  1                  5
  STAGE II                  1                  5
  STAGE IIA                62                291
  STAGE IIB                46                206
  STAGE III                 1                  1
  STAGE IIIA               30                124
  STAGE IIIB                5                 24
  STAGE IIIC               12                 53
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED    44 121  20   8
  19P LOSS WILD-TYPE 232 503 116  32
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1               44                232
  T2              121                503
  T3               20                116
  T4                8                 32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19P LOSS MUTATED    80  73  21  15
  19P LOSS WILD-TYPE 427 285  98  62
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               80                427
  N1               73                285
  N2               21                 98
  N3               15                 62
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   161   6
  19P LOSS WILD-TYPE 728  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    161    6
  19P LOSS WILD-TYPE  728   16
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0              161                728
  1                6                 16
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED   190   3
  19P LOSS WILD-TYPE 878   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED    190    3
  19P LOSS WILD-TYPE  878    9
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE              190                878
  MALE                  3                  9
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    80  95
  19P LOSS WILD-TYPE 349 423
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     80   95
  19P LOSS WILD-TYPE  349  423
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                80                349
  YES               95                423
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19P LOSS MUTATED                            0                           168
  19P LOSS WILD-TYPE                          1                           602
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19P LOSS MUTATED                                8                   1
  19P LOSS WILD-TYPE                            192                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19P LOSS MUTATED                       3                                4
  19P LOSS WILD-TYPE                     6                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19P LOSS MUTATED                    4              4
  19P LOSS WILD-TYPE                 13             43
D75V9, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 168                602
  INFILTRATING LOBULAR CARCINOMA                  8                192
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              4                 13
  OTHER  SPECIFY                                  4                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0    16
  19P LOSS WILD-TYPE                                1    44
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                          47   109
  19P LOSS WILD-TYPE                       134   636
D75V11, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          16                 44
  BLACK OR AFRICAN AMERICAN                      47                134
  WHITE                                         109                636
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     9 151
  19P LOSS WILD-TYPE  30 724
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9  151
  19P LOSS WILD-TYPE   30  724
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 30
  NOT HISPANIC OR LATINO              151                724
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED   135  26
  19Q LOSS WILD-TYPE 782 121
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               161                903 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                26                121 
$`19Q LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SQ TCGA-A2-A04U TCGA-A2-A04X TCGA-A2-A0CM TCGA-A2-A0D1 
        9.96        18.21        87.25        55.43        24.79        34.55 
TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T7 TCGA-A2-A0YG TCGA-A2-A0YT TCGA-A2-A1FW 
       80.28        27.12        20.75        21.90        23.77        17.36 
TCGA-A2-A1G1 TCGA-A2-A3XT TCGA-A7-A13E TCGA-A7-A2KD TCGA-A7-A56D TCGA-A8-A06Q 
       19.20        91.07        20.19        22.32        14.73         1.02 
TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A076 TCGA-A8-A07G TCGA-A8-A07L TCGA-A8-A07O 
       17.98        53.06        53.98        18.97        32.05         9.99 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A09A 
       33.01        19.96        12.00        31.00        33.01         9.99 
TCGA-A8-A09C TCGA-A8-A09I TCGA-A8-A09M TCGA-A8-A09N TCGA-AC-A23C TCGA-AC-A2BM 
        1.02        45.07        33.07         1.02         0.95        99.35 
TCGA-AC-A2FM TCGA-AC-A62V TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A04A TCGA-AN-A0AS 
       26.04        11.44         1.12         0.23         2.96         0.33 
TCGA-AN-A0FT TCGA-AN-A0FV TCGA-AN-A0FZ TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P 
        7.04         0.33         0.33        80.28        66.77        95.70 
TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JD TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A1KQ 
       21.40        52.18        72.00        55.33        71.80        61.87 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A0Y5 TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A1AJ 
       17.79        24.79         5.65        83.87       134.14       101.00 
TCGA-AR-A1AQ TCGA-AR-A24H TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A252 TCGA-AR-A2LK 
       99.32       160.90       112.77        97.84        93.30        54.21 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0IB TCGA-B6-A0WX TCGA-B6-A1KF TCGA-B6-A1KN 
       10.59        77.62       129.57        21.47       101.52       139.17 
TCGA-B6-A400 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-BH-A0BT TCGA-BH-A0C0 
        7.07        70.16        68.12        18.84        45.57        41.75 
TCGA-BH-A0C7 TCGA-BH-A0DQ TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0H0 TCGA-BH-A0H7 
       90.97         3.22        24.49        31.00        15.16        23.08 
TCGA-BH-A0HY TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18S TCGA-BH-A1FU 
       50.79        23.05        32.91        35.93        66.05        72.07 
TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A5IZ TCGA-C8-A12M TCGA-C8-A12P TCGA-C8-A12Q 
       83.31       130.16        18.64        11.77        11.77        12.66 
TCGA-C8-A12U TCGA-C8-A12Z TCGA-C8-A1HF TCGA-C8-A1HL TCGA-C8-A26X TCGA-C8-A26Y 
       12.66        12.56        10.92        10.42        12.36        12.95 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A8HQ TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A1JC 
        9.50        24.56        12.49        19.46        56.81        15.78 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1XA TCGA-D8-A1XQ TCGA-D8-A1XT 
       18.97        20.09        19.40        27.58        16.41        16.64 
TCGA-D8-A1XY TCGA-D8-A1Y3 TCGA-D8-A27M TCGA-E2-A109 TCGA-E2-A14O TCGA-E2-A159 
       16.54        14.14        13.48        46.59        44.68        25.05 
TCGA-E2-A15H TCGA-E2-A15S TCGA-E2-A1AZ TCGA-E2-A573 TCGA-E2-A574 TCGA-E9-A1N6 
       12.92        14.07        76.57        34.92        38.76        22.29 
TCGA-E9-A1NF TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R3 TCGA-E9-A1R7 TCGA-E9-A1RB 
       35.24         9.86        24.82         2.56        48.23        32.09 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A22D TCGA-E9-A22G TCGA-E9-A244 TCGA-E9-A2JS 
       46.59        34.45        41.03        40.73         0.69        29.72 
TCGA-E9-A5UO TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PC 
       25.81        22.82        29.95        40.41        18.90         6.15 
TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A3U0 TCGA-EW-A6SA TCGA-GM-A2DC TCGA-GM-A2DF 
       55.00        52.73        17.49        16.77        83.34        70.85 
TCGA-GM-A2DH TCGA-LL-A7T0 TCGA-OL-A5D7 TCGA-OL-A5RY TCGA-OL-A6VO TCGA-PL-A8LX 
       72.10        12.36        58.52        24.72        28.21         0.16 
TCGA-S3-A6ZF TCGA-S3-AA14 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-WT-AB44 
       18.81        17.39         3.81        66.84        29.03 

$`19Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SN 
       47.24        20.88        13.68        31.79         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       28.01        19.20       143.15        18.02        78.41       121.94 
TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL 
       73.84        63.12       101.98        36.13       136.73        99.12 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D2 
        5.19        98.99       107.93        56.81        67.33        33.76 
TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       61.58        25.22       101.72        89.36       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 
       44.28        17.52        17.13         8.38        49.84        20.52 
TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       17.46        18.90        32.55        25.28        18.21        50.47 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A1FV TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G4 TCGA-A2-A1G6 
       23.47        60.72        22.45        20.25        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV 
       10.59        36.23        39.65        33.93        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CE TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 
       38.30        35.31        34.29        35.47        30.61        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13F TCGA-A7-A13G 
       35.67        33.11        29.79        31.73        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF 
       20.61        11.34        10.59        10.29        11.28        13.41 
TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE 
       14.70        11.97        14.93        13.74        14.50        21.17 
TCGA-A7-A4SF TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW 
       17.92        12.10        10.72        11.05        10.29         9.37 
TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A06X 
       10.42         8.75        13.02        13.02        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A079 TCGA-A8-A07B TCGA-A8-A07E 
       26.01         1.02        17.03         9.01        43.00        19.99 
TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S 
       18.97        14.01        12.00        10.98         8.98         7.99 
TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 
       24.99         9.99        45.07        15.06        36.95        13.02 
TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
        0.99        38.01        28.96        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 
        0.99       112.08        43.00        40.01        33.01        30.97 
TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09B TCGA-A8-A09D 
       17.95        41.98        12.00         9.99        12.00        50.04 
TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       49.05        29.98        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23E TCGA-AC-A23G 
        0.99        27.02        17.03        38.04        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72         1.48        73.05        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ 
       60.92        87.12        74.14        33.04        19.33        14.66 
TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ 
       32.45         6.48        16.31        14.83        22.19        24.13 
TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI 
       25.05        14.99        16.57        19.79        15.48        23.24 
TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU 
       24.79        29.26        16.80        14.53        19.33        14.96 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        8.22         0.03        20.19         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ 
        0.33         0.33         0.62         1.78         1.71         9.96 
TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD 
        7.36         7.46         0.16         0.33         0.33         6.44 
TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        5.65         7.96         7.00         7.59         7.17         6.90 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO 
        0.36         0.33         0.33         5.36         0.33        12.33 
TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AN-A0XV 
        0.30         0.33         0.33         0.33         0.33         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        61.35        81.63        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 
       29.13        32.78        26.04        37.48        20.32        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 
       26.24        50.24        62.04       115.27        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       48.36        41.62        40.57        14.73        82.62        70.39 
TCGA-AO-A1KS TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N 
        0.53        26.93       130.09        15.62        32.52         2.56 
TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS 
       32.91        19.20       140.55        98.33         5.26        84.10 
TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0TY TCGA-AR-A0TZ 
      109.02        75.22        98.93        64.83        55.86       107.24 
TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AK 
       65.36       133.22       107.21       125.16       108.36       103.86 
TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AR 
       97.68        98.33        96.00        86.07        93.90        17.23 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY 
       37.81        94.29        61.28        86.53        86.43        33.73 
TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P 
       50.89        94.22       120.33        99.78       118.59         2.76 
TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
      104.28       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.66        89.00        99.62        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC TCGA-B6-A0IE 
      143.38       281.29        12.13       275.87        50.70        65.72 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP 
      234.28        81.17        78.02       263.28       162.05       102.77 
TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS 
      140.48       100.70        89.46       282.90       157.41        97.48 
TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 
      188.68        79.63        18.35       113.79       206.86       129.70 
TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KI 
      245.10        28.27        68.94        58.88        43.59        73.51 
TCGA-B6-A2IU TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
      170.17        37.87        85.35       103.63        71.15        62.93 
TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 TCGA-BH-A0B2 
       59.84        20.45        25.55        63.09        81.44        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        70.22        81.63        84.13        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C1 TCGA-BH-A0C3 
       53.95        49.94        77.95        49.05        44.02        89.06 
TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK 
       45.83        77.98        23.44        38.01        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        17.26        15.65         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 
       70.88        16.27         4.41        15.68        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0GZ 
       44.81        46.19        32.58        24.43        30.35        10.78 
TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB 
       37.78        53.26        24.56        41.00        52.96        26.50 
TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU 
       20.38         5.85         2.50        13.61        36.85        12.89 
TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 
       51.32        27.25         5.59        23.93        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A18G TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
       44.81         4.90        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18T TCGA-BH-A18U 
       37.74        30.28        55.63        37.55         7.36        51.39 
TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU 
       51.16        67.50        91.99       113.82        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 TCGA-BH-A1F2 
       12.00        55.69        49.58        17.69        25.81        31.53 
TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FD 
       89.16        97.48        24.62       120.62       114.15        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 
       72.07       144.59        28.14        26.14        38.60        57.83 
TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V 
       10.65         6.44        20.12        10.52       109.28        20.88 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 
       23.51         9.63         5.26         9.70        18.87        21.76 
TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12V TCGA-C8-A12W 
        9.44        11.93        11.77        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 
       12.66        48.53         3.16        13.51         1.87        12.59 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI 
       12.92         4.11         4.08        12.33        11.34        11.28 
TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V 
        0.16        12.03        12.33        12.95        12.33        20.25 
TCGA-C8-A26W TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A27B 
       12.53         8.28         9.67         9.53         0.03        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A13Z TCGA-D8-A140 
       33.99        12.95        13.02        13.41        20.88        13.25 
TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 
       20.58        13.97        14.17        13.48        21.14        19.20 
TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JD TCGA-D8-A1JE 
       14.17        17.49        16.50        55.50        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JN 
       12.03        53.00        14.01        20.12        20.09        20.38 
TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       21.01        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       16.73        25.74        23.90        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM 
       15.22        14.73        21.80        14.50        19.92        17.69 
TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       55.30        15.85        16.31        12.99        15.16        43.04 
TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27F 
       15.32        15.52         9.93        14.24        17.42        16.04 
TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N 
       13.45        13.05        14.43        48.03        16.41         4.80 
TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 
        1.61        10.09        13.08        12.53        12.26        33.37 
TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 
       18.51        21.67        16.18        12.66        25.22        43.00 
TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       34.42        27.52        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S 
       28.87        47.15        40.96        38.24        38.60        33.17 
TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y 
       75.98        43.33        34.26        32.02        31.96        69.34 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       18.51        63.62        69.96        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E 
       23.87        14.79        23.34        22.82        17.29        20.71 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       21.63        18.21        55.63        53.92         9.04        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1B0 
       11.05        50.79        19.56        56.94        51.39        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ 
       77.65        37.41        70.36        33.73        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE 
       60.36        73.64        19.66        24.59        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 
       50.07       106.75       102.61         8.75        43.04        26.99 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A576 TCGA-E2-A9RU 
       34.55        43.56         8.28        30.61        34.29        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       34.82        32.88        36.82        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1R0 
       39.55        41.62        35.77        25.84        18.94        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RC 
       34.95         6.12         3.02        11.15        45.01        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A227 
        1.12        46.65         6.58        21.27        47.64        32.05 
TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22E TCGA-E9-A22H 
       42.25        37.74        39.09        38.37        41.72        40.50 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
       20.12        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X 
        9.47        38.07        32.91        30.18        30.44        23.90 
TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW 
       23.84        26.70         0.79        26.40        27.85        12.20 
TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 
       39.72         8.48        18.21        18.90        13.25        16.57 
TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        28.77        25.94        29.85        41.13        39.78 
TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 
       52.96        29.82        23.11        18.48        30.08         7.86 
TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH 
       19.99        13.94        10.52        14.43        34.55        19.96 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       25.91        22.09        34.03        10.16        23.51        15.22 
TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 
       24.99        31.30        33.21         7.40       109.87        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DD TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
      216.76        79.10        75.02        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL 
       69.30        66.38        72.03        13.55        18.12         2.60 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       62.47        11.84        11.57        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       17.06        15.32        14.70        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ 
        2.63        16.08        15.68         7.46        14.50        19.53 
TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 
       19.59        17.49        27.91        22.39         2.10        36.30 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       22.32        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VQ TCGA-OL-A6VR 
       42.77        26.04        17.36        14.07        19.73        40.11 
TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ 
        8.91        47.01        64.21        86.96         0.26         9.93 
TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 
       18.48        21.07        20.68        19.27        13.84        18.87 
TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 
       17.26        13.94        17.03        11.41        52.96        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.16               0.03 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             160.9              282.9 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             24.79              28.50 
[1] "0.2 - 160.9 (24.8)" "0.0 - 282.9 (28.5)"
[1] "hr=" "1.4"
D76V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  19Q LOSS MUTATED        10       11        0        1        54        37
  19Q LOSS WILD-TYPE      79       74        6        5       299       215
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           1         29          3          7        6
  19Q LOSS WILD-TYPE         1        125         26         58       14
                    vv
clus                 STAGE TIS STAGE X
  19Q LOSS MUTATED           0       2
  19Q LOSS WILD-TYPE         1      11
D76V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  10                 79
  STAGE IA                 11                 74
  STAGE IB                  0                  6
  STAGE II                  1                  5
  STAGE IIA                54                299
  STAGE IIB                37                215
  STAGE III                 1                  1
  STAGE IIIA               29                125
  STAGE IIIB                3                 26
  STAGE IIIC                7                 58
  STAGE IV                  6                 14
  STAGE TIS                 0                  1
  STAGE X                   2                 11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED    40 101  15   5
  19Q LOSS WILD-TYPE 236 523 121  35
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1               40                236
  T2              101                523
  T3               15                121
  T4                5                 35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  19Q LOSS MUTATED    65  60  24  10
  19Q LOSS WILD-TYPE 442 298  95  67
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               65                442
  N1               60                298
  N2               24                 95
  N3               10                 67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   129   6
  19Q LOSS WILD-TYPE 760  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    129    6
  19Q LOSS WILD-TYPE  760   16
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0              129                760
  1                6                 16
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED   158   3
  19Q LOSS WILD-TYPE 910   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED    158    3
  19Q LOSS WILD-TYPE  910    9
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE              158                910
  MALE                  3                  9
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    64  82
  19Q LOSS WILD-TYPE 365 436
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     64   82
  19Q LOSS WILD-TYPE  365  436
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                64                365
  YES               82                436
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  19Q LOSS MUTATED                            0                           141
  19Q LOSS WILD-TYPE                          1                           629
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  19Q LOSS MUTATED                                5                   1
  19Q LOSS WILD-TYPE                            195                   5
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  19Q LOSS MUTATED                       0                                4
  19Q LOSS WILD-TYPE                     9                               25
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  19Q LOSS MUTATED                    4              5
  19Q LOSS WILD-TYPE                 13             42
D76V9, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 141                629
  INFILTRATING LOBULAR CARCINOMA                  5                195
  MEDULLARY CARCINOMA                             1                  5
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                4                 25
  MUCINOUS CARCINOMA                              4                 13
  OTHER  SPECIFY                                  5                 42
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0    13
  19Q LOSS WILD-TYPE                                1    47
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                          37    93
  19Q LOSS WILD-TYPE                       144   652
D76V11, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          13                 47
  BLACK OR AFRICAN AMERICAN                      37                144
  WHITE                                          93                652
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V12, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5 129
  19Q LOSS WILD-TYPE  34 746
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5  129
  19Q LOSS WILD-TYPE   34  746
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              129                746
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    75  16
  20P LOSS WILD-TYPE 842 131
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                91                973 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                16                131 
$`20P LOSS MUTATED`
TCGA-5T-A9QA TCGA-A1-A0SK TCGA-A2-A04T TCGA-A2-A0YE TCGA-A2-A3XU TCGA-A2-A4S3 
        9.96        31.79        73.84        18.21        29.98        21.90 
TCGA-A7-A0CE TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A4SE TCGA-A8-A06Q TCGA-A8-A079 
       35.31        31.36        21.73        21.17         1.02         9.01 
TCGA-A8-A07L TCGA-A8-A08F TCGA-A8-A08L TCGA-A8-A08O TCGA-A8-A0AB TCGA-AC-A3W5 
       32.05        33.01         9.99        31.00        17.03        16.57 
TCGA-AC-A62X TCGA-AN-A0AM TCGA-AN-A0XW TCGA-AO-A0J6 TCGA-AO-A1KT TCGA-AQ-A04J 
       13.71         0.16         5.59        37.48        17.79        26.93 
TCGA-AQ-A54N TCGA-AR-A0TZ TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 
        2.56       107.24       134.14        17.23        50.89        99.62 
TCGA-B6-A0I9 TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0RL TCGA-B6-A0RS TCGA-B6-A0X1 
       12.13       233.62        18.77        81.17       100.70       245.10 
TCGA-B6-A1KN TCGA-B6-A400 TCGA-BH-A0AV TCGA-BH-A0B4 TCGA-BH-A0B9 TCGA-BH-A0BR 
      139.17         7.07        59.84        39.16        51.68        76.60 
TCGA-BH-A0DH TCGA-BH-A0E1 TCGA-BH-A18V TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FM 
       38.01        15.68        51.16       114.15        33.17        45.63 
TCGA-C8-A12M TCGA-C8-A134 TCGA-C8-A8HQ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JM 
       11.77        12.59        12.49        20.12        20.09        19.40 
TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XQ TCGA-D8-A1Y3 TCGA-D8-A27F 
       27.58        21.80        14.50        16.41        14.14        16.04 
TCGA-D8-A27H TCGA-D8-A27R TCGA-E2-A14N TCGA-E2-A14R TCGA-E2-A15A TCGA-E2-A15E 
       13.05        10.09        47.15        38.60        23.34        20.71 
TCGA-E2-A2P5 TCGA-E2-A573 TCGA-E9-A1N5 TCGA-E9-A1NC TCGA-E9-A1R6 TCGA-E9-A1RE 
       26.99        34.92        36.82        39.55        11.15        46.65 
TCGA-E9-A22G TCGA-E9-A244 TCGA-EW-A1P4 TCGA-EW-A1P8 TCGA-EW-A2FR TCGA-EW-A2FW 
       40.73         0.69        29.82         7.86        55.00        22.09 
TCGA-EW-A3U0 TCGA-EW-A423 TCGA-GM-A2DF TCGA-JL-A3YX TCGA-LL-A5YP TCGA-MS-A51U 
       17.49        10.16        70.85        11.57        14.79        22.39 
TCGA-OL-A5RW TCGA-OL-A5S0 TCGA-OL-A66O TCGA-OL-A6VO TCGA-PL-A8LX TCGA-S3-AA0Z 
       36.36        20.38        17.36        28.21         0.16        20.68 
TCGA-WT-AB44 
       29.03 

$`20P LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
       48.36         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO 
       47.24        20.88        13.68         7.96        39.32        28.01 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R 
       19.20        18.21       143.15        18.02        78.41       121.94 
TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK 
       87.25        63.12       101.98        55.43        36.13       136.73 
TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR 
       99.12        24.79       114.81        92.48        88.60       107.93 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0CX 
       77.19        75.25         5.19        98.99       107.93        56.81 
TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0D4 TCGA-A2-A0EM 
       67.33        34.55        33.76        61.58        25.22       101.72 
TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER TCGA-A2-A0ES 
       89.36        80.28       118.45        79.76        74.40        72.00 
TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX TCGA-A2-A0EY 
       35.05        34.29        31.82        61.94        24.72        63.29 
TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       99.19        54.64        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YF TCGA-A2-A0YG 
       18.90        20.75        32.55        25.28        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        91.07        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ 
       26.96        21.14        38.30        34.29        35.47        30.61 
TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E 
       37.45        35.67        33.11        29.79        31.73        20.19 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       25.15        23.61        29.56        24.26        23.74        23.80 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 
       20.61        22.32        11.34        10.59        10.29        11.28 
TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD 
       13.41        14.70        11.97        14.93        13.74        14.50 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV 
       17.92        14.73        12.10        10.72        11.05        10.29 
TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R 
        9.37        10.42         8.75        13.02        13.02        17.98 
TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 
       53.06        29.03        31.00        26.01         1.02        17.03 
TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I 
       53.98        43.00        19.99        18.97        18.97        14.01 
TCGA-A8-A07J TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U 
       12.00         9.99        10.98         8.98         7.99        24.99 
TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A 
        9.99        45.07        15.06        36.95        13.02         0.99 
TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P 
       38.01        28.96        19.96        12.00        37.05        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
        0.99        27.02        38.04         0.95        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W6 TCGA-AC-A3W7 
       22.19        24.13        25.05        14.99        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS 
       23.24        24.79        29.26        16.80        14.53        19.33 
TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX 
       14.96        11.44        17.42        18.67        13.58        12.26 
TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR 
        1.68         8.22         0.03        20.19         1.12         1.32 
TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 
        2.30         0.33         0.33         0.23         0.33         0.62 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL 
        2.96         1.78         1.71         9.96         7.36         7.46 
TCGA-AN-A0AR TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF TCGA-AN-A0FJ 
        0.33         0.33         0.33         6.44         5.65         7.96 
TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FV 
        7.00         7.59         7.17         6.90         7.04         0.33 
TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL TCGA-AN-A0XN 
        0.36         0.33         0.33         0.33         5.36         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU 
       12.33         0.30         0.33         0.33         0.33         0.33 
TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P 
        5.33        80.28        61.35        66.77        81.63        95.70 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       52.18        26.04        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 
       61.87        70.39         0.53        24.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        32.52        32.91        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 TCGA-AR-A1AH 
       55.86        65.36       133.22        83.87       107.21       125.16 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       86.07        93.90        99.32        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L TCGA-AR-A24M 
       86.53        86.43        33.73       160.90        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S 
       99.78       118.59         2.76       104.28       112.77        97.84 
TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z 
      105.27        77.69       105.30        32.58        98.76        98.66 
TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LE 
       89.00        93.30        85.64        71.05        93.83       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
       20.25        86.53        54.21        66.15        63.62        38.17 
TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP 
       39.39        40.54        57.27        73.35        33.30        38.96 
TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0IA TCGA-B6-A0IB 
       10.59        77.62       143.38       281.29       275.87       129.57 
TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IM TCGA-B6-A0IN 
       50.70        65.72       146.50       112.37       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 
       18.35        21.47       113.79       206.86       129.70        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52        73.51       170.17 
TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
       37.87        85.35        70.16        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        62.93        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0BA 
       40.83        39.55        70.22        81.63        84.13        37.22 
TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL 
       32.02        18.21        43.53        61.51        21.70        74.89 
TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT 
       61.68        72.23        75.48        74.14        53.95        45.57 
TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 
       49.94        77.95        49.05        41.75        44.02        89.06 
TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK 
       90.97        45.83        77.98        23.44        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       78.28        17.26        15.65         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E2 TCGA-BH-A0E6 
       67.86        70.88        16.27         4.41        14.30         9.63 
TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
       44.81        46.19        32.58        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK 
       23.08        41.00        52.96        26.50        20.38         5.85 
TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX 
        2.50        13.61        36.85        12.89        51.32        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 
       50.79         5.59        23.93        24.95        42.35        44.81 
TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K 
       23.05        32.91         4.90        35.93        20.12        90.84 
TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       26.66        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES 
       66.05         7.36        51.39        67.50        91.99       113.82 
TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY 
       82.85        42.28        12.00        55.69        49.58        17.69 
TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB 
       25.81        31.53        89.16        97.48        24.62       120.62 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN 
       74.73       122.89        36.92        63.35        55.00        72.07 
TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 
      144.59        72.07        28.14        26.14        38.60        83.31 
TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42T 
       57.83       130.16        10.65         6.44        20.12        10.52 
TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 
      109.28        20.88        18.64        23.51         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W 
       12.66        11.77        12.66        12.66        12.66        12.66 
TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56         3.16        13.51         1.87 
TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HF TCGA-C8-A1HG 
       12.92         4.11         4.08        12.33        10.92        11.34 
TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
       11.28         0.16        12.03        10.42        12.33        12.95 
TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        20.25        12.53        12.36        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B 
        9.67         9.53         0.03         9.50        24.56        14.43 
TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y 
       33.99        12.95        13.02        13.41        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       21.14        19.20        14.17        17.49        16.50        55.50 
TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH 
       15.78        18.15        18.90        12.03        53.00        14.01 
TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT 
       18.97        20.09        20.38        21.01        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 
       14.70        18.58        17.79        16.73        25.74        23.90 
TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL 
       18.15        12.39        17.16        15.22        14.73        19.92 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        55.30        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        43.04        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       14.24        17.42        13.45        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27T TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         1.61        13.08        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q 
       40.11        28.44        28.87        44.68        40.96        38.24 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 
       69.34        18.51        63.62        69.96        23.24        19.43 
TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15C TCGA-E2-A15D 
       21.04        23.87        14.79        25.05        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K 
       21.63        18.21        12.92        55.63        53.92         9.04 
TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S 
       20.58        11.05        50.79        19.56        56.94        14.07 
TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 
       51.39        76.57        53.62        87.22        33.01        32.35 
TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG 
       28.50        16.47        37.25        77.65        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 
       60.99        11.08        54.18        60.36        73.64        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       24.59        75.81        28.90        50.07       106.75       102.61 
TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
        8.75        43.04        34.55        43.56         8.28        30.61 
TCGA-E2-A574 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N6 
       38.76        34.29        17.69        34.82        32.88        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       34.16        36.20        36.56        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         6.12         3.02        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12         6.58        21.27        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 
       41.03        41.72        40.50        20.12        38.99         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO 
        7.13        24.56        12.33        29.72         9.47        38.07 
TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK 
       32.91        30.18        30.44        23.90        23.84        26.70 
TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
        0.79        25.81        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 
        8.48        18.21        18.90        13.25        16.57        15.68 
TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ 
       28.77        25.94        22.82        29.95        29.85        40.41 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 
       41.13        39.78        52.96        23.11        18.48        30.08 
TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       18.90        19.99         6.15        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A424 
       34.55        19.96        52.73        25.91        34.03        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 
       15.22        16.77        24.99        31.30        33.21         7.40 
TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD 
      109.87        59.57       216.76        79.10        83.34        75.02 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.47        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       32.75        29.23        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        19.53        12.36        19.59        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A66H TCGA-OL-A66I 
       34.92        28.87        24.72        22.32        26.70        23.47 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P TCGA-OL-A6VQ 
       65.62        41.92        42.77        26.04        14.07        19.73 
TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY 
       40.11         8.91        47.01        64.21        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.81        18.48        21.07        19.27        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       18.87        17.39        17.26        13.94        17.03         3.81 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 
       66.84        11.41        52.96        15.35        16.04       108.07 
TCGA-Z7-A8R6 
      107.05 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.16               0.03 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             245.1              282.9 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             22.09              28.44 
[1] "0.2 - 245.1 (22.1)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1.5"
D77V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20P LOSS MUTATED         3        6        0        0        37        20
  20P LOSS WILD-TYPE      86       79        6        6       316       232
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           0         15          3          6        3
  20P LOSS WILD-TYPE         2        139         26         59       17
                    vv
clus                 STAGE TIS STAGE X
  20P LOSS MUTATED           0       0
  20P LOSS WILD-TYPE         1      13
D77V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   3                 86
  STAGE IA                  6                 79
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                37                316
  STAGE IIB                20                232
  STAGE III                 0                  2
  STAGE IIIA               15                139
  STAGE IIIB                3                 26
  STAGE IIIC                6                 59
  STAGE IV                  3                 17
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED    16  65   8   4
  20P LOSS WILD-TYPE 260 559 128  36
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1               16                260
  T2               65                559
  T3                8                128
  T4                4                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20P LOSS MUTATED    41  31  11   8
  20P LOSS WILD-TYPE 466 327 108  69
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               41                466
  N1               31                327
  N2               11                108
  N3                8                 69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    73   5
  20P LOSS WILD-TYPE 816  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     73    5
  20P LOSS WILD-TYPE  816   17
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               73                816
  1                5                 17
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    92   1
  20P LOSS WILD-TYPE 976  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     92    1
  20P LOSS WILD-TYPE  976   11
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               92                976
  MALE                  1                 11
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    30  53
  20P LOSS WILD-TYPE 399 465
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     30   53
  20P LOSS WILD-TYPE  399  465
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                30                399
  YES               53                465
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20P LOSS MUTATED                            0                            76
  20P LOSS WILD-TYPE                          1                           694
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20P LOSS MUTATED                                8                   2
  20P LOSS WILD-TYPE                            192                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20P LOSS MUTATED                       0                                2
  20P LOSS WILD-TYPE                     9                               27
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20P LOSS MUTATED                    1              4
  20P LOSS WILD-TYPE                 16             43
D77V9, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  76                694
  INFILTRATING LOBULAR CARCINOMA                  8                192
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                2                 27
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  4                 43
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     5
  20P LOSS WILD-TYPE                                1    55
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                          24    56
  20P LOSS WILD-TYPE                       157   689
D77V11, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 55
  BLACK OR AFRICAN AMERICAN                      24                157
  WHITE                                          56                689
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V12, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     5  71
  20P LOSS WILD-TYPE  34 804
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5   71
  20P LOSS WILD-TYPE   34  804
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO               71                804
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED    43  10
  20Q LOSS WILD-TYPE 874 137
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                53               1011 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                10                137 
$`20Q LOSS MUTATED`
TCGA-A1-A0SK TCGA-A2-A3XU TCGA-A7-A0CE TCGA-A7-A0DA TCGA-A7-A26E TCGA-A7-A26I 
       31.79        29.98        35.31        35.67        31.36        21.73 
TCGA-A7-A6VW TCGA-A8-A06Q TCGA-A8-A07B TCGA-A8-A08O TCGA-A8-A0AB TCGA-AC-A62X 
        9.37         1.02        43.00        31.00        17.03        13.71 
TCGA-AN-A0AR TCGA-AN-A0XW TCGA-AO-A03P TCGA-AO-A0J6 TCGA-AO-A1KS TCGA-AQ-A04J 
        0.33         5.59        95.70        37.48         0.53        26.93 
TCGA-AQ-A54N TCGA-AR-A0U3 TCGA-AR-A1AR TCGA-AR-A24K TCGA-AR-A251 TCGA-B6-A0RS 
        2.56       134.14        17.23        50.89        99.62       100.70 
TCGA-B6-A0X1 TCGA-B6-A400 TCGA-BH-A0AV TCGA-BH-A18V TCGA-BH-A1FC TCGA-C8-A12M 
      245.10         7.07        59.84        51.16       114.15        11.77 
TCGA-C8-A27B TCGA-C8-A8HQ TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1XJ TCGA-D8-A1XK 
       14.43        12.49        20.12        20.09        21.80        14.50 
TCGA-E2-A14N TCGA-E2-A15E TCGA-E2-A2P5 TCGA-E9-A1NC TCGA-E9-A22G TCGA-EW-A1P4 
       47.15        20.71        26.99        39.55        40.73        29.82 
TCGA-EW-A1P8 TCGA-EW-A2FW TCGA-EW-A3U0 TCGA-JL-A3YX TCGA-LL-A5YP TCGA-MS-A51U 
        7.86        22.09        17.49        11.57        14.79        22.39 
TCGA-OL-A5RW TCGA-OL-A66O TCGA-OL-A6VO TCGA-S3-AA0Z TCGA-WT-AB44 
       36.36        17.36        28.21        20.68        29.03 

$`20Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 
      129.14       131.67        42.81        40.14        11.44        48.56 
TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF 
       48.36         9.96         8.52        14.37        43.43        48.10 
TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN 
       14.27        47.24        20.88        13.68         7.96        39.32 
TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q 
       28.01        19.20        18.21       143.15        18.02        78.41 
TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04V TCGA-A2-A04W TCGA-A2-A04X 
      121.94        73.84        87.25        63.12       101.98        55.43 
TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO TCGA-A2-A0CP 
       36.13       136.73        99.12        24.79       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CU TCGA-A2-A0CV 
       88.60       107.93        77.19        75.25         5.19        98.99 
TCGA-A2-A0CW TCGA-A2-A0CX TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
      107.93        56.81        67.33        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SV TCGA-A2-A0SW 
       24.72        63.29        99.19        54.64        27.12        44.88 
TCGA-A2-A0SX TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 
       50.43        44.28        17.52        17.13         8.38        49.84 
TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD 
       20.52        17.46        18.90        20.75        32.55        25.28 
TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ 
       18.21        50.47        21.90        21.67        49.48        18.61 
TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW 
       19.33        48.46        31.73        23.77        23.47        17.36 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E 
       52.47       107.70        42.44        17.19        18.15       105.34 
TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XV 
       10.59        36.23        39.65        33.93        91.07        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW 
       56.28        47.31        35.93        50.37        50.83         7.30 
TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 
       24.39        21.30        23.21        26.96        21.14        21.90 
TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0D9 TCGA-A7-A0DB 
       38.30        34.29        35.47        30.61        37.45        33.11 
TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H 
       29.79        31.73        20.19        25.15        23.61        29.56 
TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.74        23.80        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       14.93        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A7-A6VY 
       12.10        10.72        11.05        10.29        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06U TCGA-A8-A06X 
       13.02        13.02        17.98        53.06        29.03        31.00 
TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07E 
       26.01         1.02        17.03        53.98         9.01        19.99 
TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O 
       18.97        18.97        14.01        12.00        32.05         9.99 
TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z 
       10.98         8.98         7.99        24.99         9.99        45.07 
TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C 
       15.06        36.95        13.02         0.99        38.01        28.96 
TCGA-A8-A08F TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08L TCGA-A8-A08P 
       33.01        19.96        12.00        37.05         9.99        31.00 
TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
        0.99        33.01       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09A 
       30.97        17.95        41.98        12.00         9.99         9.99 
TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K 
       12.00         1.02        50.04        49.05        45.07        29.98 
TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09V 
       33.07         1.02        25.02         8.98        19.04        15.02 
TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A6 
        0.99        14.01        12.00        19.04        13.02        21.04 
TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
        0.99        27.02        38.04         0.95        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE 
        5.72         1.48        73.05        99.35        40.57        86.66 
TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH 
       90.71        60.92        87.12        26.04        74.14        33.04 
TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD 
       19.33        14.66        32.45         6.48        16.31        14.83 
TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 
       22.19        24.13        25.05        14.99        16.57        19.79 
TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A5EI 
       15.48        23.24        24.79        29.26        16.80        14.53 
TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW 
       19.33        14.96        11.44        17.42        18.67        13.58 
TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ 
       12.26         1.68         8.22         0.03        20.19         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.32         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK 
        0.62         2.96         1.78         1.71         9.96         7.36 
TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FF 
        7.46         0.16         0.33         0.33         6.44         5.65 
TCGA-AN-A0FJ TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        7.96         7.00         7.59         7.17         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XL 
        0.33         0.36         0.33         0.33         0.33         5.36 
TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XT 
        0.33        12.33         0.30         0.33         0.33         0.33 
TCGA-AN-A0XU TCGA-AN-A0XV TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O 
        0.33         5.33        80.28        61.35        66.77        81.63 
TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J3 
       68.75        47.87        58.95        29.13        32.78        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA 
       52.18        26.04        20.32        22.36        53.03        21.53 
TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JG 
       50.70        50.86        72.00        76.77        65.10        26.24 
TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 TCGA-AO-A125 
       50.24        62.04        55.33        71.80       115.27        99.25 
TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D 
      108.72       106.78       108.03        90.58        98.27        64.04 
TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       57.30        48.36        41.62        40.57        14.73        82.62 
TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04L TCGA-AQ-A0Y5 
       61.87        70.39        17.79        24.79       130.09         5.65 
TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ 
       15.62        32.52        32.91        19.20       140.55        98.33 
TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
        5.26        84.10       109.02        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A0U4 
       55.86       107.24        65.36       133.22        83.87       107.21 
TCGA-AR-A1AH TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM 
      125.16       108.36       101.00       103.86        97.68        98.33 
TCGA-AR-A1AN TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AS TCGA-AR-A1AU 
       96.00        86.07        93.90        99.32        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24L 
       61.28        86.53        86.43        33.73       160.90        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R 
      120.33        99.78       118.59         2.76       104.28       112.77 
TCGA-AR-A24S TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X 
       97.84       105.27        77.69       105.30        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A256 
       98.66        89.00        93.30        85.64        71.05        93.83 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK TCGA-AR-A2LL TCGA-AR-A2LM 
      166.42        20.25        86.53        54.21        66.15        63.62 
TCGA-AR-A2LN TCGA-AR-A2LO TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN 
       38.17        39.39        40.54        57.27        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE TCGA-B6-A0IG TCGA-B6-A0IH 
      275.87       129.57        50.70        65.72       146.50       112.37 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP 
      233.62        18.77       127.33        84.59       165.76       129.07 
TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH TCGA-B6-A0RI TCGA-B6-A0RL 
      140.88       255.68        68.45       212.25       234.28        81.17 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RT 
       78.02       263.28       162.05       102.77       140.48        89.46 
TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WW 
      282.90       157.41        97.48       188.68        79.63        18.35 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       113.79       206.86       129.70        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A1KN TCGA-B6-A2IU 
       58.88        43.59       101.52        73.51       139.17       170.17 
TCGA-B6-A3ZX TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
       37.87        85.35        70.16        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B0 
       71.15        62.93        20.45        25.55        63.09        81.44 
TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 
       40.83        39.55        39.16        70.22        81.63        84.13 
TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG 
       51.68        37.22        32.02        18.21        43.53        61.51 
TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ 
       21.70        74.89        61.68        72.23        75.48        74.14 
TCGA-BH-A0BR TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ 
       76.60        53.95        45.57        49.94        77.95        49.05 
TCGA-BH-A0C0 TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE 
       41.75        44.02        89.06        90.97        45.83        77.98 
TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO 
       23.44        38.01        29.98        13.91        78.28        17.26 
TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DX 
       15.65         3.22         2.56        38.47        67.86        70.88 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E6 TCGA-BH-A0E7 
       16.27         4.41        15.68        14.30         9.63        44.81 
TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0GY 
       46.19        32.58        24.49        31.00        24.43        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 
       10.78        15.16        37.78        53.26        24.56        23.08 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0HX TCGA-BH-A0HY 
       13.61        36.85        12.89        51.32        27.25        50.79 
TCGA-BH-A0RX TCGA-BH-A0W3 TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
        5.59        23.93        24.95        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L 
       32.91         4.90        35.93        20.12        90.84        26.66 
TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S 
       72.56        37.74        30.28        55.63        37.55        66.05 
TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
        7.36        51.39        67.50        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FD 
       31.53        89.16        97.48        24.62       120.62        33.17 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FM 
       74.73       122.89        36.92        63.35        55.00        45.63 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 
       10.52       109.28        20.88        18.64        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12V 
       11.77        12.66        11.77        12.66        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 
       12.66        12.66        48.53        12.56         3.16        13.51 
TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE 
        1.87        12.59        12.92         4.11         4.08        12.33 
TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HK TCGA-C8-A1HL 
       10.92        11.34        11.28         0.16        12.03        10.42 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       12.33        12.95        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 TCGA-C8-A278 
       12.95         8.28         9.67         9.53         0.03         9.50 
TCGA-C8-A27A TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP TCGA-C8-A8HR TCGA-C8-A9FZ 
       24.56        33.99        12.95        13.02        13.41        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       56.81        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J8 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.48        21.14        19.20        14.17        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF TCGA-D8-A1JG 
       55.50        15.78        18.15        18.90        12.03        53.00 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       14.01        18.97        20.09        19.40        20.38        21.01 
TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 
       12.20        13.32        14.70        18.58        17.79        16.73 
TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD 
       25.74        23.90        27.58        18.15        12.39        17.16 
TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       15.22        14.73        19.92        17.69        55.30        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H TCGA-D8-A27I TCGA-D8-A27K 
       17.42        16.04        13.45        13.05        14.43        48.03 
TCGA-D8-A27L TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27T 
       16.41        13.48         4.80         1.61        10.09        13.08 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U 
       12.53        12.26        33.37        18.51        21.67        16.18 
TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 
       12.66        25.22        43.00        34.42        27.52        46.59 
TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14O 
       40.41        37.51        40.11        28.44        28.87        44.68 
TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U 
       40.96        38.24        38.60        33.17        75.98        43.33 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 
       34.26        32.02        31.96        69.34        18.51        63.62 
TCGA-E2-A152 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 TCGA-E2-A156 TCGA-E2-A158 
       69.96        23.24        19.43        21.04        23.87        14.79 
TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15F TCGA-E2-A15G 
       25.05        23.34        22.82        17.29        21.63        18.21 
TCGA-E2-A15H TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       12.92        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       50.79        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        87.22        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II 
       37.25        77.65        37.41        70.36        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU 
       28.44        59.18         3.88        22.19        60.99        11.08 
TCGA-E2-A1L6 TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB 
       54.18        60.36        73.64        19.66        24.59        75.81 
TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL 
       28.90        50.07       106.75       102.61         8.75        43.04 
TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 
       34.55        43.56         8.28        30.61        34.92        38.76 
TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.29        17.69        34.82        32.88        36.82        22.29 
TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF 
       34.16        36.20        36.56        41.62        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       25.84        18.94         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
        2.56         6.12         3.02        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG 
       32.09        40.24         1.12        46.65         6.58        21.27 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 
       46.59        47.64        34.45        32.05        42.25        37.74 
TCGA-E9-A22A TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 
       39.09        38.37        41.03        41.72        40.50        20.12 
TCGA-E9-A244 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 
        0.69        38.99         1.94         7.13        24.56        12.33 
TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 
       29.72         9.47        38.07        32.91        30.18        30.44 
TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A5UP 
       23.90        23.84        26.70         0.79        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 
       27.85        12.20        39.72         8.48        18.21        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1J6 TCGA-EW-A1OV TCGA-EW-A1OW 
       13.25        16.57        15.68        28.77        25.94        22.82 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 
       29.95        29.85        40.41        41.13        39.78        52.96 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48        30.08        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A3E8 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 
       52.73        25.91        34.03        10.16        23.51        15.22 
TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-GI-A2C8 TCGA-GI-A2C9 
       16.77        24.99        31.30        33.21         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN 
       72.10        85.15        86.96       115.69       106.06       101.62 
TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN 
       85.35       110.50        38.20        43.73        69.30        66.38 
TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2NL TCGA-HN-A2OB TCGA-JL-A3YW 
       72.03        13.55        18.12         2.60        62.47        11.84 
TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 
       21.24        13.22         7.10        13.28        10.62        24.95 
TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN 
       32.75        29.23        25.05        17.06        15.32        14.70 
TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       14.47        22.26         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-LQ-A4E4 
       14.50        19.53        12.36        19.59        17.49        27.91 
TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU 
        2.10        36.30        58.52        31.99        58.62        40.08 
TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5RZ TCGA-OL-A5S0 TCGA-OL-A66H 
       34.92        28.87        24.72        22.32        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66P 
       23.47        65.62        41.92        42.77        26.04        14.07 
TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       19.73        40.11         8.91        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH 
        0.16         0.26         9.93        18.81        18.48        21.07 
TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 
       19.27        13.84        18.87        17.39        17.26        13.94 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 
       17.03         3.81        66.84        11.41        52.96        15.35 
TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       16.04       108.07       107.05 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              0.33               0.03 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             245.1              282.9 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             22.39              28.14 
[1] "0.3 - 245.1 (22.4)" "0.0 - 282.9 (28.1)"
[1] "hr=" "1.6"
D78V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  20Q LOSS MUTATED         1        2        0        0        26        14
  20Q LOSS WILD-TYPE      88       83        6        6       327       238
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           0          8          1          2        1
  20Q LOSS WILD-TYPE         2        146         28         63       19
                    vv
clus                 STAGE TIS STAGE X
  20Q LOSS MUTATED           0       0
  20Q LOSS WILD-TYPE         1      13
D78V3, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   1                 88
  STAGE IA                  2                 83
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                26                327
  STAGE IIB                14                238
  STAGE III                 0                  2
  STAGE IIIA                8                146
  STAGE IIIB                1                 28
  STAGE IIIC                2                 63
  STAGE IV                  1                 19
  STAGE TIS                 0                  1
  STAGE X                   0                 13
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     7  42   5   1
  20Q LOSS WILD-TYPE 269 582 131  39
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                7                269
  T2               42                582
  T3                5                131
  T4                1                 39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  20Q LOSS MUTATED    28  19   5   3
  20Q LOSS WILD-TYPE 479 339 114  74
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0               28                479
  N1               19                339
  N2                5                114
  N3                3                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    44   2
  20Q LOSS WILD-TYPE 845  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     44    2
  20Q LOSS WILD-TYPE  845   20
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0               44                845
  1                2                 20
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                    0    1
  20Q LOSS MUTATED     55    0
  20Q LOSS WILD-TYPE 1013   12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     55    0
  20Q LOSS WILD-TYPE 1013   12
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE               55               1013
  MALE                  0                 12
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED    22  28
  20Q LOSS WILD-TYPE 407 490
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED     22   28
  20Q LOSS WILD-TYPE  407  490
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                22                407
  YES               28                490
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  20Q LOSS MUTATED                            0                            40
  20Q LOSS WILD-TYPE                          1                           730
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  20Q LOSS MUTATED                                7                   3
  20Q LOSS WILD-TYPE                            193                   3
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  20Q LOSS MUTATED                       0                                1
  20Q LOSS WILD-TYPE                     9                               28
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  20Q LOSS MUTATED                    1              3
  20Q LOSS WILD-TYPE                 16             44
D78V9, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                  40                730
  INFILTRATING LOBULAR CARCINOMA                  7                193
  MEDULLARY CARCINOMA                             3                  3
  METAPLASTIC CARCINOMA                           0                  9
  MIXED HISTOLOGY (PLEASE SPECIFY)                1                 28
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  3                 44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     5
  20Q LOSS WILD-TYPE                                1    55
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                          16    29
  20Q LOSS WILD-TYPE                       165   716
D78V11, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                           5                 55
  BLACK OR AFRICAN AMERICAN                      16                165
  WHITE                                          29                716
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V12, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4  43
  20Q LOSS WILD-TYPE  35 832
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4   43
  20Q LOSS WILD-TYPE   35  832
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 35
  NOT HISPANIC OR LATINO               43                832
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   152  26
  21Q LOSS WILD-TYPE 765 121
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               178                886 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                26                121 
$`21Q LOSS MUTATED`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-5L-AAT1 TCGA-A1-A0SN TCGA-A2-A04T TCGA-A2-A0CW 
      131.67        42.81        48.36        39.32        73.84       107.93 
TCGA-A2-A0D0 TCGA-A2-A0EU TCGA-A2-A0SU TCGA-A2-A0YJ TCGA-A2-A0YT TCGA-A2-A1FV 
       67.33        34.29        54.64        18.61        23.77        23.47 
TCGA-A2-A1FW TCGA-A2-A25B TCGA-A2-A3XY TCGA-A2-A3Y0 TCGA-A7-A0CJ TCGA-A7-A26G 
       17.36        42.44        35.93        50.83        30.61        23.74 
TCGA-A7-A4SD TCGA-A8-A06P TCGA-A8-A06U TCGA-A8-A079 TCGA-A8-A08F TCGA-A8-A08G 
       14.50        13.02        29.03         9.01        33.01        19.96 
TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A09A TCGA-A8-A09B 
       12.00        37.05        31.00        33.01         9.99        12.00 
TCGA-A8-A09I TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A0A2 TCGA-A8-A0A4 TCGA-A8-A0A9 
       45.07        25.02         8.98        19.04        13.02        27.02 
TCGA-AC-A2BK TCGA-AC-A2BM TCGA-AC-A4ZE TCGA-AC-A7VB TCGA-AC-A8OP TCGA-AC-A8OQ 
       73.05        99.35        29.26         8.22        20.19         1.12 
TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A0AM TCGA-AN-A0FF TCGA-AN-A0FJ TCGA-AN-A0FV 
        2.96         1.78         0.16         5.65         7.96         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AO-A03L TCGA-AO-A03P TCGA-AO-A03R TCGA-AO-A0J3 
        0.33         0.33        80.28        95.70        68.75        21.40 
TCGA-AO-A0J4 TCGA-AO-A0J7 TCGA-AO-A0JD TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AR-A0TP 
       52.18        20.32        72.00       130.09         5.65       140.55 
TCGA-AR-A0TT TCGA-AR-A0TZ TCGA-AR-A0U1 TCGA-AR-A0U2 TCGA-AR-A1AP TCGA-AR-A24S 
      109.02       107.24       133.22        83.87        93.90        97.84 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A256 
       77.69       105.30        32.58        89.00        93.30        93.83 
TCGA-AR-A2LK TCGA-B6-A0IB TCGA-B6-A0IE TCGA-B6-A0RP TCGA-B6-A0RS TCGA-B6-A0WW 
       54.21       129.57        65.72       102.77       100.70        18.35 
TCGA-B6-A0X1 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KN TCGA-B6-A2IU TCGA-B6-A408 
      245.10        58.88        43.59       139.17       170.17        68.12 
TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0B9 TCGA-BH-A0BG TCGA-BH-A0BP TCGA-BH-A0DE 
       62.93        59.84        51.68        61.51        75.48        77.98 
TCGA-BH-A0DP TCGA-BH-A0E9 TCGA-BH-A0H7 TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0HY 
       15.65        46.19        23.08        12.89        27.25        50.79 
TCGA-BH-A0W3 TCGA-BH-A18L TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1FM TCGA-BH-A5J0 
       23.93        26.66        51.39        51.16        45.63        23.51 
TCGA-C8-A12O TCGA-C8-A12Q TCGA-C8-A12U TCGA-C8-A12W TCGA-C8-A137 TCGA-C8-A138 
       12.66        12.66        12.66        12.66         4.11         4.08 
TCGA-C8-A1HF TCGA-C8-A1HK TCGA-C8-A1HN TCGA-C8-A26W TCGA-C8-A27A TCGA-C8-A27B 
       10.92        12.03        12.95        12.53        24.56        14.43 
TCGA-C8-A8HP TCGA-C8-A8HR TCGA-D8-A145 TCGA-D8-A1J8 TCGA-D8-A1JD TCGA-D8-A1JF 
       13.02        13.41        13.48        14.17        18.15        12.03 
TCGA-D8-A1JM TCGA-D8-A1X6 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XF TCGA-D8-A1XL 
       19.40        17.79        27.58        18.15        15.22        19.92 
TCGA-D8-A1XR TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y1 TCGA-D8-A27M TCGA-D8-A27T 
       15.85        16.54        15.32         9.93        13.48        13.08 
TCGA-D8-A27W TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10C TCGA-E2-A152 TCGA-E2-A15E 
       12.26        34.42        46.59        40.11        69.96        20.71 
TCGA-E2-A15G TCGA-E2-A15H TCGA-E2-A1IH TCGA-E2-A1L8 TCGA-E2-A1LL TCGA-E2-A56Z 
       18.21        12.92        33.73        73.64        43.04         8.28 
TCGA-E2-A574 TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1ND TCGA-E9-A1NH TCGA-E9-A1R0 
       38.76        34.16        36.56        41.62        18.94        28.27 
TCGA-E9-A1R4 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RG TCGA-E9-A226 TCGA-E9-A22G 
        6.12        45.01        32.09        21.27        34.45        40.73 
TCGA-E9-A243 TCGA-E9-A247 TCGA-E9-A248 TCGA-E9-A3QA TCGA-E9-A5FL TCGA-EW-A1IW 
       20.12        38.99         1.94        30.18         0.79        12.20 
TCGA-EW-A1J6 TCGA-EW-A2FS TCGA-EW-A6SD TCGA-GI-A2C9 TCGA-GM-A2DL TCGA-GM-A4E0 
       28.77        52.73        33.21       109.87       115.69        72.03 
TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A5YM TCGA-OL-A5RZ TCGA-OL-A66N TCGA-OL-A6VQ 
        2.60        11.57        15.32        22.32        26.04        19.73 
TCGA-PL-A8LX TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA17 
        0.16        18.81        18.48        13.94 

$`21Q LOSS WILD-TYPE`
TCGA-3C-AAAU TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5T-A9QA TCGA-A1-A0SB 
      129.14        40.14        11.44        48.56         9.96         8.52 
TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SH TCGA-A1-A0SI 
       14.37        43.43        48.10        14.27        47.24        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SK TCGA-A1-A0SM TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68        31.79         7.96        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04R TCGA-A2-A04U TCGA-A2-A04V 
      143.15        18.02        78.41       121.94        87.25        63.12 
TCGA-A2-A04W TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM 
      101.98        55.43        36.13       136.73        99.12        24.79 
TCGA-A2-A0CO TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS TCGA-A2-A0CT 
      114.81        92.48        88.60       107.93        77.19        75.25 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 
        5.19        98.99        56.81        34.55        33.76        61.58 
TCGA-A2-A0D4 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EO TCGA-A2-A0EP TCGA-A2-A0EQ 
       25.22       101.72        89.36        80.28       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       74.40        72.00        35.05        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SV TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        27.12        44.88        50.43        44.28 
TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       17.52        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.90        21.67        49.48        19.33        48.46        31.73 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 
       60.72        22.45        20.25        19.20        19.56        16.47 
TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F 
       52.47       107.70        17.19        18.15       105.34        10.59 
TCGA-A2-A3KC TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XT TCGA-A2-A3XU TCGA-A2-A3XV 
       36.23        39.65        33.93        91.07        29.98        32.75 
TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY 
       56.28        47.31        50.37         7.30        24.39        21.30 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A2-A4S3 TCGA-A7-A0CD TCGA-A7-A0CE 
       23.21        26.96        21.14        21.90        38.30        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC 
       34.29        35.47        37.45        35.67        33.11        29.79 
TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E 
       31.73        20.19        25.15        23.61        29.56        31.36 
TCGA-A7-A26F TCGA-A7-A26H TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY 
       24.26        23.80        21.73        20.61        22.32        11.34 
TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3J1 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A426 
       10.59        10.29        11.28        13.41        14.70        11.97 
TCGA-A7-A4SA TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A5ZV 
       14.93        13.74        21.17        17.92        14.73        12.10 
TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY 
       10.72        11.05        10.29         9.37        10.42         8.75 
TCGA-A8-A06O TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T TCGA-A8-A06X TCGA-A8-A06Y 
       13.02         1.02        17.98        53.06        31.00        26.01 
TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F 
        1.02        17.03        53.98        43.00        19.99        18.97 
TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L TCGA-A8-A07O TCGA-A8-A07P 
       18.97        14.01        12.00        32.05         9.99        10.98 
TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W TCGA-A8-A07Z TCGA-A8-A084 
        8.98         7.99        24.99         9.99        45.07        15.06 
TCGA-A8-A085 TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08L 
       36.95        13.02         0.99        38.01        28.96         9.99 
TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 
       31.00         0.99       112.08        43.00        40.01        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A099 TCGA-A8-A09C 
       30.97        17.95        41.98        12.00         9.99         1.02 
TCGA-A8-A09D TCGA-A8-A09E TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09N TCGA-A8-A09T 
       50.04        49.05        29.98        33.07         1.02        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A6 TCGA-A8-A0A7 
       15.02         0.99        14.01        12.00        21.04         0.99 
TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G TCGA-AC-A23H 
       17.03        38.04         0.95        22.95        73.91         5.72 
TCGA-AC-A2B8 TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        40.57        86.66        90.71        60.92        87.12 
TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3BB 
       26.04        74.14        33.04        19.33        14.66        32.45 
TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP TCGA-AC-A3QQ TCGA-AC-A3TM 
        6.48        16.31        14.83        22.19        24.13        25.05 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 TCGA-AC-A3YI TCGA-AC-A3YJ 
       14.99        16.57        19.79        15.48        23.24        24.79 
TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X 
       16.80        14.53        19.33        14.96        11.44        13.71 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VC 
       17.42        18.67        13.58        12.26         1.68         0.03 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 
        1.32         2.30         0.33         0.33         0.23         0.33 
TCGA-AN-A049 TCGA-AN-A04D TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0AL TCGA-AN-A0AR 
        0.62         1.71         9.96         7.36         7.46         0.33 
TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN 
        0.33         0.33         6.44         7.00         7.59         7.17 
TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ 
        6.90         7.04         0.36         0.33         0.33         0.33 
TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XU 
        5.36         0.33        12.33         0.30         0.33         0.33 
TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03T 
        5.33         5.59        61.35        66.77        81.63        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0J8 
       58.95        29.13        32.78        26.04        37.48        22.36 
TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JE TCGA-AO-A0JF 
       53.03        21.53        50.70        50.86        76.77        65.10 
TCGA-AO-A0JG TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A124 
       26.24        50.24        62.04        55.33        71.80       115.27 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO 
       64.04        57.30        48.36        41.62        40.57        14.73 
TCGA-AO-A1KP TCGA-AO-A1KQ TCGA-AO-A1KR TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H 
       82.62        61.87        70.39         0.53        17.79        24.79 
TCGA-AQ-A04J TCGA-AQ-A1H2 TCGA-AQ-A1H3 TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 
       26.93        15.62        32.52         2.56        32.91        19.20 
TCGA-AR-A0TQ TCGA-AR-A0TR TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TW TCGA-AR-A0TX 
       98.33         5.26        84.10        75.22        98.93        64.83 
TCGA-AR-A0TY TCGA-AR-A0U0 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AI 
       55.86        65.36       134.14       107.21       125.16       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV TCGA-AR-A1AW 
       99.32        17.23        37.81        94.29        61.28        86.53 
TCGA-AR-A1AX TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M 
       86.43        33.73       160.90        50.89        94.22       120.33 
TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24T 
       99.78       118.59         2.76       104.28       112.77       105.27 
TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A255 TCGA-AR-A2LE 
       98.76        98.66        99.62        85.64        71.05       166.42 
TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LO 
       20.25        86.53        66.15        63.62        38.17        39.39 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ 
       40.54        57.27        73.35        33.30        38.96        10.59 
TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IC 
       77.62       143.38       281.29        12.13       275.87        50.70 
TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IN 
      146.50       112.37       233.62        18.77       127.33        84.59 
TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RH 
      165.76       129.07       140.88       255.68        68.45       212.25 
TCGA-B6-A0RI TCGA-B6-A0RL TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RQ 
      234.28        81.17        78.02       263.28       162.05       140.48 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X4 TCGA-B6-A0X5 
       21.47       113.79       206.86       129.70        28.27        68.94 
TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 
      101.52        73.51        37.87         7.07        85.35        70.16 
TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ 
       18.84       103.63        71.15        20.45        25.55        63.09 
TCGA-BH-A0B0 TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       81.44        40.83        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BJ 
       84.13        37.22        32.02        18.21        43.53        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BQ TCGA-BH-A0BR TCGA-BH-A0BS 
       74.89        61.68        72.23        74.14        76.60        53.95 
TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       45.57        49.94        77.95        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DG TCGA-BH-A0DH TCGA-BH-A0DI 
       89.06        90.97        45.83        23.44        38.01        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT 
       13.91        78.28        17.26         3.22         2.56        38.47 
TCGA-BH-A0DV TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       67.86        70.88        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0EI 
        9.63        44.81        32.58        24.49        31.00        24.43 
TCGA-BH-A0GY TCGA-BH-A0GZ TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       30.35        10.78        15.16        37.78        53.26        24.56 
TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       41.00        52.96        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HW TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 
       13.61        36.85        51.32         5.59        24.95        42.35 
TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J 
       44.81        23.05        32.91         4.90        35.93        20.12 
TCGA-BH-A18K TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R 
       90.84        72.56        37.74        30.28        55.63        37.55 
TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ES TCGA-BH-A1ET 
       66.05         7.36        67.50        91.99       113.82        82.85 
TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1EY TCGA-BH-A1F0 
       42.28        12.00        55.69        49.58        17.69        25.81 
TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1F8 TCGA-BH-A1FB TCGA-BH-A1FC 
       31.53        89.16        97.48        24.62       120.62       114.15 
TCGA-BH-A1FD TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
       33.17        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 
       83.31        57.83       130.16        10.65         6.44        20.12 
TCGA-BH-A42T TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5IZ TCGA-BH-A6R8 TCGA-BH-A6R9 
       10.52       109.28        20.88        18.64         9.63         5.26 
TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M 
        9.70        18.87        21.76         9.44        11.93        11.77 
TCGA-C8-A12N TCGA-C8-A12P TCGA-C8-A12V TCGA-C8-A12X TCGA-C8-A12Y TCGA-C8-A12Z 
       11.77        11.77        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A1HE 
        3.16        13.51         1.87        12.59        12.92        12.33 
TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HO 
       11.34        11.28         0.16        10.42        12.33        12.33 
TCGA-C8-A26V TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 
       20.25        12.36        12.95         8.28         9.67         9.53 
TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A9FZ 
        0.03         9.50        33.99        12.95        12.49        19.46 
TCGA-D8-A13Y TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       56.81        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A146 TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB TCGA-D8-A1JC 
       21.14        19.20        17.49        16.50        55.50        15.78 
TCGA-D8-A1JE TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JK 
       18.90        53.00        14.01        18.97        20.09        20.12 
TCGA-D8-A1JL TCGA-D8-A1JN TCGA-D8-A1JP TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU 
       20.09        20.38        21.01        12.20        13.32        14.70 
TCGA-D8-A1X5 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1X9 TCGA-D8-A1XC TCGA-D8-A1XD 
       18.58        16.73        25.74        23.90        12.39        17.16 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XQ 
       14.73        21.80        14.50        17.69        55.30        16.41 
TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1Y0 
       16.31        16.64        12.99        15.16        43.04        15.52 
TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G TCGA-D8-A27H 
       14.24        14.14        17.42        16.04        13.45        13.05 
TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       14.43        48.03        16.41         4.80         1.61        10.09 
TCGA-D8-A27V TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        33.37        18.51        21.67        16.18        12.66 
TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A108 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10E 
       25.22        43.00        27.52        40.41        37.51        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A155 
       69.34        18.51        63.62        23.24        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       23.87        14.79        25.05        23.34        22.82        17.29 
TCGA-E2-A15F TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M 
       21.63        55.63        53.92         9.04        20.58        11.05 
TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A15T TCGA-E2-A1AZ 
       50.79        19.56        56.94        14.07        51.39        76.57 
TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC 
       53.62        87.22        33.01        32.35        28.50        16.47 
TCGA-E2-A1BD TCGA-E2-A1IE TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1II TCGA-E2-A1IJ 
       37.25        77.65        37.41        70.36        33.70        28.44 
TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 
       59.18         3.88        22.19        60.99        11.08        54.18 
TCGA-E2-A1L7 TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG 
       60.36        19.66        24.59        75.81        28.90        50.07 
TCGA-E2-A1LH TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX 
      106.75       102.61         8.75        26.99        34.55        43.56 
TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A576 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N4 
       30.61        34.92        34.29        17.69        34.82        32.88 
TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1NC TCGA-E9-A1NE TCGA-E9-A1NF 
       36.82        22.29        36.20        39.55        35.77        35.24 
TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 
       25.84         9.86        24.82        34.95         2.56         3.02 
TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF 
       11.15        48.23        40.24         1.12        46.65         6.58 
TCGA-E9-A1RH TCGA-E9-A1RI TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       46.59        47.64        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A249 
       38.37        41.03        41.72        40.50         0.69         7.13 
TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3HO TCGA-E9-A3Q9 
       24.56        12.33        29.72         9.47        38.07        32.91 
TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5UO TCGA-E9-A5UP 
       30.44        23.90        23.84        26.70        25.81        26.40 
TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J1 TCGA-EW-A1J2 
       27.85        39.72         8.48        18.21        18.90        13.25 
TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OW TCGA-EW-A1OX TCGA-EW-A1OY 
       16.57        15.68        25.94        22.82        29.95        29.85 
TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 
       40.41        41.13        39.78        52.96        29.82        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PB TCGA-EW-A1PC 
       18.48        30.08         7.86        18.90        19.99         6.15 
TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR 
       13.94        10.52        14.43        34.55        19.96        55.00 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GM-A2D9 
       15.22        16.77        24.99        31.30         7.40        59.57 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DH 
      216.76        79.10        83.34        75.02        70.85        72.10 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       85.15        86.96       106.06       101.62        85.35       110.50 
TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A5PV TCGA-GM-A5PX 
       38.20        43.73        69.30        66.38        13.55        18.12 
TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 
       62.47        11.84        21.24        13.22         7.10        13.28 
TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL 
       10.62        24.95        32.75        29.23        25.05        17.06 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR 
       14.70        14.47        14.79        22.26         2.63        16.08 
TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 
       15.68         7.46        14.50        19.53        12.36        19.59 
TCGA-LL-A9Q3 TCGA-LQ-A4E4 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 
       17.49        27.91        22.39         2.10        36.30        58.52 
TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RX 
       31.99        58.62        40.08        34.92        36.36        28.87 
TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K 
       24.72        20.38        26.70        23.47        65.62        41.92 
TCGA-OL-A66L TCGA-OL-A66O TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VR TCGA-OL-A97C 
       42.77        17.36        14.07        28.21        40.11         8.91 
TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZH 
       47.01        64.21        86.96         0.26         9.93        21.07 
TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 
       20.68        19.27        13.84        18.87        17.39        17.26 
TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 
       17.03         3.81        66.84        11.41        52.96        29.03 
TCGA-XX-A899 TCGA-XX-A89A TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       15.35        16.04       108.07       107.05 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.16               0.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             245.1              282.9 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            27.135             28.075 
[1] "0.2 - 245.1 (27.1)" "0.0 - 282.9 (28.1)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  21Q LOSS MUTATED        11       13        0        0        51        50
  21Q LOSS WILD-TYPE      78       72        6        6       302       202
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           1         29         10          5        6
  21Q LOSS WILD-TYPE         1        125         19         60       14
                    vv
clus                 STAGE TIS STAGE X
  21Q LOSS MUTATED           1       3
  21Q LOSS WILD-TYPE         0      10
D79V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  11                 78
  STAGE IA                 13                 72
  STAGE IB                  0                  6
  STAGE II                  0                  6
  STAGE IIA                51                302
  STAGE IIB                50                202
  STAGE III                 1                  1
  STAGE IIIA               29                125
  STAGE IIIB               10                 19
  STAGE IIIC                5                 60
  STAGE IV                  6                 14
  STAGE TIS                 1                  0
  STAGE X                   3                 10
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED    40 108  20  11
  21Q LOSS WILD-TYPE 236 516 116  29
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               40                236
  T2              108                516
  T3               20                116
  T4               11                 29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  21Q LOSS MUTATED    74  64  30   9
  21Q LOSS WILD-TYPE 433 294  89  68
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               74                433
  N1               64                294
  N2               30                 89
  N3                9                 68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   149   8
  21Q LOSS WILD-TYPE 740  14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    149    8
  21Q LOSS WILD-TYPE  740   14
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              149                740
  1                8                 14
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   180   0
  21Q LOSS WILD-TYPE 888  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    180    0
  21Q LOSS WILD-TYPE  888   12
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE              180                888
  MALE                  0                 12
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    81  86
  21Q LOSS WILD-TYPE 348 432
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     81   86
  21Q LOSS WILD-TYPE  348  432
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                81                348
  YES               86                432
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  21Q LOSS MUTATED                            0                           145
  21Q LOSS WILD-TYPE                          1                           625
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  21Q LOSS MUTATED                               20                   2
  21Q LOSS WILD-TYPE                            180                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  21Q LOSS MUTATED                       2                                7
  21Q LOSS WILD-TYPE                     7                               22
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  21Q LOSS MUTATED                    1              3
  21Q LOSS WILD-TYPE                 16             44
D79V9, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 145                625
  INFILTRATING LOBULAR CARCINOMA                 20                180
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           2                  7
  MIXED HISTOLOGY (PLEASE SPECIFY)                7                 22
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                  3                 44
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0    17
  21Q LOSS WILD-TYPE                                1    43
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          35   110
  21Q LOSS WILD-TYPE                       146   635
D79V11, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          17                 43
  BLACK OR AFRICAN AMERICAN                      35                146
  WHITE                                         110                635
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V12, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     5 143
  21Q LOSS WILD-TYPE  34 732
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      5  143
  21Q LOSS WILD-TYPE   34  732
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    5                 34
  NOT HISPANIC OR LATINO              143                732
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   409  70
  22Q LOSS WILD-TYPE 508  77
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               479                585 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                70                 77 
$`22Q LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-3C-AALJ TCGA-A1-A0SD TCGA-A1-A0SG TCGA-A1-A0SJ 
      129.14       131.67        42.81        14.37        14.27        13.68 
TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04V 
       39.32        28.01       143.15        18.02        78.41        63.12 
TCGA-A2-A04Y TCGA-A2-A0CM TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CS 
       36.13        24.79        92.48        88.60       107.93        77.19 
TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D4 TCGA-A2-A0EN 
        5.19        98.99       107.93        67.33        25.22        89.36 
TCGA-A2-A0EO TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0SU 
       80.28        35.05        34.29        31.82        61.94        54.64 
TCGA-A2-A0SV TCGA-A2-A0SX TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T6 TCGA-A2-A0T7 
       27.12        50.43        49.84        20.52        18.90        20.75 
TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YT 
       25.28        18.21        50.47        21.90        21.67        23.77 
TCGA-A2-A1FW TCGA-A2-A1G0 TCGA-A2-A25A TCGA-A2-A25B TCGA-A2-A3XS TCGA-A2-A3XT 
       17.36        20.25       107.70        42.44        33.93        91.07 
TCGA-A2-A3XU TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RY TCGA-A2-A4S3 TCGA-A7-A0CE 
       29.98        50.37        50.83        21.30        21.90        35.31 
TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A13D 
       34.29        35.47        30.61        35.67        33.11        31.73 
TCGA-A7-A13E TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3J1 
       20.19        29.56        31.36        21.73        20.61        11.28 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A4SF TCGA-A7-A56D 
       11.97        13.74        14.50        21.17        17.92        14.73 
TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R TCGA-A8-A06T 
        9.37         8.75        13.02         1.02        17.98        53.06 
TCGA-A8-A06U TCGA-A8-A06X TCGA-A8-A06Y TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 
       29.03        31.00        26.01         1.02        17.03        53.98 
TCGA-A8-A07B TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       43.00        19.99        18.97        14.01        12.00        32.05 
TCGA-A8-A07R TCGA-A8-A07W TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08G TCGA-A8-A08I 
        8.98         9.99        15.06        36.95        19.96        12.00 
TCGA-A8-A08J TCGA-A8-A08O TCGA-A8-A08S TCGA-A8-A08Z TCGA-A8-A097 TCGA-A8-A09B 
       37.05        31.00        33.01        40.01        12.00        12.00 
TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09N TCGA-A8-A09R TCGA-A8-A09T TCGA-A8-A09W 
        1.02        50.04         1.02         8.98        19.04         0.99 
TCGA-A8-A0A4 TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-A8-A0AB TCGA-AC-A23G 
       13.02        21.04         0.99        27.02        17.03        73.91 
TCGA-AC-A2BK TCGA-AC-A2FF TCGA-AC-A2FM TCGA-AC-A2QH TCGA-AC-A3BB TCGA-AC-A3HN 
       73.05        90.71        26.04        33.04        32.45        16.31 
TCGA-AC-A3QP TCGA-AC-A3TM TCGA-AC-A3W7 TCGA-AC-A5EH TCGA-AC-A5XS TCGA-AC-A5XU 
       22.19        25.05        15.48        16.80        19.33        14.96 
TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A8OP 
       17.42        18.67        12.26         1.68         8.22        20.19 
TCGA-AN-A041 TCGA-AN-A049 TCGA-AN-A0AJ TCGA-AN-A0AK TCGA-AN-A0FD TCGA-AN-A0FF 
        0.23         0.62         9.96         7.36         6.44         5.65 
TCGA-AN-A0FK TCGA-AN-A0FW TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XO TCGA-AN-A0XR 
        7.00         0.36         0.33         0.33        12.33         0.33 
TCGA-AN-A0XS TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03L TCGA-AO-A03N TCGA-AO-A03P 
        0.33         0.33         0.33        80.28        66.77        95.70 
TCGA-AO-A0J3 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JA TCGA-AO-A0JB 
       21.40        20.32        22.36        53.03        21.53        50.70 
TCGA-AO-A0JD TCGA-AO-A0JG TCGA-AO-A12A TCGA-AO-A12E TCGA-AO-A1KP TCGA-AO-A1KQ 
       72.00        26.24        90.58        57.30        82.62        61.87 
TCGA-AO-A1KS TCGA-AQ-A54N TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TR TCGA-AR-A0TT 
        0.53         2.56        32.91        19.20         5.26       109.02 
TCGA-AR-A0TW TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U0 TCGA-AR-A0U2 TCGA-AR-A0U3 
       98.93        55.86       107.24        65.36        83.87       134.14 
TCGA-AR-A1AH TCGA-AR-A1AJ TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AP TCGA-AR-A1AQ 
      125.16       101.00        98.33        96.00        93.90        99.32 
TCGA-AR-A1AR TCGA-AR-A1AV TCGA-AR-A1AY TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       17.23        61.28        33.73       160.90        50.89        94.22 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24W TCGA-AR-A24X 
      118.59         2.76       112.77        97.84        32.58        98.76 
TCGA-AR-A24Z TCGA-AR-A250 TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LK 
       98.66        89.00        93.30        71.05        93.83        54.21 
TCGA-AR-A2LO TCGA-AR-A5QN TCGA-AR-A5QP TCGA-B6-A0IG TCGA-B6-A0IH TCGA-B6-A0IN 
       39.39        33.30        38.96       146.50       112.37        84.59 
TCGA-B6-A0IO TCGA-B6-A0IQ TCGA-B6-A0RE TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RN 
      165.76       140.88       255.68        68.45        81.17       263.28 
TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0WW TCGA-B6-A0WX TCGA-B6-A0WY TCGA-B6-A1KN 
      162.05       102.77        18.35        21.47       113.79       139.17 
TCGA-B6-A3ZX TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU 
       37.87        68.12        18.84       103.63        71.15        62.93 
TCGA-BH-A0AY TCGA-BH-A0B0 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       25.55        81.44        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BF TCGA-BH-A0BJ TCGA-BH-A0BL 
       84.13        51.68        37.22        43.53        21.70        74.89 
TCGA-BH-A0BR TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C3 TCGA-BH-A0C7 
       76.60        45.57        49.94        49.05        89.06        90.97 
TCGA-BH-A0DH TCGA-BH-A0DQ TCGA-BH-A0E0 TCGA-BH-A0E6 TCGA-BH-A0EB TCGA-BH-A0GY 
       38.01         3.22         4.41         9.63        24.49        30.35 
TCGA-BH-A0GZ TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HA TCGA-BH-A0HB TCGA-BH-A0HQ 
       10.78        23.08        41.00        52.96        26.50        36.85 
TCGA-BH-A0HU TCGA-BH-A0HX TCGA-BH-A0W3 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA 
       12.89        27.25        23.93        42.35        44.81        23.05 
TCGA-BH-A18F TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
       32.91        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18T TCGA-BH-A18V TCGA-BH-A1ES TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EX 
        7.36        51.16       113.82        82.85        42.28        49.58 
TCGA-BH-A1EY TCGA-BH-A1F5 TCGA-BH-A1F8 TCGA-BH-A1FC TCGA-BH-A1FD TCGA-BH-A1FL 
       17.69        89.16        24.62       114.15        33.17        55.00 
TCGA-BH-A1FM TCGA-BH-A1FN TCGA-BH-A204 TCGA-BH-A209 TCGA-BH-A42T TCGA-BH-A5IZ 
       45.63        72.07        83.31       130.16        10.52        18.64 
TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-C8-A12M TCGA-C8-A12U TCGA-C8-A12Y TCGA-C8-A132 
       23.51         9.63        11.77        12.66        48.53         1.87 
TCGA-C8-A138 TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HL TCGA-C8-A1HM TCGA-C8-A1HN 
        4.08        11.28        12.03        10.42        12.33        12.95 
TCGA-C8-A26Z TCGA-C8-A274 TCGA-C8-A27A TCGA-C8-A8HP TCGA-C8-A9FZ TCGA-D8-A13Y 
        8.28         9.53        24.56        13.02        19.46        56.81 
TCGA-D8-A13Z TCGA-D8-A143 TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JB 
       20.88        14.17        13.48        21.14        14.17        55.50 
TCGA-D8-A1JD TCGA-D8-A1JG TCGA-D8-A1JJ TCGA-D8-A1JM TCGA-D8-A1JN TCGA-D8-A1JP 
       18.15        53.00        20.09        19.40        20.38        21.01 
TCGA-D8-A1X5 TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XB TCGA-D8-A1XD TCGA-D8-A1XK 
       18.58        23.90        27.58        18.15        17.16        14.50 
TCGA-D8-A1XM TCGA-D8-A1XO TCGA-D8-A1XR TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1Y0 
       17.69        55.30        15.85        16.64        12.99        15.52 
TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 TCGA-D8-A27I TCGA-D8-A27L TCGA-D8-A27T 
        9.93        14.24        14.14        14.43        16.41        13.08 
TCGA-D8-A3Z5 TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A109 TCGA-E2-A10A 
       33.37        25.22        43.00        34.42        46.59        40.41 
TCGA-E2-A10C TCGA-E2-A10F TCGA-E2-A14O TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14T 
       40.11        28.87        44.68        38.24        38.60        75.98 
TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A159 
       34.26        32.02        18.51        63.62        23.24        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15H 
       23.34        22.82        20.71        21.63        18.21        12.92 
TCGA-E2-A15I TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15P TCGA-E2-A15T TCGA-E2-A1AZ 
       55.63        11.05        50.79        19.56        51.39        76.57 
TCGA-E2-A1B1 TCGA-E2-A1B5 TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IH TCGA-E2-A1II 
       87.22        32.35        37.25        37.41        33.73        33.70 
TCGA-E2-A1IJ TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1L8 TCGA-E2-A1LE 
       28.44         3.88        22.19        60.99        73.64        28.90 
TCGA-E2-A1LK TCGA-E2-A2P5 TCGA-E2-A56Z TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A576 
        8.75        26.99         8.28        34.92        38.76        34.29 
TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
       17.69        34.82        36.82        34.16        36.20        36.56 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NH TCGA-E9-A1NI 
       41.62        35.77        35.24        25.84        18.94         9.86 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R6 TCGA-E9-A1RA TCGA-E9-A1RB TCGA-E9-A1RC 
       34.95         2.56        11.15        45.01        32.09        40.24 
TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RG TCGA-E9-A1RI TCGA-E9-A229 
        1.12        46.65         6.58        21.27        47.64        37.74 
TCGA-E9-A22A TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A244 TCGA-E9-A247 
       39.09        41.03        41.72        40.50         0.69        38.99 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A3HO TCGA-E9-A3X8 TCGA-E9-A54Y 
        1.94         7.13        24.56        38.07        30.44        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UO TCGA-E9-A6HE TCGA-EW-A1IX TCGA-EW-A1J1 
       26.70         0.79        25.81        27.85        39.72        18.90 
TCGA-EW-A1J2 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OY TCGA-EW-A1P3 TCGA-EW-A1P5 
       13.25        28.77        22.82        29.85        52.96        23.11 
TCGA-EW-A1P6 TCGA-EW-A1P8 TCGA-EW-A1PA TCGA-EW-A1PC TCGA-EW-A1PH TCGA-EW-A2FV 
       18.48         7.86        18.90         6.15        19.96        25.91 
TCGA-EW-A423 TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD 
       10.16        15.22        16.77        24.99        31.30        33.21 
TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A3NY 
      216.76        79.10        83.34        86.96       115.69        38.20 
TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-HN-A2NL TCGA-JL-A3YW TCGA-JL-A3YX TCGA-LD-A66U 
       66.38        72.03         2.60        11.84        11.57        21.24 
TCGA-LD-A7W5 TCGA-LL-A442 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A6FP TCGA-LL-A7T0 
        7.10        29.23        14.70        14.47        22.26        12.36 
TCGA-LQ-A4E4 TCGA-OL-A5D7 TCGA-OL-A5RV TCGA-OL-A5RW TCGA-OL-A5RZ TCGA-OL-A66K 
       27.91        58.52        34.92        36.36        22.32        41.92 
TCGA-OL-A66L TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PE-A5DE 
       42.77        28.21        19.73        47.01        64.21        86.96 
TCGA-PL-A8LX TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-S3-AA10 
        0.16         9.93        18.81        18.48        21.07        19.27 
TCGA-UL-AAZ6 TCGA-V7-A7HQ TCGA-WT-AB44 TCGA-XX-A89A TCGA-Z7-A8R5 
       17.03        66.84        29.03        16.04       108.07 

$`22Q LOSS WILD-TYPE`
TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA TCGA-A1-A0SB 
       40.14        11.44        48.56        48.36         9.96         8.52 
TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SH TCGA-A1-A0SI TCGA-A1-A0SK TCGA-A1-A0SM 
       43.43        48.10        47.24        20.88        31.79         7.96 
TCGA-A1-A0SP TCGA-A1-A0SQ TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U TCGA-A2-A04W 
       19.20        18.21       121.94        73.84        87.25       101.98 
TCGA-A2-A04X TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CT TCGA-A2-A0CX 
       55.43       136.73        99.12       114.81        75.25        56.81 
TCGA-A2-A0D1 TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EP TCGA-A2-A0EQ 
       34.55        33.76        61.58       101.72       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SW 
       74.40        72.00        24.72        63.29        99.19        44.88 
TCGA-A2-A0SY TCGA-A2-A0T0 TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T5 TCGA-A2-A0YC 
       44.28        17.52        17.13         8.38        17.46        32.55 
TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM TCGA-A2-A1FV 
       49.48        18.61        19.33        48.46        31.73        23.47 
TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 
       60.72        22.45        19.20        19.56        16.47        52.47 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY TCGA-A2-A4RW TCGA-A2-A4RX 
       32.75        56.28        47.31        35.93         7.30        24.39 
TCGA-A2-A4S0 TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0D9 TCGA-A7-A0DC 
       23.21        26.96        21.14        38.30        37.45        29.79 
TCGA-A7-A13F TCGA-A7-A13G TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A2KD 
       25.15        23.61        24.26        23.74        23.80        22.32 
TCGA-A7-A3IY TCGA-A7-A3IZ TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 TCGA-A7-A4SA 
       11.34        10.59        10.29        13.41        14.70        14.93 
TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O 
       12.10        10.72        11.05        10.29        10.42        13.02 
TCGA-A8-A079 TCGA-A8-A07G TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07S TCGA-A8-A07U 
        9.01        18.97         9.99        10.98         7.99        24.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       45.07        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08L TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A091 
        9.99        31.00         0.99       112.08        43.00        33.01 
TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 TCGA-A8-A099 TCGA-A8-A09A TCGA-A8-A09E 
       30.97        17.95        41.98         9.99         9.99        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09V TCGA-A8-A09X 
       45.07        29.98        33.07        25.02        15.02        14.01 
TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0AD TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23H 
       12.00        19.04        38.04         0.95        22.95         5.72 
TCGA-AC-A2B8 TCGA-AC-A2BM TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FG TCGA-AC-A2FK 
        1.48        99.35        40.57        86.66        60.92        87.12 
TCGA-AC-A2FO TCGA-AC-A2QI TCGA-AC-A2QJ TCGA-AC-A3EH TCGA-AC-A3OD TCGA-AC-A3QQ 
       74.14        19.33        14.66         6.48        14.83        24.13 
TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A4ZE 
       14.99        16.57        19.79        23.24        24.79        29.26 
TCGA-AC-A5EI TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A7VC TCGA-AC-A8OQ 
       14.53        11.44        13.71        13.58         0.03         1.12 
TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y TCGA-AN-A046 TCGA-AN-A04A 
        1.32         2.30         0.33         0.33         0.33         2.96 
TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AS 
        1.78         1.71         7.46         0.16         0.33         0.33 
TCGA-AN-A0AT TCGA-AN-A0FJ TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT 
        0.33         7.96         7.59         7.17         6.90         7.04 
TCGA-AN-A0FV TCGA-AN-A0FX TCGA-AN-A0XL TCGA-AN-A0XN TCGA-AN-A0XP TCGA-AN-A0XV 
        0.33         0.33         5.36         0.33         0.30         5.33 
TCGA-AN-A0XW TCGA-AO-A03M TCGA-AO-A03O TCGA-AO-A03R TCGA-AO-A03T TCGA-AO-A03U 
        5.59        61.35        81.63        68.75        47.87        58.95 
TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 TCGA-AO-A0JC 
       29.13        32.78        52.18        26.04        37.48        50.86 
TCGA-AO-A0JE TCGA-AO-A0JF TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       76.77        65.10        50.24        62.04        55.33        71.80 
TCGA-AO-A124 TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12B 
      115.27        99.25       108.72       106.78       108.03        98.27 
TCGA-AO-A12D TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KR 
       64.04        48.36        41.62        40.57        14.73        70.39 
TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 TCGA-AQ-A1H2 
       17.79        24.79        26.93       130.09         5.65        15.62 
TCGA-AQ-A1H3 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS TCGA-AR-A0TV TCGA-AR-A0TX 
       32.52       140.55        98.33        84.10        75.22        64.83 
TCGA-AR-A0U1 TCGA-AR-A0U4 TCGA-AR-A1AI TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AO 
      133.22       107.21       108.36       103.86        97.68        86.07 
TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24M TCGA-AR-A24N 
       37.81        94.29        86.53        86.43       120.33        99.78 
TCGA-AR-A24Q TCGA-AR-A24T TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A251 TCGA-AR-A254 
      104.28       105.27        77.69       105.30        99.62        85.64 
TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN 
      166.42        20.25        86.53        66.15        63.62        38.17 
TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 
       40.54        57.27        73.35        10.59        77.62       143.38 
TCGA-B6-A0I5 TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IE 
      281.29        12.13       275.87       129.57        50.70        65.72 
TCGA-B6-A0IJ TCGA-B6-A0IK TCGA-B6-A0IM TCGA-B6-A0IP TCGA-B6-A0RH TCGA-B6-A0RI 
      233.62        18.77       127.33       129.07       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RQ TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV 
       78.02       140.48       100.70        89.46       282.90       157.41 
TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 
       97.48       188.68        79.63       206.86       129.70       245.10 
TCGA-B6-A0X4 TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI 
       28.27        68.94        58.88        43.59       101.52        73.51 
TCGA-B6-A2IU TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-BH-A0AV TCGA-BH-A0AW 
      170.17         7.07        85.35        70.16        59.84        20.45 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BG TCGA-BH-A0BM 
       63.09        40.83        32.02        18.21        61.51        61.68 
TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BW TCGA-BH-A0C0 
       72.23        75.48        74.14        53.95        77.95        41.75 
TCGA-BH-A0C1 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DG TCGA-BH-A0DI TCGA-BH-A0DK 
       44.02        45.83        77.98        23.44        29.98        13.91 
TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       78.28        17.26        15.65         2.56        38.47        67.86 
TCGA-BH-A0DX TCGA-BH-A0DZ TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       70.88        16.27        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EE TCGA-BH-A0EI TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 
       32.58        31.00        24.43        15.16        37.78        53.26 
TCGA-BH-A0H6 TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HW 
       24.56        20.38         5.85         2.50        13.61        51.32 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A18G TCGA-BH-A18N TCGA-BH-A18P 
       50.79         5.59        24.95         4.90        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18U TCGA-BH-A1EN TCGA-BH-A1EO 
       55.63        37.55        66.05        51.39        67.50        91.99 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F6 TCGA-BH-A1FB 
       12.00        55.69        25.81        31.53        97.48       120.62 
TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FR TCGA-BH-A1FU 
       74.73       122.89        36.92        63.35       144.59        72.07 
TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q 
       28.14        26.14        38.60        57.83        10.65         6.44 
TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.12       109.28        20.88         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P 
       21.76         9.44        11.93        11.77        12.66        11.77 
TCGA-C8-A12Q TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12X TCGA-C8-A12Z TCGA-C8-A130 
       12.66        12.66        12.66        12.66        12.56         3.16 
TCGA-C8-A131 TCGA-C8-A134 TCGA-C8-A135 TCGA-C8-A137 TCGA-C8-A1HE TCGA-C8-A1HF 
       13.51        12.59        12.92         4.11        12.33        10.92 
TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A26X 
       11.34         0.16        12.33        20.25        12.53        12.36 
TCGA-C8-A26Y TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A278 TCGA-C8-A27B TCGA-C8-A3M7 
       12.95         9.67         0.03         9.50        14.43        33.99 
TCGA-C8-A3M8 TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 
       12.95        12.49        13.41        13.25        20.58        13.97 
TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JC TCGA-D8-A1JE TCGA-D8-A1JF 
       19.20        17.49        16.50        15.78        18.90        12.03 
TCGA-D8-A1JH TCGA-D8-A1JI TCGA-D8-A1JK TCGA-D8-A1JL TCGA-D8-A1JS TCGA-D8-A1JT 
       14.01        18.97        20.12        20.09        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XC TCGA-D8-A1XF 
       14.70        17.79        16.73        25.74        12.39        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XL TCGA-D8-A1XQ TCGA-D8-A1XS TCGA-D8-A1XV 
       14.73        21.80        19.92        16.41        16.31        15.16 
TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A27E TCGA-D8-A27F TCGA-D8-A27G 
       43.04        16.54        15.32        17.42        16.04        13.45 
TCGA-D8-A27H TCGA-D8-A27K TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R 
       13.05        48.03        13.48         4.80         1.61        10.09 
TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W 
       12.53        12.26        18.51        21.67        16.18        12.66 
TCGA-E2-A108 TCGA-E2-A10B TCGA-E2-A10E TCGA-E2-A14N TCGA-E2-A14P TCGA-E2-A14S 
       27.52        37.51        28.44        47.15        40.96        33.17 
TCGA-E2-A14U TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A152 TCGA-E2-A154 TCGA-E2-A155 
       43.33        31.96        69.34        69.96        19.43        21.04 
TCGA-E2-A156 TCGA-E2-A158 TCGA-E2-A15D TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L 
       23.87        14.79        17.29        53.92         9.04        20.58 
TCGA-E2-A15R TCGA-E2-A15S TCGA-E2-A1B0 TCGA-E2-A1B4 TCGA-E2-A1B6 TCGA-E2-A1BC 
       56.94        14.07        53.62        33.01        28.50        16.47 
TCGA-E2-A1IE TCGA-E2-A1IG TCGA-E2-A1IK TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L7 
       77.65        70.36        59.18        11.08        54.18        60.36 
TCGA-E2-A1L9 TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LG TCGA-E2-A1LH TCGA-E2-A1LI 
       19.66        24.59        75.81        50.07       106.75       102.61 
TCGA-E2-A1LL TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A570 TCGA-E9-A1N4 TCGA-E9-A1N6 
       43.04        34.55        43.56        30.61        32.88        22.29 
TCGA-E9-A1NC TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R4 TCGA-E9-A1R5 TCGA-E9-A1R7 
       39.55        24.82        28.27         6.12         3.02        48.23 
TCGA-E9-A1RH TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A22B TCGA-E9-A22G 
       46.59        34.45        32.05        42.25        38.37        40.73 
TCGA-E9-A243 TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 TCGA-E9-A3QA 
       20.12        12.33        29.72         9.47        32.91        30.18 
TCGA-E9-A54X TCGA-E9-A5UP TCGA-EW-A1IW TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J3 
       23.90        26.40        12.20         8.48        18.21        16.57 
TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OZ TCGA-EW-A1P0 TCGA-EW-A1P1 
       15.68        25.94        29.95        40.41        41.13        39.78 
TCGA-EW-A1P4 TCGA-EW-A1P7 TCGA-EW-A1PB TCGA-EW-A1PD TCGA-EW-A1PE TCGA-EW-A1PF 
       29.82        30.08        19.99        13.94        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 
       34.55        55.00        52.73        22.09        34.03        17.49 
TCGA-EW-A424 TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DD TCGA-GM-A2DF 
       23.51         7.40       109.87        59.57        75.02        70.85 
TCGA-GM-A2DH TCGA-GM-A2DI TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW 
       72.10        85.15       106.06       101.62        85.35       110.50 
TCGA-GM-A3XG TCGA-GM-A3XL TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB TCGA-LD-A74U 
       43.73        69.30        13.55        18.12        62.47        13.22 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A50Y TCGA-LL-A5YL 
       13.28        10.62        24.95        32.75        25.05        17.06 
TCGA-LL-A5YM TCGA-LL-A5YP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z 
       15.32        14.79         2.63        16.08        15.68         7.46 
TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 
       14.50        19.53        19.59        17.49        22.39         2.10 
TCGA-OL-A5D6 TCGA-OL-A5D8 TCGA-OL-A5DA TCGA-OL-A5RU TCGA-OL-A5RX TCGA-OL-A5RY 
       36.30        31.99        58.62        40.08        28.87        24.72 
TCGA-OL-A5S0 TCGA-OL-A66H TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66N TCGA-OL-A66O 
       20.38        26.70        23.47        65.62        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VR TCGA-OL-A97C TCGA-PL-A8LY TCGA-S3-AA0Z TCGA-S3-AA11 
       14.07        40.11         8.91         0.26        20.68        13.84 
TCGA-S3-AA12 TCGA-S3-AA14 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UU-A93S TCGA-W8-A86G 
       18.87        17.39        17.26        13.94         3.81        11.41 
TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R6 
       52.96        15.35       107.05 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.16               0.03 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            263.28             282.90 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             28.90              26.04 
[1] "0.2 - 263.3 (28.9)" "0.0 - 282.9 (26.0)"
[1] "hr=" "1.2"
D80V2, continuous
                    vv
clus                 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  22Q LOSS MUTATED        36       36        1        2       150       123
  22Q LOSS WILD-TYPE      53       49        5        4       203       129
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           1         70         12         35        8
  22Q LOSS WILD-TYPE         1         84         17         30       12
                    vv
clus                 STAGE TIS STAGE X
  22Q LOSS MUTATED           0       7
  22Q LOSS WILD-TYPE         1       6
D80V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  36                 53
  STAGE IA                 36                 49
  STAGE IB                  1                  5
  STAGE II                  2                  4
  STAGE IIA               150                203
  STAGE IIB               123                129
  STAGE III                 1                  1
  STAGE IIIA               70                 84
  STAGE IIIB               12                 17
  STAGE IIIC               35                 30
  STAGE IV                  8                 12
  STAGE TIS                 0                  1
  STAGE X                   7                  6
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED   115 294  54  17
  22Q LOSS WILD-TYPE 161 330  82  23
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1              115                161
  T2              294                330
  T3               54                 82
  T4               17                 23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2  N3
  22Q LOSS MUTATED   217 164  55  41
  22Q LOSS WILD-TYPE 290 194  64  36
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0              217                290
  N1              164                194
  N2               55                 64
  N3               41                 36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   403   9
  22Q LOSS WILD-TYPE 486  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    403    9
  22Q LOSS WILD-TYPE  486   13
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              403                486
  1                9                 13
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   475   7
  22Q LOSS WILD-TYPE 593   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    475    7
  22Q LOSS WILD-TYPE  593    5
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE              475                593
  MALE                  7                  5
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   176 256
  22Q LOSS WILD-TYPE 253 262
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    176  256
  22Q LOSS WILD-TYPE  253  262
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               176                253
  YES              256                262
[1] 2 2
[1] FALSE
                    vv
clus                 INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  22Q LOSS MUTATED                            0                           357
  22Q LOSS WILD-TYPE                          1                           413
                    vv
clus                 INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  22Q LOSS MUTATED                               88                   2
  22Q LOSS WILD-TYPE                            112                   4
                    vv
clus                 METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  22Q LOSS MUTATED                       3                               19
  22Q LOSS WILD-TYPE                     6                               10
                    vv
clus                 MUCINOUS CARCINOMA OTHER  SPECIFY
  22Q LOSS MUTATED                    1             11
  22Q LOSS WILD-TYPE                 16             36
D80V9, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                      0                  1
  INFILTRATING DUCTAL CARCINOMA                 357                413
  INFILTRATING LOBULAR CARCINOMA                 88                112
  MEDULLARY CARCINOMA                             2                  4
  METAPLASTIC CARCINOMA                           3                  6
  MIXED HISTOLOGY (PLEASE SPECIFY)               19                 10
  MUCINOUS CARCINOMA                              1                 16
  OTHER  SPECIFY                                 11                 36
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0    22
  22Q LOSS WILD-TYPE                                1    38
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          85   333
  22Q LOSS WILD-TYPE                        96   412
D80V11, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  1
  ASIAN                                          22                 38
  BLACK OR AFRICAN AMERICAN                      85                 96
  WHITE                                         333                412
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V12, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    16 386
  22Q LOSS WILD-TYPE  23 489
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     16  386
  22Q LOSS WILD-TYPE   23  489
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   16                 23
  NOT HISPANIC OR LATINO              386                489
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED   165  23
  XP LOSS WILD-TYPE 752 124
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              188               876 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               23               124 
$`XP LOSS MUTATED`
TCGA-3C-AAAU TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A2-A04R TCGA-A2-A04T TCGA-A2-A04U 
      129.14        47.24        31.79       121.94        73.84        87.25 
TCGA-A2-A0CM TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 
       24.79        77.19        75.25       107.93        67.33        34.55 
TCGA-A2-A0D4 TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A3XT TCGA-A2-A4S3 
       25.22        80.28        27.12        17.52        91.07        21.90 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A2KD TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SA 
       35.31        30.61        22.32        10.59        11.28        14.93 
TCGA-A7-A4SD TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06T 
       14.50        17.92        14.73         9.37         8.75        53.06 
TCGA-A8-A06U TCGA-A8-A06Y TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08L TCGA-A8-A08O 
       29.03        26.01        15.06        36.95         9.99        31.00 
TCGA-A8-A099 TCGA-A8-A09N TCGA-A8-A09W TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A2BM 
        9.99         1.02         0.99        17.03        38.04        99.35 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A7VB TCGA-AN-A04A TCGA-AN-A0AK TCGA-AN-A0AM 
       29.26        16.80         8.22         2.96         7.36         0.16 
TCGA-AN-A0AR TCGA-AN-A0FD TCGA-AN-A0FJ TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XT 
        0.33         6.44         7.96         0.33         5.36         0.33 
TCGA-AN-A0XU TCGA-AO-A03R TCGA-AO-A0J2 TCGA-AO-A0J3 TCGA-AO-A0J4 TCGA-AO-A0JA 
        0.33        68.75        32.78        21.40        52.18        21.53 
TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A124 TCGA-AO-A12F TCGA-AO-A1KQ TCGA-AO-A1KR 
       76.77        50.24       115.27        48.36        61.87        70.39 
TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ TCGA-AR-A0U1 
       15.62         2.56        75.22        55.86       107.24       133.22 
TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AY TCGA-AR-A24Q TCGA-AR-A24R 
      134.14       107.21       125.16        33.73       104.28       112.77 
TCGA-AR-A251 TCGA-AR-A254 TCGA-AR-A256 TCGA-AR-A2LO TCGA-B6-A0IE TCGA-B6-A0IG 
       99.62        85.64        93.83        39.39        65.72       146.50 
TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0RU TCGA-B6-A0WV 
       18.77       140.88        68.45        81.17       282.90        79.63 
TCGA-B6-A0WX TCGA-B6-A1KN TCGA-BH-A0AV TCGA-BH-A0B0 TCGA-BH-A0BW TCGA-BH-A0DG 
       21.47       139.17        59.84        81.44        77.95        23.44 
TCGA-BH-A0DH TCGA-BH-A0DL TCGA-BH-A0DX TCGA-BH-A0E6 TCGA-BH-A0EI TCGA-BH-A0GZ 
       38.01        78.28        70.88         9.63        24.43        10.78 
TCGA-BH-A0HA TCGA-BH-A0HW TCGA-BH-A0W3 TCGA-BH-A0WA TCGA-BH-A1ES TCGA-BH-A1EY 
       52.96        51.32        23.93        23.05       113.82        17.69 
TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12Q 
       24.62        33.17        45.63        10.52        18.64        12.66 
TCGA-C8-A12X TCGA-C8-A135 TCGA-C8-A1HF TCGA-C8-A1HG TCGA-C8-A1HJ TCGA-C8-A1HL 
       12.66        12.92        10.92        11.34         0.16        10.42 
TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A274 TCGA-C8-A278 TCGA-C8-A8HQ TCGA-C8-A8HR 
       20.25        12.53         9.53         9.50        12.49        13.41 
TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA TCGA-D8-A1JB 
       19.46        56.81        19.20        17.49        16.50        55.50 
TCGA-D8-A1JI TCGA-D8-A1JM TCGA-D8-A1JP TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XO 
       18.97        19.40        21.01        23.90        27.58        55.30 
TCGA-D8-A27F TCGA-D8-A27H TCGA-D8-A27R TCGA-D8-A27T TCGA-E2-A14Y TCGA-E2-A152 
       16.04        13.05        10.09        13.08        69.34        69.96 
TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A15H TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A1IE 
       21.04        14.79        12.92        19.56        14.07        77.65 
TCGA-E2-A1L7 TCGA-E2-A1L8 TCGA-E2-A1LA TCGA-E2-A1LH TCGA-E2-A576 TCGA-E9-A1N4 
       60.36        73.64        24.59       106.75        34.29        32.88 
TCGA-E9-A1N8 TCGA-E9-A1NA TCGA-E9-A1NC TCGA-E9-A1NH TCGA-E9-A1R4 TCGA-E9-A1RG 
       34.16        36.56        39.55        18.94         6.12        21.27 
TCGA-E9-A22G TCGA-E9-A247 TCGA-E9-A3HO TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 
       40.73        38.99        38.07        25.81        18.90        28.77 
TCGA-EW-A1OW TCGA-EW-A1OZ TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A6SB TCGA-EW-A6SD 
       22.82        40.41        18.90        13.94        24.99        33.21 
TCGA-GM-A2DH TCGA-HN-A2NL TCGA-JL-A3YX TCGA-LL-A6FR TCGA-LQ-A4E4 TCGA-OL-A5RW 
       72.10         2.60        11.57        16.08        27.91        36.36 
TCGA-OL-A5RZ TCGA-OL-A66I TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZH 
       22.32        23.47        47.01        64.21         0.16        21.07 
TCGA-S3-AA14 TCGA-XX-A89A 
       17.39        16.04 

$`XP LOSS WILD-TYPE`
TCGA-3C-AALI TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 
      131.67        42.81        40.14        11.44        48.56        48.36 
TCGA-5T-A9QA TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG 
        9.96         8.52        14.37        43.43        48.10        14.27 
TCGA-A1-A0SI TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP 
       20.88        13.68         7.96        39.32        28.01        19.20 
TCGA-A1-A0SQ TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04V TCGA-A2-A04W 
       18.21       143.15        18.02        78.41        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CO TCGA-A2-A0CP 
       55.43        36.13       136.73        99.12       114.81        92.48 
TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX TCGA-A2-A0D2 
       88.60       107.93         5.19        98.99        56.81        33.76 
TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ TCGA-A2-A0ER 
       61.58       101.72        89.36       118.45        79.76        74.40 
TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW TCGA-A2-A0EX 
       72.00        35.05        34.29        31.82        61.94        24.72 
TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX TCGA-A2-A0SY 
       63.29        99.19        54.64        44.88        50.43        44.28 
TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 TCGA-A2-A0T6 
       17.13         8.38        49.84        20.52        17.46        18.90 
TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF TCGA-A2-A0YG 
       20.75        32.55        25.28        18.21        50.47        21.90 
TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL TCGA-A2-A0YM 
       21.67        49.48        18.61        19.33        48.46        31.73 
TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ TCGA-A2-A1G0 
       23.77        23.47        17.36        60.72        22.45        20.25 
TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A TCGA-A2-A25B 
       19.20        19.56        16.47        52.47       107.70        42.44 
TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC TCGA-A2-A3KD 
       17.19        18.15       105.34        10.59        36.23        39.65 
TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX TCGA-A2-A3XY 
       33.93        29.98        32.75        56.28        47.31        35.93 
TCGA-A2-A3XZ TCGA-A2-A3Y0 TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       50.37        50.83         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       26.96        21.14        38.30        34.29        35.47        37.45 
TCGA-A7-A0DA TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F 
       35.67        33.11        29.79        31.73        20.19        25.15 
TCGA-A7-A13G TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H 
       23.61        29.56        31.36        24.26        23.74        23.80 
TCGA-A7-A26I TCGA-A7-A26J TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       21.73        20.61        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW TCGA-A7-A5ZX 
       11.97        13.74        21.17        12.10        10.72        11.05 
TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q TCGA-A8-A06R 
       10.29        10.42        13.02        13.02         1.02        17.98 
TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A075 TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       31.00         1.02        17.03        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       45.07        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08I TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S 
       19.96        12.00        37.05        31.00         0.99        33.01 
TCGA-A8-A08T TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 
      112.08        43.00        40.01        33.01        30.97        17.95 
TCGA-A8-A095 TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D 
       41.98        12.00         9.99        12.00         1.02        50.04 
TCGA-A8-A09E TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R 
       49.05        45.07        29.98        33.07        25.02         8.98 
TCGA-A8-A09T TCGA-A8-A09V TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       19.04        15.02        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       21.04         0.99        27.02         0.95        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72         1.48        73.05        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        14.53        19.33        14.96        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OQ TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X 
        0.03        20.19         1.12         1.32         2.30         0.33 
TCGA-AN-A03Y TCGA-AN-A041 TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04C TCGA-AN-A04D 
        0.33         0.23         0.33         0.62         1.78         1.71 
TCGA-AN-A0AJ TCGA-AN-A0AL TCGA-AN-A0AS TCGA-AN-A0AT TCGA-AN-A0FF TCGA-AN-A0FK 
        9.96         7.46         0.33         0.33         5.65         7.00 
TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX 
        7.59         7.17         6.90         7.04         0.36         0.33 
TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR 
        0.33         0.33         0.33        12.33         0.30         0.33 
TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N 
        0.33         5.33         5.59        80.28        61.35        66.77 
TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J5 
       81.63        95.70        47.87        58.95        29.13        26.04 
TCGA-AO-A0J6 TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC 
       37.48        20.32        22.36        53.03        50.70        50.86 
TCGA-AO-A0JD TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JJ TCGA-AO-A0JL TCGA-AO-A0JM 
       72.00        65.10        26.24        62.04        55.33        71.80 
TCGA-AO-A125 TCGA-AO-A126 TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B 
       99.25       108.72       106.78       108.03        90.58        98.27 
TCGA-AO-A12D TCGA-AO-A12E TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP 
       64.04        57.30        41.62        40.57        14.73        82.62 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TR 
       32.52        32.91        19.20       140.55        98.33         5.26 
TCGA-AR-A0TS TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U2 
       84.10       109.02        98.93        64.83        65.36        83.87 
TCGA-AR-A1AI TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN 
      108.36       101.00       103.86        97.68        98.33        96.00 
TCGA-AR-A1AO TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU 
       86.07        93.90        99.32        17.23        37.81        94.29 
TCGA-AR-A1AV TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24H TCGA-AR-A24K TCGA-AR-A24L 
       61.28        86.53        86.43       160.90        50.89        94.22 
TCGA-AR-A24M TCGA-AR-A24N TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24S TCGA-AR-A24T 
      120.33        99.78       118.59         2.76        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       77.69       105.30        32.58        98.76        98.66        89.00 
TCGA-AR-A252 TCGA-AR-A255 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       93.30        71.05       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A2LR TCGA-AR-A5QM 
       66.15        63.62        38.17        40.54        57.27        73.35 
TCGA-AR-A5QN TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 
       33.30        38.96        10.59        77.62       143.38       281.29 
TCGA-B6-A0I9 TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ 
       12.13       275.87       129.57        50.70       112.37       233.62 
TCGA-B6-A0IM TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH 
      127.33        84.59       165.76       129.07       255.68       212.25 
TCGA-B6-A0RI TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ 
      234.28        78.02       263.28       162.05       102.77       140.48 
TCGA-B6-A0RS TCGA-B6-A0RT TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WW 
      100.70        89.46       157.41        97.48       188.68        18.35 
TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 TCGA-B6-A0X5 
      113.79       206.86       129.70       245.10        28.27        68.94 
TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU TCGA-B6-A3ZX 
       58.88        43.59       101.52        73.51       170.17        37.87 
TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B 
        7.07        85.35        70.16        68.12        18.84       103.63 
TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AW TCGA-BH-A0AY TCGA-BH-A0AZ TCGA-BH-A0B2 
       71.15        62.93        20.45        25.55        63.09        40.83 
TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 TCGA-BH-A0B7 TCGA-BH-A0B9 
       39.55        39.16        70.22        81.63        84.13        51.68 
TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF TCGA-BH-A0BG TCGA-BH-A0BJ 
       37.22        32.02        18.21        43.53        61.51        21.70 
TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP TCGA-BH-A0BQ TCGA-BH-A0BR 
       74.89        61.68        72.23        75.48        74.14        76.60 
TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BV TCGA-BH-A0BZ TCGA-BH-A0C0 TCGA-BH-A0C1 
       53.95        45.57        49.94        49.05        41.75        44.02 
TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DI TCGA-BH-A0DK 
       89.06        90.97        45.83        77.98        29.98        13.91 
TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS TCGA-BH-A0DT TCGA-BH-A0DV 
       17.26        15.65         3.22         2.56        38.47        67.86 
TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 TCGA-BH-A0E7 TCGA-BH-A0E9 
       16.27         4.41        15.68        14.30        44.81        46.19 
TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 
       32.58        24.49        31.00        30.35        15.16        37.78 
TCGA-BH-A0H5 TCGA-BH-A0H6 TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI 
       53.26        24.56        23.08        41.00        26.50        20.38 
TCGA-BH-A0HK TCGA-BH-A0HO TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HU TCGA-BH-A0HX 
        5.85         2.50        13.61        36.85        12.89        27.25 
TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A18F 
       50.79         5.59        24.95        42.35        44.81        32.91 
TCGA-BH-A18G TCGA-BH-A18I TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M 
        4.90        35.93        20.12        90.84        26.66        72.56 
TCGA-BH-A18N TCGA-BH-A18P TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T 
       37.74        30.28        55.63        37.55        66.05         7.36 
TCGA-BH-A18U TCGA-BH-A18V TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU 
       51.39        51.16        67.50        91.99        82.85        42.28 
TCGA-BH-A1EV TCGA-BH-A1EW TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 
       12.00        55.69        49.58        25.81        31.53        89.16 
TCGA-BH-A1F6 TCGA-BH-A1FB TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH 
       97.48       120.62       114.15        74.73       122.89        36.92 
TCGA-BH-A1FJ TCGA-BH-A1FL TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 
       63.35        55.00        72.07       144.59        72.07        28.14 
TCGA-BH-A202 TCGA-BH-A203 TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A209 TCGA-BH-A28O 
       26.14        38.60        83.31        57.83       130.16        10.65 
TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 
        6.44        20.12       109.28        20.88        23.51         9.63 
TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L 
        5.26         9.70        18.87        21.76         9.44        11.93 
TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V 
       11.77        11.77        12.66        11.77        12.66        12.66 
TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 
       12.66        48.53        12.56         3.16        13.51         1.87 
TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 TCGA-C8-A1HE TCGA-C8-A1HI TCGA-C8-A1HK 
       12.59         4.11         4.08        12.33        11.28        12.03 
TCGA-C8-A1HM TCGA-C8-A1HN TCGA-C8-A1HO TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z 
       12.33        12.95        12.33        12.36        12.95         8.28 
TCGA-C8-A273 TCGA-C8-A275 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 
        9.67         0.03        24.56        14.43        33.99        12.95 
TCGA-C8-A8HP TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 
       13.02        20.88        13.25        20.58        13.97        14.17 
TCGA-D8-A145 TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE 
       13.48        21.14        14.17        15.78        18.15        18.90 
TCGA-D8-A1JF TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JJ TCGA-D8-A1JK TCGA-D8-A1JL 
       12.03        53.00        14.01        20.09        20.12        20.09 
TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 
       20.38        12.20        13.32        14.70        18.58        17.79 
TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF 
       16.73        25.74        18.15        12.39        17.16        15.22 
TCGA-D8-A1XG TCGA-D8-A1XJ TCGA-D8-A1XK TCGA-D8-A1XL TCGA-D8-A1XM TCGA-D8-A1XQ 
       14.73        21.80        14.50        19.92        17.69        16.41 
TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU TCGA-D8-A1XV TCGA-D8-A1XW 
       15.85        16.31        16.64        12.99        15.16        43.04 
TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 TCGA-D8-A1Y2 TCGA-D8-A1Y3 
       16.54        15.32        15.52         9.93        14.24        14.14 
TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L TCGA-D8-A27M 
       17.42        13.45        14.43        48.03        16.41        13.48 
TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27V TCGA-D8-A27W TCGA-D8-A3Z5 TCGA-D8-A3Z6 
        4.80         1.61        12.53        12.26        33.37        18.51 
TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-E2-A105 TCGA-E2-A107 
       21.67        16.18        12.66        25.22        43.00        34.42 
TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B TCGA-E2-A10C TCGA-E2-A10E 
       27.52        46.59        40.41        37.51        40.11        28.44 
TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P TCGA-E2-A14Q TCGA-E2-A14R 
       28.87        47.15        44.68        40.96        38.24        38.60 
TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V TCGA-E2-A14W TCGA-E2-A14X 
       33.17        75.98        43.33        34.26        32.02        31.96 
TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 
       18.51        63.62        23.24        19.43        23.87        25.05 
TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G 
       23.34        22.82        17.29        20.71        21.63        18.21 
TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15K TCGA-E2-A15L TCGA-E2-A15M TCGA-E2-A15O 
       55.63        53.92         9.04        20.58        11.05        50.79 
TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 TCGA-E2-A1B1 TCGA-E2-A1B4 
       56.94        51.39        76.57        53.62        87.22        33.01 
TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD TCGA-E2-A1IF TCGA-E2-A1IG 
       32.35        28.50        16.47        37.25        37.41        70.36 
TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK TCGA-E2-A1IL TCGA-E2-A1IN 
       33.73        33.70        28.44        59.18         3.88        22.19 
TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 TCGA-E2-A1LB TCGA-E2-A1LE 
       60.99        11.08        54.18        19.66        75.81        28.90 
TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 
       50.07       102.61         8.75        43.04        26.99        34.55 
TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU 
       43.56         8.28        30.61        34.92        38.76        17.69 
TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 TCGA-E9-A1N9 TCGA-E9-A1ND TCGA-E9-A1NE 
       34.82        36.82        22.29        36.20        41.62        35.77 
TCGA-E9-A1NF TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 TCGA-E9-A1R2 
       35.24        25.84         9.86        24.82        28.27        34.95 
TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA TCGA-E9-A1RB 
        2.56         3.02        11.15        48.23        45.01        32.09 
TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH TCGA-E9-A1RI 
       40.24         1.12        46.65         6.58        46.59        47.64 
TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A TCGA-E9-A22B 
       34.45        32.05        42.25        37.74        39.09        38.37 
TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 TCGA-E9-A248 
       41.03        41.72        40.50        20.12         0.69         1.94 
TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT TCGA-E9-A3Q9 
        7.13        24.56        12.33        29.72         9.47        32.91 
TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y TCGA-E9-A5FK TCGA-E9-A5FL 
       30.18        30.44        23.90        23.84        26.70         0.79 
TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX TCGA-EW-A1IY TCGA-EW-A1IZ 
       26.40        27.85        12.20        39.72         8.48        18.21 
TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV TCGA-EW-A1OX TCGA-EW-A1OY 
       13.25        16.57        15.68        25.94        29.95        29.85 
TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 TCGA-EW-A1P5 TCGA-EW-A1P6 
       41.13        39.78        52.96        29.82        23.11        18.48 
TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC TCGA-EW-A1PE TCGA-EW-A1PF 
       30.08         7.86        19.99         6.15        10.52        14.43 
TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS TCGA-EW-A2FV TCGA-EW-A2FW 
       34.55        19.96        55.00        52.73        25.91        22.09 
TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 TCGA-EW-A6S9 TCGA-EW-A6SA 
       34.03        17.49        10.16        23.51        15.22        16.77 
TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB 
       31.30         7.40       109.87        59.57       216.76        79.10 
TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL 
       83.34        75.02        70.85        85.15        86.96       115.69 
TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG 
      106.06       101.62        85.35       110.50        38.20        43.73 
TCGA-GM-A3XL TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV TCGA-GM-A5PX TCGA-HN-A2OB 
       69.30        66.38        72.03        13.55        18.12        62.47 
TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LD-A9QF 
       11.84        21.24        13.22         7.10        13.28        10.62 
TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y TCGA-LL-A5YL TCGA-LL-A5YM 
       24.95        32.75        29.23        25.05        17.06        15.32 
TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A73Y 
       14.70        14.47        14.79        22.26         2.63        15.68 
TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-LL-A9Q3 
        7.46        14.50        19.53        12.36        19.59        17.49 
TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 TCGA-OL-A5DA 
       22.39         2.10        36.30        58.52        31.99        58.62 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       40.08        34.92        28.87        24.72        20.38        26.70 
TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O TCGA-OL-A66P 
       65.62        41.92        42.77        26.04        17.36        14.07 
TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE TCGA-PL-A8LY 
       28.21        19.73        40.11         8.91        86.96         0.26 
TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 TCGA-S3-AA11 
        9.93        18.81        18.48        20.68        19.27        13.84 
TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S TCGA-V7-A7HQ 
       18.87        17.26        13.94        17.03         3.81        66.84 
TCGA-W8-A86G TCGA-WT-AB41 TCGA-WT-AB44 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       11.41        52.96        29.03        15.35       108.07       107.05 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.16              0.03 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           282.90            281.29 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           25.105            28.355 
[1] "0.2 - 282.9 (25.1)" "0.0 - 281.3 (28.4)"
[1] "hr=" "1.2"
D81V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XP LOSS MUTATED        14       17        0        1        68        45
  XP LOSS WILD-TYPE      75       68        6        5       285       207
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           0         24          5          6        5
  XP LOSS WILD-TYPE         2        130         24         59       15
                   vv
clus                STAGE TIS STAGE X
  XP LOSS MUTATED           1       2
  XP LOSS WILD-TYPE         0      11
D81V3, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 14                75
  STAGE IA                17                68
  STAGE IB                 0                 6
  STAGE II                 1                 5
  STAGE IIA               68               285
  STAGE IIB               45               207
  STAGE III                0                 2
  STAGE IIIA              24               130
  STAGE IIIB               5                24
  STAGE IIIC               6                59
  STAGE IV                 5                15
  STAGE TIS                1                 0
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED    46 120  14   8
  XP LOSS WILD-TYPE 230 504 122  32
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              46               230
  T2             120               504
  T3              14               122
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XP LOSS MUTATED    93  63  22  10
  XP LOSS WILD-TYPE 414 295  97  67
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              93               414
  N1              63               295
  N2              22                97
  N3              10                67
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   164   6
  XP LOSS WILD-TYPE 725  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    164    6
  XP LOSS WILD-TYPE  725   16
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0             164               725
  1               6                16
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED   187   3
  XP LOSS WILD-TYPE 881   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED    187    3
  XP LOSS WILD-TYPE  881    9
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE             187               881
  MALE                 3                 9
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    80  90
  XP LOSS WILD-TYPE 349 428
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     80   90
  XP LOSS WILD-TYPE  349  428
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               80               349
  YES              90               428
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XP LOSS MUTATED                            0                           152
  XP LOSS WILD-TYPE                          1                           618
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XP LOSS MUTATED                               21                   0
  XP LOSS WILD-TYPE                            179                   6
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XP LOSS MUTATED                       0                                6
  XP LOSS WILD-TYPE                     9                               23
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XP LOSS MUTATED                    3              7
  XP LOSS WILD-TYPE                 14             40
D81V9, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                152               618
  INFILTRATING LOBULAR CARCINOMA                21               179
  MEDULLARY CARCINOMA                            0                 6
  METAPLASTIC CARCINOMA                          0                 9
  MIXED HISTOLOGY (PLEASE SPECIFY)               6                23
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 7                40
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0    17
  XP LOSS WILD-TYPE                                1    43
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          41   115
  XP LOSS WILD-TYPE                       140   630
D81V11, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         17                43
  BLACK OR AFRICAN AMERICAN                     41               140
  WHITE                                        115               630
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V12, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     7 155
  XP LOSS WILD-TYPE  32 720
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      7  155
  XP LOSS WILD-TYPE   32  720
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             155               720
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED   163  25
  XQ LOSS WILD-TYPE 754 122
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              188               876 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               25               122 
$`XQ LOSS MUTATED`
TCGA-3C-AAAU TCGA-3C-AALI TCGA-A1-A0SH TCGA-A1-A0SK TCGA-A2-A04R TCGA-A2-A04U 
      129.14       131.67        47.24        31.79       121.94        87.25 
TCGA-A2-A0CS TCGA-A2-A0CT TCGA-A2-A0CW TCGA-A2-A0D0 TCGA-A2-A0D1 TCGA-A2-A0D4 
       77.19        75.25       107.93        67.33        34.55        25.22 
TCGA-A2-A0EO TCGA-A2-A0SV TCGA-A2-A0T0 TCGA-A2-A3XT TCGA-A2-A3Y0 TCGA-A2-A4S3 
       80.28        27.12        17.52        91.07        50.83        21.90 
TCGA-A7-A0CE TCGA-A7-A0CJ TCGA-A7-A0DA TCGA-A7-A3IZ TCGA-A7-A3J1 TCGA-A7-A4SA 
       35.31        30.61        35.67        10.59        11.28        14.93 
TCGA-A7-A4SF TCGA-A7-A56D TCGA-A7-A6VW TCGA-A7-A6VY TCGA-A8-A06T TCGA-A8-A06U 
       17.92        14.73         9.37         8.75        53.06        29.03 
TCGA-A8-A06Y TCGA-A8-A075 TCGA-A8-A084 TCGA-A8-A085 TCGA-A8-A08I TCGA-A8-A08L 
       26.01        17.03        15.06        36.95        12.00         9.99 
TCGA-A8-A08O TCGA-A8-A099 TCGA-A8-A09N TCGA-A8-A0AB TCGA-A8-A0AD TCGA-AC-A2BM 
       31.00         9.99         1.02        17.03        38.04        99.35 
TCGA-AC-A4ZE TCGA-AC-A5EH TCGA-AC-A7VB TCGA-AC-A8OQ TCGA-AN-A041 TCGA-AN-A0AJ 
       29.26        16.80         8.22         1.12         0.23         9.96 
TCGA-AN-A0AK TCGA-AN-A0AM TCGA-AN-A0AR TCGA-AN-A0AT TCGA-AN-A0FD TCGA-AN-A0FJ 
        7.36         0.16         0.33         0.33         6.44         7.96 
TCGA-AN-A0FV TCGA-AN-A0XL TCGA-AN-A0XT TCGA-AN-A0XU TCGA-AO-A03R TCGA-AO-A0J3 
        0.33         5.36         0.33         0.33        68.75        21.40 
TCGA-AO-A0JA TCGA-AO-A0JE TCGA-AO-A0JI TCGA-AO-A0JJ TCGA-AO-A124 TCGA-AO-A1KQ 
       21.53        76.77        50.24        62.04       115.27        61.87 
TCGA-AQ-A1H2 TCGA-AQ-A54N TCGA-AR-A0TR TCGA-AR-A0TV TCGA-AR-A0TY TCGA-AR-A0TZ 
       15.62         2.56         5.26        75.22        55.86       107.24 
TCGA-AR-A0U2 TCGA-AR-A0U3 TCGA-AR-A0U4 TCGA-AR-A1AH TCGA-AR-A1AY TCGA-AR-A24H 
       83.87       134.14       107.21       125.16        33.73       160.90 
TCGA-AR-A251 TCGA-AR-A255 TCGA-AR-A256 TCGA-AR-A2LO TCGA-AR-A2LR TCGA-B6-A0IE 
       99.62        71.05        93.83        39.39        57.27        65.72 
TCGA-B6-A0IG TCGA-B6-A0IK TCGA-B6-A0IQ TCGA-B6-A0RG TCGA-B6-A0RL TCGA-B6-A0WX 
      146.50        18.77       140.88        68.45        81.17        21.47 
TCGA-B6-A1KN TCGA-BH-A0B0 TCGA-BH-A0BR TCGA-BH-A0BV TCGA-BH-A0DG TCGA-BH-A0DH 
      139.17        81.44        76.60        49.94        23.44        38.01 
TCGA-BH-A0DX TCGA-BH-A0GZ TCGA-BH-A0HA TCGA-BH-A0HU TCGA-BH-A0HW TCGA-BH-A0W3 
       70.88        10.78        52.96        12.89        51.32        23.93 
TCGA-BH-A1ES TCGA-BH-A1EY TCGA-BH-A1F8 TCGA-BH-A1FD TCGA-BH-A1FM TCGA-BH-A209 
      113.82        17.69        24.62        33.17        45.63       130.16 
TCGA-BH-A42T TCGA-BH-A5IZ TCGA-C8-A12Q TCGA-C8-A12X TCGA-C8-A135 TCGA-C8-A1HF 
       10.52        18.64        12.66        12.66        12.92        10.92 
TCGA-C8-A1HJ TCGA-C8-A1HL TCGA-C8-A1HO TCGA-C8-A26V TCGA-C8-A26W TCGA-C8-A8HQ 
        0.16        10.42        12.33        20.25        12.53        12.49 
TCGA-C8-A8HR TCGA-C8-A9FZ TCGA-D8-A13Y TCGA-D8-A147 TCGA-D8-A1J9 TCGA-D8-A1JA 
       13.41        19.46        56.81        19.20        17.49        16.50 
TCGA-D8-A1JB TCGA-D8-A1JI TCGA-D8-A1JJ TCGA-D8-A1JL TCGA-D8-A1JM TCGA-D8-A1JP 
       55.50        18.97        20.09        20.09        19.40        21.01 
TCGA-D8-A1X9 TCGA-D8-A1XA TCGA-D8-A1XJ TCGA-D8-A1XO TCGA-D8-A1Y3 TCGA-D8-A27F 
       23.90        27.58        21.80        55.30        14.14        16.04 
TCGA-D8-A27H TCGA-D8-A27T TCGA-E2-A152 TCGA-E2-A155 TCGA-E2-A158 TCGA-E2-A15H 
       13.05        13.08        69.96        21.04        14.79        12.92 
TCGA-E2-A15K TCGA-E2-A15P TCGA-E2-A15S TCGA-E2-A1IE TCGA-E2-A1L7 TCGA-E2-A1L8 
        9.04        19.56        14.07        77.65        60.36        73.64 
TCGA-E2-A1LH TCGA-E2-A576 TCGA-E9-A1N4 TCGA-E9-A1N8 TCGA-E9-A1N9 TCGA-E9-A1NA 
      106.75        34.29        32.88        34.16        36.20        36.56 
TCGA-E9-A1NC TCGA-E9-A1NF TCGA-E9-A1NH TCGA-E9-A1R4 TCGA-E9-A1RG TCGA-E9-A22G 
       39.55        35.24        18.94         6.12        21.27        40.73 
TCGA-E9-A247 TCGA-E9-A5UO TCGA-EW-A1J1 TCGA-EW-A1J6 TCGA-EW-A1OW TCGA-EW-A1OZ 
       38.99        25.81        18.90        28.77        22.82        40.41 
TCGA-EW-A1PA TCGA-EW-A1PD TCGA-EW-A6SD TCGA-GM-A2DH TCGA-GM-A3XL TCGA-HN-A2NL 
       18.90        13.94        33.21        72.10        69.30         2.60 
TCGA-JL-A3YX TCGA-LL-A6FR TCGA-LL-A7T0 TCGA-LQ-A4E4 TCGA-OL-A5DA TCGA-OL-A5RW 
       11.57        16.08        12.36        27.91        58.62        36.36 
TCGA-OL-A5RZ TCGA-PE-A5DC TCGA-PE-A5DD TCGA-PL-A8LX TCGA-S3-A6ZH TCGA-S3-AA14 
       22.32        47.01        64.21         0.16        21.07        17.39 
TCGA-WT-AB44 TCGA-XX-A89A 
       29.03        16.04 

$`XQ LOSS WILD-TYPE`
TCGA-3C-AALJ TCGA-3C-AALK TCGA-4H-AAAK TCGA-5L-AAT0 TCGA-5L-AAT1 TCGA-5T-A9QA 
       42.81        40.14        11.44        48.56        48.36         9.96 
TCGA-A1-A0SB TCGA-A1-A0SD TCGA-A1-A0SE TCGA-A1-A0SF TCGA-A1-A0SG TCGA-A1-A0SI 
        8.52        14.37        43.43        48.10        14.27        20.88 
TCGA-A1-A0SJ TCGA-A1-A0SM TCGA-A1-A0SN TCGA-A1-A0SO TCGA-A1-A0SP TCGA-A1-A0SQ 
       13.68         7.96        39.32        28.01        19.20        18.21 
TCGA-A2-A04N TCGA-A2-A04P TCGA-A2-A04Q TCGA-A2-A04T TCGA-A2-A04V TCGA-A2-A04W 
      143.15        18.02        78.41        73.84        63.12       101.98 
TCGA-A2-A04X TCGA-A2-A04Y TCGA-A2-A0CK TCGA-A2-A0CL TCGA-A2-A0CM TCGA-A2-A0CO 
       55.43        36.13       136.73        99.12        24.79       114.81 
TCGA-A2-A0CP TCGA-A2-A0CQ TCGA-A2-A0CR TCGA-A2-A0CU TCGA-A2-A0CV TCGA-A2-A0CX 
       92.48        88.60       107.93         5.19        98.99        56.81 
TCGA-A2-A0D2 TCGA-A2-A0D3 TCGA-A2-A0EM TCGA-A2-A0EN TCGA-A2-A0EP TCGA-A2-A0EQ 
       33.76        61.58       101.72        89.36       118.45        79.76 
TCGA-A2-A0ER TCGA-A2-A0ES TCGA-A2-A0ET TCGA-A2-A0EU TCGA-A2-A0EV TCGA-A2-A0EW 
       74.40        72.00        35.05        34.29        31.82        61.94 
TCGA-A2-A0EX TCGA-A2-A0EY TCGA-A2-A0ST TCGA-A2-A0SU TCGA-A2-A0SW TCGA-A2-A0SX 
       24.72        63.29        99.19        54.64        44.88        50.43 
TCGA-A2-A0SY TCGA-A2-A0T1 TCGA-A2-A0T2 TCGA-A2-A0T3 TCGA-A2-A0T4 TCGA-A2-A0T5 
       44.28        17.13         8.38        49.84        20.52        17.46 
TCGA-A2-A0T6 TCGA-A2-A0T7 TCGA-A2-A0YC TCGA-A2-A0YD TCGA-A2-A0YE TCGA-A2-A0YF 
       18.90        20.75        32.55        25.28        18.21        50.47 
TCGA-A2-A0YG TCGA-A2-A0YH TCGA-A2-A0YI TCGA-A2-A0YJ TCGA-A2-A0YK TCGA-A2-A0YL 
       21.90        21.67        49.48        18.61        19.33        48.46 
TCGA-A2-A0YM TCGA-A2-A0YT TCGA-A2-A1FV TCGA-A2-A1FW TCGA-A2-A1FX TCGA-A2-A1FZ 
       31.73        23.77        23.47        17.36        60.72        22.45 
TCGA-A2-A1G0 TCGA-A2-A1G1 TCGA-A2-A1G4 TCGA-A2-A1G6 TCGA-A2-A259 TCGA-A2-A25A 
       20.25        19.20        19.56        16.47        52.47       107.70 
TCGA-A2-A25B TCGA-A2-A25C TCGA-A2-A25D TCGA-A2-A25E TCGA-A2-A25F TCGA-A2-A3KC 
       42.44        17.19        18.15       105.34        10.59        36.23 
TCGA-A2-A3KD TCGA-A2-A3XS TCGA-A2-A3XU TCGA-A2-A3XV TCGA-A2-A3XW TCGA-A2-A3XX 
       39.65        33.93        29.98        32.75        56.28        47.31 
TCGA-A2-A3XY TCGA-A2-A3XZ TCGA-A2-A4RW TCGA-A2-A4RX TCGA-A2-A4RY TCGA-A2-A4S0 
       35.93        50.37         7.30        24.39        21.30        23.21 
TCGA-A2-A4S1 TCGA-A2-A4S2 TCGA-A7-A0CD TCGA-A7-A0CG TCGA-A7-A0CH TCGA-A7-A0D9 
       26.96        21.14        38.30        34.29        35.47        37.45 
TCGA-A7-A0DB TCGA-A7-A0DC TCGA-A7-A13D TCGA-A7-A13E TCGA-A7-A13F TCGA-A7-A13G 
       33.11        29.79        31.73        20.19        25.15        23.61 
TCGA-A7-A13H TCGA-A7-A26E TCGA-A7-A26F TCGA-A7-A26G TCGA-A7-A26H TCGA-A7-A26I 
       29.56        31.36        24.26        23.74        23.80        21.73 
TCGA-A7-A26J TCGA-A7-A2KD TCGA-A7-A3IY TCGA-A7-A3J0 TCGA-A7-A3RF TCGA-A7-A425 
       20.61        22.32        11.34        10.29        13.41        14.70 
TCGA-A7-A426 TCGA-A7-A4SB TCGA-A7-A4SD TCGA-A7-A4SE TCGA-A7-A5ZV TCGA-A7-A5ZW 
       11.97        13.74        14.50        21.17        12.10        10.72 
TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VX TCGA-A8-A06O TCGA-A8-A06P TCGA-A8-A06Q 
       11.05        10.29        10.42        13.02        13.02         1.02 
TCGA-A8-A06R TCGA-A8-A06X TCGA-A8-A06Z TCGA-A8-A076 TCGA-A8-A079 TCGA-A8-A07B 
       17.98        31.00         1.02        53.98         9.01        43.00 
TCGA-A8-A07E TCGA-A8-A07F TCGA-A8-A07G TCGA-A8-A07I TCGA-A8-A07J TCGA-A8-A07L 
       19.99        18.97        18.97        14.01        12.00        32.05 
TCGA-A8-A07O TCGA-A8-A07P TCGA-A8-A07R TCGA-A8-A07S TCGA-A8-A07U TCGA-A8-A07W 
        9.99        10.98         8.98         7.99        24.99         9.99 
TCGA-A8-A07Z TCGA-A8-A086 TCGA-A8-A08A TCGA-A8-A08B TCGA-A8-A08C TCGA-A8-A08F 
       45.07        13.02         0.99        38.01        28.96        33.01 
TCGA-A8-A08G TCGA-A8-A08J TCGA-A8-A08P TCGA-A8-A08R TCGA-A8-A08S TCGA-A8-A08T 
       19.96        37.05        31.00         0.99        33.01       112.08 
TCGA-A8-A08X TCGA-A8-A08Z TCGA-A8-A091 TCGA-A8-A092 TCGA-A8-A093 TCGA-A8-A095 
       43.00        40.01        33.01        30.97        17.95        41.98 
TCGA-A8-A097 TCGA-A8-A09A TCGA-A8-A09B TCGA-A8-A09C TCGA-A8-A09D TCGA-A8-A09E 
       12.00         9.99        12.00         1.02        50.04        49.05 
TCGA-A8-A09I TCGA-A8-A09K TCGA-A8-A09M TCGA-A8-A09Q TCGA-A8-A09R TCGA-A8-A09T 
       45.07        29.98        33.07        25.02         8.98        19.04 
TCGA-A8-A09V TCGA-A8-A09W TCGA-A8-A09X TCGA-A8-A0A1 TCGA-A8-A0A2 TCGA-A8-A0A4 
       15.02         0.99        14.01        12.00        19.04        13.02 
TCGA-A8-A0A6 TCGA-A8-A0A7 TCGA-A8-A0A9 TCGA-AC-A23C TCGA-AC-A23E TCGA-AC-A23G 
       21.04         0.99        27.02         0.95        22.95        73.91 
TCGA-AC-A23H TCGA-AC-A2B8 TCGA-AC-A2BK TCGA-AC-A2FB TCGA-AC-A2FE TCGA-AC-A2FF 
        5.72         1.48        73.05        40.57        86.66        90.71 
TCGA-AC-A2FG TCGA-AC-A2FK TCGA-AC-A2FM TCGA-AC-A2FO TCGA-AC-A2QH TCGA-AC-A2QI 
       60.92        87.12        26.04        74.14        33.04        19.33 
TCGA-AC-A2QJ TCGA-AC-A3BB TCGA-AC-A3EH TCGA-AC-A3HN TCGA-AC-A3OD TCGA-AC-A3QP 
       14.66        32.45         6.48        16.31        14.83        22.19 
TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3TN TCGA-AC-A3W5 TCGA-AC-A3W6 TCGA-AC-A3W7 
       24.13        25.05        14.99        16.57        19.79        15.48 
TCGA-AC-A3YI TCGA-AC-A3YJ TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V 
       23.24        24.79        14.53        19.33        14.96        11.44 
TCGA-AC-A62X TCGA-AC-A62Y TCGA-AC-A6IV TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO 
       13.71        17.42        18.67        13.58        12.26         1.68 
TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AC-A8OR TCGA-AC-A8OS TCGA-AN-A03X TCGA-AN-A03Y 
        0.03        20.19         1.32         2.30         0.33         0.33 
TCGA-AN-A046 TCGA-AN-A049 TCGA-AN-A04A TCGA-AN-A04C TCGA-AN-A04D TCGA-AN-A0AL 
        0.33         0.62         2.96         1.78         1.71         7.46 
TCGA-AN-A0AS TCGA-AN-A0FF TCGA-AN-A0FK TCGA-AN-A0FL TCGA-AN-A0FN TCGA-AN-A0FS 
        0.33         5.65         7.00         7.59         7.17         6.90 
TCGA-AN-A0FT TCGA-AN-A0FW TCGA-AN-A0FX TCGA-AN-A0FY TCGA-AN-A0FZ TCGA-AN-A0XN 
        7.04         0.36         0.33         0.33         0.33         0.33 
TCGA-AN-A0XO TCGA-AN-A0XP TCGA-AN-A0XR TCGA-AN-A0XS TCGA-AN-A0XV TCGA-AN-A0XW 
       12.33         0.30         0.33         0.33         5.33         5.59 
TCGA-AO-A03L TCGA-AO-A03M TCGA-AO-A03N TCGA-AO-A03O TCGA-AO-A03P TCGA-AO-A03T 
       80.28        61.35        66.77        81.63        95.70        47.87 
TCGA-AO-A03U TCGA-AO-A03V TCGA-AO-A0J2 TCGA-AO-A0J4 TCGA-AO-A0J5 TCGA-AO-A0J6 
       58.95        29.13        32.78        52.18        26.04        37.48 
TCGA-AO-A0J7 TCGA-AO-A0J8 TCGA-AO-A0J9 TCGA-AO-A0JB TCGA-AO-A0JC TCGA-AO-A0JD 
       20.32        22.36        53.03        50.70        50.86        72.00 
TCGA-AO-A0JF TCGA-AO-A0JG TCGA-AO-A0JL TCGA-AO-A0JM TCGA-AO-A125 TCGA-AO-A126 
       65.10        26.24        55.33        71.80        99.25       108.72 
TCGA-AO-A128 TCGA-AO-A129 TCGA-AO-A12A TCGA-AO-A12B TCGA-AO-A12D TCGA-AO-A12E 
      106.78       108.03        90.58        98.27        64.04        57.30 
TCGA-AO-A12F TCGA-AO-A12G TCGA-AO-A12H TCGA-AO-A1KO TCGA-AO-A1KP TCGA-AO-A1KR 
       48.36        41.62        40.57        14.73        82.62        70.39 
TCGA-AO-A1KS TCGA-AO-A1KT TCGA-AQ-A04H TCGA-AQ-A04J TCGA-AQ-A04L TCGA-AQ-A0Y5 
        0.53        17.79        24.79        26.93       130.09         5.65 
TCGA-AQ-A1H3 TCGA-AQ-A54O TCGA-AQ-A7U7 TCGA-AR-A0TP TCGA-AR-A0TQ TCGA-AR-A0TS 
       32.52        32.91        19.20       140.55        98.33        84.10 
TCGA-AR-A0TT TCGA-AR-A0TW TCGA-AR-A0TX TCGA-AR-A0U0 TCGA-AR-A0U1 TCGA-AR-A1AI 
      109.02        98.93        64.83        65.36       133.22       108.36 
TCGA-AR-A1AJ TCGA-AR-A1AK TCGA-AR-A1AL TCGA-AR-A1AM TCGA-AR-A1AN TCGA-AR-A1AO 
      101.00       103.86        97.68        98.33        96.00        86.07 
TCGA-AR-A1AP TCGA-AR-A1AQ TCGA-AR-A1AR TCGA-AR-A1AS TCGA-AR-A1AU TCGA-AR-A1AV 
       93.90        99.32        17.23        37.81        94.29        61.28 
TCGA-AR-A1AW TCGA-AR-A1AX TCGA-AR-A24K TCGA-AR-A24L TCGA-AR-A24M TCGA-AR-A24N 
       86.53        86.43        50.89        94.22       120.33        99.78 
TCGA-AR-A24O TCGA-AR-A24P TCGA-AR-A24Q TCGA-AR-A24R TCGA-AR-A24S TCGA-AR-A24T 
      118.59         2.76       104.28       112.77        97.84       105.27 
TCGA-AR-A24U TCGA-AR-A24V TCGA-AR-A24W TCGA-AR-A24X TCGA-AR-A24Z TCGA-AR-A250 
       77.69       105.30        32.58        98.76        98.66        89.00 
TCGA-AR-A252 TCGA-AR-A254 TCGA-AR-A2LE TCGA-AR-A2LH TCGA-AR-A2LJ TCGA-AR-A2LK 
       93.30        85.64       166.42        20.25        86.53        54.21 
TCGA-AR-A2LL TCGA-AR-A2LM TCGA-AR-A2LN TCGA-AR-A2LQ TCGA-AR-A5QM TCGA-AR-A5QN 
       66.15        63.62        38.17        40.54        73.35        33.30 
TCGA-AR-A5QP TCGA-AR-A5QQ TCGA-B6-A0I1 TCGA-B6-A0I2 TCGA-B6-A0I5 TCGA-B6-A0I9 
       38.96        10.59        77.62       143.38       281.29        12.13 
TCGA-B6-A0IA TCGA-B6-A0IB TCGA-B6-A0IC TCGA-B6-A0IH TCGA-B6-A0IJ TCGA-B6-A0IM 
      275.87       129.57        50.70       112.37       233.62       127.33 
TCGA-B6-A0IN TCGA-B6-A0IO TCGA-B6-A0IP TCGA-B6-A0RE TCGA-B6-A0RH TCGA-B6-A0RI 
       84.59       165.76       129.07       255.68       212.25       234.28 
TCGA-B6-A0RM TCGA-B6-A0RN TCGA-B6-A0RO TCGA-B6-A0RP TCGA-B6-A0RQ TCGA-B6-A0RS 
       78.02       263.28       162.05       102.77       140.48       100.70 
TCGA-B6-A0RT TCGA-B6-A0RU TCGA-B6-A0RV TCGA-B6-A0WS TCGA-B6-A0WT TCGA-B6-A0WV 
       89.46       282.90       157.41        97.48       188.68        79.63 
TCGA-B6-A0WW TCGA-B6-A0WY TCGA-B6-A0WZ TCGA-B6-A0X0 TCGA-B6-A0X1 TCGA-B6-A0X4 
       18.35       113.79       206.86       129.70       245.10        28.27 
TCGA-B6-A0X5 TCGA-B6-A0X7 TCGA-B6-A1KC TCGA-B6-A1KF TCGA-B6-A1KI TCGA-B6-A2IU 
       68.94        58.88        43.59       101.52        73.51       170.17 
TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-B6-A402 TCGA-B6-A408 TCGA-B6-A409 
       37.87         7.07        85.35        70.16        68.12        18.84 
TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A0AU TCGA-BH-A0AV TCGA-BH-A0AW TCGA-BH-A0AY 
      103.63        71.15        62.93        59.84        20.45        25.55 
TCGA-BH-A0AZ TCGA-BH-A0B2 TCGA-BH-A0B3 TCGA-BH-A0B4 TCGA-BH-A0B5 TCGA-BH-A0B6 
       63.09        40.83        39.55        39.16        70.22        81.63 
TCGA-BH-A0B7 TCGA-BH-A0B9 TCGA-BH-A0BA TCGA-BH-A0BC TCGA-BH-A0BD TCGA-BH-A0BF 
       84.13        51.68        37.22        32.02        18.21        43.53 
TCGA-BH-A0BG TCGA-BH-A0BJ TCGA-BH-A0BL TCGA-BH-A0BM TCGA-BH-A0BO TCGA-BH-A0BP 
       61.51        21.70        74.89        61.68        72.23        75.48 
TCGA-BH-A0BQ TCGA-BH-A0BS TCGA-BH-A0BT TCGA-BH-A0BW TCGA-BH-A0BZ TCGA-BH-A0C0 
       74.14        53.95        45.57        77.95        49.05        41.75 
TCGA-BH-A0C1 TCGA-BH-A0C3 TCGA-BH-A0C7 TCGA-BH-A0DD TCGA-BH-A0DE TCGA-BH-A0DI 
       44.02        89.06        90.97        45.83        77.98        29.98 
TCGA-BH-A0DK TCGA-BH-A0DL TCGA-BH-A0DO TCGA-BH-A0DP TCGA-BH-A0DQ TCGA-BH-A0DS 
       13.91        78.28        17.26        15.65         3.22         2.56 
TCGA-BH-A0DT TCGA-BH-A0DV TCGA-BH-A0DZ TCGA-BH-A0E0 TCGA-BH-A0E1 TCGA-BH-A0E2 
       38.47        67.86        16.27         4.41        15.68        14.30 
TCGA-BH-A0E6 TCGA-BH-A0E7 TCGA-BH-A0E9 TCGA-BH-A0EA TCGA-BH-A0EB TCGA-BH-A0EE 
        9.63        44.81        46.19        32.58        24.49        31.00 
TCGA-BH-A0EI TCGA-BH-A0GY TCGA-BH-A0H0 TCGA-BH-A0H3 TCGA-BH-A0H5 TCGA-BH-A0H6 
       24.43        30.35        15.16        37.78        53.26        24.56 
TCGA-BH-A0H7 TCGA-BH-A0H9 TCGA-BH-A0HB TCGA-BH-A0HI TCGA-BH-A0HK TCGA-BH-A0HO 
       23.08        41.00        26.50        20.38         5.85         2.50 
TCGA-BH-A0HP TCGA-BH-A0HQ TCGA-BH-A0HX TCGA-BH-A0HY TCGA-BH-A0RX TCGA-BH-A0W4 
       13.61        36.85        27.25        50.79         5.59        24.95 
TCGA-BH-A0W5 TCGA-BH-A0W7 TCGA-BH-A0WA TCGA-BH-A18F TCGA-BH-A18G TCGA-BH-A18I 
       42.35        44.81        23.05        32.91         4.90        35.93 
TCGA-BH-A18J TCGA-BH-A18K TCGA-BH-A18L TCGA-BH-A18M TCGA-BH-A18N TCGA-BH-A18P 
       20.12        90.84        26.66        72.56        37.74        30.28 
TCGA-BH-A18Q TCGA-BH-A18R TCGA-BH-A18S TCGA-BH-A18T TCGA-BH-A18U TCGA-BH-A18V 
       55.63        37.55        66.05         7.36        51.39        51.16 
TCGA-BH-A1EN TCGA-BH-A1EO TCGA-BH-A1ET TCGA-BH-A1EU TCGA-BH-A1EV TCGA-BH-A1EW 
       67.50        91.99        82.85        42.28        12.00        55.69 
TCGA-BH-A1EX TCGA-BH-A1F0 TCGA-BH-A1F2 TCGA-BH-A1F5 TCGA-BH-A1F6 TCGA-BH-A1FB 
       49.58        25.81        31.53        89.16        97.48       120.62 
TCGA-BH-A1FC TCGA-BH-A1FE TCGA-BH-A1FG TCGA-BH-A1FH TCGA-BH-A1FJ TCGA-BH-A1FL 
      114.15        74.73       122.89        36.92        63.35        55.00 
TCGA-BH-A1FN TCGA-BH-A1FR TCGA-BH-A1FU TCGA-BH-A201 TCGA-BH-A202 TCGA-BH-A203 
       72.07       144.59        72.07        28.14        26.14        38.60 
TCGA-BH-A204 TCGA-BH-A208 TCGA-BH-A28O TCGA-BH-A28Q TCGA-BH-A2L8 TCGA-BH-A42U 
       83.31        57.83        10.65         6.44        20.12       109.28 
TCGA-BH-A42V TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ 
       20.88        23.51         9.63         5.26         9.70        18.87 
TCGA-BH-A8G0 TCGA-BH-AB28 TCGA-C8-A12L TCGA-C8-A12M TCGA-C8-A12N TCGA-C8-A12O 
       21.76         9.44        11.93        11.77        11.77        12.66 
TCGA-C8-A12P TCGA-C8-A12U TCGA-C8-A12V TCGA-C8-A12W TCGA-C8-A12Y TCGA-C8-A12Z 
       11.77        12.66        12.66        12.66        48.53        12.56 
TCGA-C8-A130 TCGA-C8-A131 TCGA-C8-A132 TCGA-C8-A134 TCGA-C8-A137 TCGA-C8-A138 
        3.16        13.51         1.87        12.59         4.11         4.08 
TCGA-C8-A1HE TCGA-C8-A1HG TCGA-C8-A1HI TCGA-C8-A1HK TCGA-C8-A1HM TCGA-C8-A1HN 
       12.33        11.34        11.28        12.03        12.33        12.95 
TCGA-C8-A26X TCGA-C8-A26Y TCGA-C8-A26Z TCGA-C8-A273 TCGA-C8-A274 TCGA-C8-A275 
       12.36        12.95         8.28         9.67         9.53         0.03 
TCGA-C8-A278 TCGA-C8-A27A TCGA-C8-A27B TCGA-C8-A3M7 TCGA-C8-A3M8 TCGA-C8-A8HP 
        9.50        24.56        14.43        33.99        12.95        13.02 
TCGA-D8-A13Z TCGA-D8-A140 TCGA-D8-A141 TCGA-D8-A142 TCGA-D8-A143 TCGA-D8-A145 
       20.88        13.25        20.58        13.97        14.17        13.48 
TCGA-D8-A146 TCGA-D8-A1J8 TCGA-D8-A1JC TCGA-D8-A1JD TCGA-D8-A1JE TCGA-D8-A1JF 
       21.14        14.17        15.78        18.15        18.90        12.03 
TCGA-D8-A1JG TCGA-D8-A1JH TCGA-D8-A1JK TCGA-D8-A1JN TCGA-D8-A1JS TCGA-D8-A1JT 
       53.00        14.01        20.12        20.38        12.20        13.32 
TCGA-D8-A1JU TCGA-D8-A1X5 TCGA-D8-A1X6 TCGA-D8-A1X7 TCGA-D8-A1X8 TCGA-D8-A1XB 
       14.70        18.58        17.79        16.73        25.74        18.15 
TCGA-D8-A1XC TCGA-D8-A1XD TCGA-D8-A1XF TCGA-D8-A1XG TCGA-D8-A1XK TCGA-D8-A1XL 
       12.39        17.16        15.22        14.73        14.50        19.92 
TCGA-D8-A1XM TCGA-D8-A1XQ TCGA-D8-A1XR TCGA-D8-A1XS TCGA-D8-A1XT TCGA-D8-A1XU 
       17.69        16.41        15.85        16.31        16.64        12.99 
TCGA-D8-A1XV TCGA-D8-A1XW TCGA-D8-A1XY TCGA-D8-A1XZ TCGA-D8-A1Y0 TCGA-D8-A1Y1 
       15.16        43.04        16.54        15.32        15.52         9.93 
TCGA-D8-A1Y2 TCGA-D8-A27E TCGA-D8-A27G TCGA-D8-A27I TCGA-D8-A27K TCGA-D8-A27L 
       14.24        17.42        13.45        14.43        48.03        16.41 
TCGA-D8-A27M TCGA-D8-A27N TCGA-D8-A27P TCGA-D8-A27R TCGA-D8-A27V TCGA-D8-A27W 
       13.48         4.80         1.61        10.09        12.53        12.26 
TCGA-D8-A3Z5 TCGA-D8-A3Z6 TCGA-D8-A4Z1 TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X 
       33.37        18.51        21.67        16.18        12.66        25.22 
TCGA-E2-A105 TCGA-E2-A107 TCGA-E2-A108 TCGA-E2-A109 TCGA-E2-A10A TCGA-E2-A10B 
       43.00        34.42        27.52        46.59        40.41        37.51 
TCGA-E2-A10C TCGA-E2-A10E TCGA-E2-A10F TCGA-E2-A14N TCGA-E2-A14O TCGA-E2-A14P 
       40.11        28.44        28.87        47.15        44.68        40.96 
TCGA-E2-A14Q TCGA-E2-A14R TCGA-E2-A14S TCGA-E2-A14T TCGA-E2-A14U TCGA-E2-A14V 
       38.24        38.60        33.17        75.98        43.33        34.26 
TCGA-E2-A14W TCGA-E2-A14X TCGA-E2-A14Y TCGA-E2-A14Z TCGA-E2-A150 TCGA-E2-A153 
       32.02        31.96        69.34        18.51        63.62        23.24 
TCGA-E2-A154 TCGA-E2-A156 TCGA-E2-A159 TCGA-E2-A15A TCGA-E2-A15C TCGA-E2-A15D 
       19.43        23.87        25.05        23.34        22.82        17.29 
TCGA-E2-A15E TCGA-E2-A15F TCGA-E2-A15G TCGA-E2-A15I TCGA-E2-A15J TCGA-E2-A15L 
       20.71        21.63        18.21        55.63        53.92        20.58 
TCGA-E2-A15M TCGA-E2-A15O TCGA-E2-A15R TCGA-E2-A15T TCGA-E2-A1AZ TCGA-E2-A1B0 
       11.05        50.79        56.94        51.39        76.57        53.62 
TCGA-E2-A1B1 TCGA-E2-A1B4 TCGA-E2-A1B5 TCGA-E2-A1B6 TCGA-E2-A1BC TCGA-E2-A1BD 
       87.22        33.01        32.35        28.50        16.47        37.25 
TCGA-E2-A1IF TCGA-E2-A1IG TCGA-E2-A1IH TCGA-E2-A1II TCGA-E2-A1IJ TCGA-E2-A1IK 
       37.41        70.36        33.73        33.70        28.44        59.18 
TCGA-E2-A1IL TCGA-E2-A1IN TCGA-E2-A1IO TCGA-E2-A1IU TCGA-E2-A1L6 TCGA-E2-A1L9 
        3.88        22.19        60.99        11.08        54.18        19.66 
TCGA-E2-A1LA TCGA-E2-A1LB TCGA-E2-A1LE TCGA-E2-A1LG TCGA-E2-A1LI TCGA-E2-A1LK 
       24.59        75.81        28.90        50.07       102.61         8.75 
TCGA-E2-A1LL TCGA-E2-A2P5 TCGA-E2-A2P6 TCGA-E2-A3DX TCGA-E2-A56Z TCGA-E2-A570 
       43.04        26.99        34.55        43.56         8.28        30.61 
TCGA-E2-A573 TCGA-E2-A574 TCGA-E2-A9RU TCGA-E9-A1N3 TCGA-E9-A1N5 TCGA-E9-A1N6 
       34.92        38.76        17.69        34.82        36.82        22.29 
TCGA-E9-A1ND TCGA-E9-A1NE TCGA-E9-A1NG TCGA-E9-A1NI TCGA-E9-A1QZ TCGA-E9-A1R0 
       41.62        35.77        25.84         9.86        24.82        28.27 
TCGA-E9-A1R2 TCGA-E9-A1R3 TCGA-E9-A1R5 TCGA-E9-A1R6 TCGA-E9-A1R7 TCGA-E9-A1RA 
       34.95         2.56         3.02        11.15        48.23        45.01 
TCGA-E9-A1RB TCGA-E9-A1RC TCGA-E9-A1RD TCGA-E9-A1RE TCGA-E9-A1RF TCGA-E9-A1RH 
       32.09        40.24         1.12        46.65         6.58        46.59 
TCGA-E9-A1RI TCGA-E9-A226 TCGA-E9-A227 TCGA-E9-A228 TCGA-E9-A229 TCGA-E9-A22A 
       47.64        34.45        32.05        42.25        37.74        39.09 
TCGA-E9-A22B TCGA-E9-A22D TCGA-E9-A22E TCGA-E9-A22H TCGA-E9-A243 TCGA-E9-A244 
       38.37        41.03        41.72        40.50        20.12         0.69 
TCGA-E9-A248 TCGA-E9-A249 TCGA-E9-A24A TCGA-E9-A295 TCGA-E9-A2JS TCGA-E9-A2JT 
        1.94         7.13        24.56        12.33        29.72         9.47 
TCGA-E9-A3HO TCGA-E9-A3Q9 TCGA-E9-A3QA TCGA-E9-A3X8 TCGA-E9-A54X TCGA-E9-A54Y 
       38.07        32.91        30.18        30.44        23.90        23.84 
TCGA-E9-A5FK TCGA-E9-A5FL TCGA-E9-A5UP TCGA-E9-A6HE TCGA-EW-A1IW TCGA-EW-A1IX 
       26.70         0.79        26.40        27.85        12.20        39.72 
TCGA-EW-A1IY TCGA-EW-A1IZ TCGA-EW-A1J2 TCGA-EW-A1J3 TCGA-EW-A1J5 TCGA-EW-A1OV 
        8.48        18.21        13.25        16.57        15.68        25.94 
TCGA-EW-A1OX TCGA-EW-A1OY TCGA-EW-A1P0 TCGA-EW-A1P1 TCGA-EW-A1P3 TCGA-EW-A1P4 
       29.95        29.85        41.13        39.78        52.96        29.82 
TCGA-EW-A1P5 TCGA-EW-A1P6 TCGA-EW-A1P7 TCGA-EW-A1P8 TCGA-EW-A1PB TCGA-EW-A1PC 
       23.11        18.48        30.08         7.86        19.99         6.15 
TCGA-EW-A1PE TCGA-EW-A1PF TCGA-EW-A1PG TCGA-EW-A1PH TCGA-EW-A2FR TCGA-EW-A2FS 
       10.52        14.43        34.55        19.96        55.00        52.73 
TCGA-EW-A2FV TCGA-EW-A2FW TCGA-EW-A3E8 TCGA-EW-A3U0 TCGA-EW-A423 TCGA-EW-A424 
       25.91        22.09        34.03        17.49        10.16        23.51 
TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-GI-A2C8 TCGA-GI-A2C9 
       15.22        16.77        24.99        31.30         7.40       109.87 
TCGA-GM-A2D9 TCGA-GM-A2DA TCGA-GM-A2DB TCGA-GM-A2DC TCGA-GM-A2DD TCGA-GM-A2DF 
       59.57       216.76        79.10        83.34        75.02        70.85 
TCGA-GM-A2DI TCGA-GM-A2DK TCGA-GM-A2DL TCGA-GM-A2DM TCGA-GM-A2DN TCGA-GM-A2DO 
       85.15        86.96       115.69       106.06       101.62        85.35 
TCGA-GM-A3NW TCGA-GM-A3NY TCGA-GM-A3XG TCGA-GM-A3XN TCGA-GM-A4E0 TCGA-GM-A5PV 
      110.50        38.20        43.73        66.38        72.03        13.55 
TCGA-GM-A5PX TCGA-HN-A2OB TCGA-JL-A3YW TCGA-LD-A66U TCGA-LD-A74U TCGA-LD-A7W5 
       18.12        62.47        11.84        21.24        13.22         7.10 
TCGA-LD-A7W6 TCGA-LD-A9QF TCGA-LL-A440 TCGA-LL-A441 TCGA-LL-A442 TCGA-LL-A50Y 
       13.28        10.62        24.95        32.75        29.23        25.05 
TCGA-LL-A5YL TCGA-LL-A5YM TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP 
       17.06        15.32        14.70        14.47        14.79        22.26 
TCGA-LL-A6FQ TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A8F5 
        2.63        15.68         7.46        14.50        19.53        19.59 
TCGA-LL-A9Q3 TCGA-MS-A51U TCGA-OK-A5Q2 TCGA-OL-A5D6 TCGA-OL-A5D7 TCGA-OL-A5D8 
       17.49        22.39         2.10        36.30        58.52        31.99 
TCGA-OL-A5RU TCGA-OL-A5RV TCGA-OL-A5RX TCGA-OL-A5RY TCGA-OL-A5S0 TCGA-OL-A66H 
       40.08        34.92        28.87        24.72        20.38        26.70 
TCGA-OL-A66I TCGA-OL-A66J TCGA-OL-A66K TCGA-OL-A66L TCGA-OL-A66N TCGA-OL-A66O 
       23.47        65.62        41.92        42.77        26.04        17.36 
TCGA-OL-A66P TCGA-OL-A6VO TCGA-OL-A6VQ TCGA-OL-A6VR TCGA-OL-A97C TCGA-PE-A5DE 
       14.07        28.21        19.73        40.11         8.91        86.96 
TCGA-PL-A8LY TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-AA0Z TCGA-S3-AA10 
        0.26         9.93        18.81        18.48        20.68        19.27 
TCGA-S3-AA11 TCGA-S3-AA12 TCGA-S3-AA15 TCGA-S3-AA17 TCGA-UL-AAZ6 TCGA-UU-A93S 
       13.84        18.87        17.26        13.94        17.03         3.81 
TCGA-V7-A7HQ TCGA-W8-A86G TCGA-WT-AB41 TCGA-XX-A899 TCGA-Z7-A8R5 TCGA-Z7-A8R6 
       66.84        11.41        52.96        15.35       108.07       107.05 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.16              0.03 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            160.9             282.9 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           24.920            28.355 
[1] "0.2 - 160.9 (24.9)" "0.0 - 282.9 (28.4)"
[1] "hr=" "1"  
D82V2, continuous
                   vv
clus                STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB
  XQ LOSS MUTATED        15       15        0        0        65        53
  XQ LOSS WILD-TYPE      74       70        6        6       288       199
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           0         22          4          6        5
  XQ LOSS WILD-TYPE         2        132         25         59       15
                   vv
clus                STAGE TIS STAGE X
  XQ LOSS MUTATED           1       2
  XQ LOSS WILD-TYPE         0      11
D82V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 15                74
  STAGE IA                15                70
  STAGE IB                 0                 6
  STAGE II                 0                 6
  STAGE IIA               65               288
  STAGE IIB               53               199
  STAGE III                0                 2
  STAGE IIIA              22               132
  STAGE IIIB               4                25
  STAGE IIIC               6                59
  STAGE IV                 5                15
  STAGE TIS                1                 0
  STAGE X                  2                11
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    41 123  16   8
  XQ LOSS WILD-TYPE 235 501 120  32
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              41               235
  T2             123               501
  T3              16               120
  T4               8                32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2  N3
  XQ LOSS MUTATED    91  69  19   9
  XQ LOSS WILD-TYPE 416 289 100  68
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              91               416
  N1              69               289
  N2              19               100
  N3               9                68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED   161   6
  XQ LOSS WILD-TYPE 728  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    161    6
  XQ LOSS WILD-TYPE  728   16
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0             161               728
  1               6                16
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED   187   3
  XQ LOSS WILD-TYPE 881   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED    187    3
  XQ LOSS WILD-TYPE  881    9
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE             187               881
  MALE                 3                 9
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    83  89
  XQ LOSS WILD-TYPE 346 429
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     83   89
  XQ LOSS WILD-TYPE  346  429
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               83               346
  YES              89               429
[1] 2 2
[1] FALSE
                   vv
clus                INFILTRATING CARCINOMA NOS INFILTRATING DUCTAL CARCINOMA
  XQ LOSS MUTATED                            0                           148
  XQ LOSS WILD-TYPE                          1                           622
                   vv
clus                INFILTRATING LOBULAR CARCINOMA MEDULLARY CARCINOMA
  XQ LOSS MUTATED                               23                   1
  XQ LOSS WILD-TYPE                            177                   5
                   vv
clus                METAPLASTIC CARCINOMA MIXED HISTOLOGY (PLEASE SPECIFY)
  XQ LOSS MUTATED                       1                                8
  XQ LOSS WILD-TYPE                     8                               21
                   vv
clus                MUCINOUS CARCINOMA OTHER  SPECIFY
  XQ LOSS MUTATED                    3              6
  XQ LOSS WILD-TYPE                 14             41
D82V9, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  INFILTRATING CARCINOMA NOS                     0                 1
  INFILTRATING DUCTAL CARCINOMA                148               622
  INFILTRATING LOBULAR CARCINOMA                23               177
  MEDULLARY CARCINOMA                            1                 5
  METAPLASTIC CARCINOMA                          1                 8
  MIXED HISTOLOGY (PLEASE SPECIFY)               8                21
  MUCINOUS CARCINOMA                             3                14
  OTHER  SPECIFY                                 6                41
[1] 8 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0    15
  XQ LOSS WILD-TYPE                                1    45
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          39   119
  XQ LOSS WILD-TYPE                       142   626
D82V11, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                         15                45
  BLACK OR AFRICAN AMERICAN                     39               142
  WHITE                                        119               626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V12, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     7 156
  XQ LOSS WILD-TYPE  32 719
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      7  156
  XQ LOSS WILD-TYPE   32  719
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                32
  NOT HISPANIC OR LATINO             156               719
[1] 2 2
[1] FALSE
