[1] "ofn"            "-oTCOADREAD-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/COADREAD-TP/22506534/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/22524545/transformed.cor.cli.txt"

nPatients in clinical file=629, in cluster file=616, common to both=614
[1]  82 614
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               564 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               564 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              113               501 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              113               501 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              123               491 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              123               491 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              122               492 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              122               492 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               75               539 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               75               539 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               98               516 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               98               516 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               594 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               594 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               593 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               21               593 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              106               508 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              106               508 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               65               549 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               65               549 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              122               492 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              122               492 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              111               503 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              111               503 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              348               266 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              348               266 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              311               303 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              311               303 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              169               445 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              169               445 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              315               299 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              315               299 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              124               490 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              124               490 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              103               511 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              103               511 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                49                565 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                49                565 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                585 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                29                585 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                85                529 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                85                529 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                78                536 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                78                536 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               128                486 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               128                486 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               114                500 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               114                500 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               372                242 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               372                242 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                43                571 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                43                571 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                599 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                15                599 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               148                466 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               148                466 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               145                469 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               145                469 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                39                575 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                39                575 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               113                501 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               113                501 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                31                583 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                31                583 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                19                595 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                19                595 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               105                509 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               105                509 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               113                501 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               113                501 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               352                262 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               352                262 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               461                153 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               461                153 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                580 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                580 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                591 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                591 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              100               514 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              100               514 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              109               505 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              109               505 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              139               475 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              139               475 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               82               532 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               82               532 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               597 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               597 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               600 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               600 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               547 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               67               547 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               44               570 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               44               570 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              195               419 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              195               419 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              189               425 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              189               425 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               84               530 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               84               530 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              120               494 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              120               494 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               46               568 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               46               568 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               546 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               68               546 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               611 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               611 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               609 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               609 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              215               399 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              215               399 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35               579 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35               579 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               75               539 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               75               539 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               77               537 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               77               537 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               101                513 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               101                513 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               110                504 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               110                504 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                540 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                74                540 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                523 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                91                523 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                71                543 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                71                543 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                71                543 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                71                543 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                18                596 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                18                596 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               205                409 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               205                409 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               229                385 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               229                385 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                574 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                40                574 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                571 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                43                571 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               338                276 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               338                276 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                521 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                93                521 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               380                234 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               380                234 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               407                207 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               407                207 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                62                552 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                62                552 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                558 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                56                558 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                64                550 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                64                550 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                606 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 8                606 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               192                422 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               192                422 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               201                413 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               201                413 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               90               524 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               90               524 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               78               536 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               78               536 
[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] "TUMOR_STAGE"                         
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "ETHNICITY"                           

Input Data has 18 rows and 614 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=111,	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=311,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	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=16,	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=18,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR_STAGE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'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 614 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "TUMOR_TISSUE_SITE"     "PATHOLOGIC_STAGE"     
 [4] "PATHOLOGY_T_STAGE"     "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"    
 [7] "GENDER"                "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"    
[10] "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES" "ETHNICITY"            
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
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 
 20 105 417  69 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 105 417  69 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 105 417  69 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 105 417  69 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
346 150 115 
[1] "table(vv)"
vv
 N0  N1  N2 
346 150 115 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
346 150 115 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
346 150 115 
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=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, binary=FALSE, numeric=TRUE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    37  13
  1P GAIN WILD-TYPE 429 115
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               50               544 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               13               115 
$`1P GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3688 TCGA-AD-6888 TCGA-CK-5912 TCGA-AG-3611 
       45.60        13.02        19.00        15.52        49.08        13.94 
TCGA-G5-6641 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3810 
       26.43        39.45        43.76        44.91        16.57        36.53 
TCGA-A6-4107 TCGA-A6-6654 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3855 
       32.45        23.87        54.02         2.01        15.02        32.05 
TCGA-AA-3973 TCGA-AA-A01D TCGA-AA-A02E TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4684 
       13.05        10.98         2.96         0.20        17.85        65.00 
TCGA-CA-5255 TCGA-CA-6716 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6167 TCGA-D5-6535 
       12.36        12.20         5.03        15.02        14.99        15.12 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A28C TCGA-DM-A28M 
        7.53        10.13        12.43       119.70        81.37        95.18 
TCGA-NH-A50T TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-2692 TCGA-AF-4110 TCGA-AG-3578 
       18.18        42.77        38.70        13.55        29.98        32.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-A026 TCGA-DC-6156 TCGA-DY-A1DF TCGA-EI-6884 
       46.03        34.03         1.94        31.00        24.13        10.78 
TCGA-EI-7004 TCGA-F5-6464 
        8.45         9.96 

$`1P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       34.03         0.99        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       21.99        39.06        21.37        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 
       79.69        17.85        10.39         8.02        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       21.24        18.28        55.76        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        1.61         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       42.28        35.11        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       61.02        78.08         6.97        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
        2.01        21.99        16.08        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       29.56         5.23        11.74         3.19        12.69        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        21.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       16.14        15.58        12.39        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        26.47       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       74.79        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       21.90        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       17.23        43.04        37.97        34.49        37.74        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02         1.02        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       26.04        31.00        12.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 
       11.51        13.64        17.46        11.97        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              0.2               0.0 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           119.70            148.01 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           18.015            22.045 
[1] "0.2 - 119.7 (18.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D1V2, continuous
D1V3, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    37  11
  1P GAIN WILD-TYPE 411 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     37   11
  1P GAIN WILD-TYPE  411  151
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON               37               411
  RECTUM              11               151
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P GAIN MUTATED         6        0        2        14         1         0
  1P GAIN WILD-TYPE      98        1       35       158        11         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P GAIN MUTATED           1          3          5          7        6
  1P GAIN WILD-TYPE        23         12         79         48       57
                   vv
clus                STAGE IVA STAGE IVB
  1P GAIN MUTATED           4         0
  1P GAIN WILD-TYPE        20         2
D1V4, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  6                98
  STAGE IA                 0                 1
  STAGE II                 2                35
  STAGE IIA               14               158
  STAGE IIB                1                11
  STAGE IIC                0                 2
  STAGE III                1                23
  STAGE IIIA               3                12
  STAGE IIIB               5                79
  STAGE IIIC               7                48
  STAGE IV                 6                57
  STAGE IVA                4                20
  STAGE IVB                0                 2
[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     1   6  35   8
  1P GAIN WILD-TYPE  19  99 382  61
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1                19
  T2               6                99
  T3              35               382
  T4               8                61
[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
  1P GAIN MUTATED    24  13  13
  1P GAIN WILD-TYPE 322 137 102
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              24               322
  N1              13               137
  N2              13               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    32   9
  1P GAIN WILD-TYPE 421  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     32    9
  1P GAIN WILD-TYPE  421   79
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              32               421
  1               9                79
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    21  29
  1P GAIN WILD-TYPE 268 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     21   29
  1P GAIN WILD-TYPE  268  296
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              21               268
  MALE                29               296
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    39   3
  1P GAIN WILD-TYPE 443  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     39    3
  1P GAIN WILD-TYPE  443   26
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO               39               443
  YES               3                26
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P GAIN MUTATED                     35                             2
  1P GAIN WILD-TYPE                  347                            60
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1P GAIN MUTATED                       8                              3
  1P GAIN WILD-TYPE                   138                             10
D1V10, multiclass
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        35               347
  COLON MUCINOUS ADENOCARCINOMA                2                60
  RECTAL ADENOCARCINOMA                        8               138
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  1P GAIN MUTATED    35   1   4   4
  1P GAIN WILD-TYPE 411   5  33  25
D1V11, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              35               411
  R1               1                 5
  R2               4                33
  RX               4                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"
D1V12, continuous
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     1  35
  1P GAIN WILD-TYPE   4 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1   35
  1P GAIN WILD-TYPE    4  317
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              35               317
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    81  29
  1Q GAIN WILD-TYPE 385  99
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              110               484 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29                99 
$`1Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3688 TCGA-AA-3939 TCGA-AD-6888 
       45.60        24.16        13.02        19.00        12.99        15.52 
TCGA-CK-5912 TCGA-AG-3611 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6641 
       49.08        13.94        36.03        31.00        51.98        26.43 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       39.45        43.76        43.76        44.91        35.11        16.57 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3561 TCGA-AA-3660 
       36.53        32.45        24.69        23.87        13.94        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3696 TCGA-AA-3848 
       54.02         2.01        47.05        15.02         5.03        10.06 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3947 TCGA-AA-3973 
       32.05        31.07        17.03        27.02        33.01        13.05 
TCGA-AA-3994 TCGA-AA-A01D TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02Y 
       27.02        10.98        35.01        26.01         2.96        39.98 
TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6606 
       14.50         0.20        17.85        65.00        12.10        11.74 
TCGA-CA-5255 TCGA-CA-6716 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5861 
       12.36        12.20        37.02        25.02        22.98        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-6533 TCGA-D5-6535 
        5.03        15.02        14.04        14.99        25.48        15.12 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A1D4 
       17.85         7.53        10.13        12.43       119.70        92.75 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       81.37        35.97        95.18         8.61        31.96        11.11 
TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6311 TCGA-NH-A50T 
       47.41        82.39        74.56        65.85        39.42        18.18 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 
        9.93        42.77        38.70        13.55        29.98        24.36 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 
       24.59        32.02        46.03        34.03        34.03         6.05 
TCGA-AG-3881 TCGA-AG-3999 TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       19.04        28.04         1.94        38.04        38.56        43.20 
TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF 
       27.55        47.44        13.97        31.00       129.27        24.13 
TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7004 TCGA-F5-6464 
       20.55         8.61        10.78        13.64         8.45         9.96 
TCGA-F5-6813 TCGA-F5-6863 
       19.66        11.87 

$`1Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T 
       15.95        21.24        18.28        55.76        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
       12.66         1.61         9.53        46.65        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       42.28        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3667 
       24.00        29.95        20.98        61.02         6.97        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3710 
       50.04        47.01        11.01         5.98        37.05        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3864 
        0.00        33.07         0.00        36.03         0.99        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        21.99        16.08        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
        1.02        33.04         1.02        37.02        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        41.00        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       27.42        26.47        16.44         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
        6.77        29.56         5.23         3.19        12.69        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       22.03        30.08        32.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       12.00        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        43.27         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41        13.35        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       14.04        26.47       119.93        60.79       117.07        98.24 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       41.42        43.04        33.67        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
      133.18         8.35        67.30        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       46.75        74.79        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       21.90        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       17.23        43.04        37.97        34.49        37.74        16.83 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
        7.07        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02         1.02        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       41.00         2.50        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       25.05        26.04        31.00        12.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        51.48        32.61         3.48         4.18 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6917 TCGA-EI-7002 
       16.34        16.31        16.41        11.51        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        12.46        47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              0.2               0.0 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.27            148.01 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            24.64             21.60 
[1] "0.2 - 129.3 (24.6)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1.2"
D2V2, continuous
D2V3, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    78  33
  1Q GAIN WILD-TYPE 370 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     78   33
  1Q GAIN WILD-TYPE  370  129
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON               78               370
  RECTUM              33               129
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1Q GAIN MUTATED        13        0        7        26         2         0
  1Q GAIN WILD-TYPE      91        1       30       146        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q GAIN MUTATED           4          4         14         15       18
  1Q GAIN WILD-TYPE        20         11         70         40       45
                   vv
clus                STAGE IVA STAGE IVB
  1Q GAIN MUTATED           6         0
  1Q GAIN WILD-TYPE        18         2
D2V4, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 13                91
  STAGE IA                 0                 1
  STAGE II                 7                30
  STAGE IIA               26               146
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                4                20
  STAGE IIIA               4                11
  STAGE IIIB              14                70
  STAGE IIIC              15                40
  STAGE IV                18                45
  STAGE IVA                6                18
  STAGE IVB                0                 2
[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     4  13  75  21
  1Q GAIN WILD-TYPE  16  92 342  48
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               4                16
  T2              13                92
  T3              75               342
  T4              21                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"
                   vv
clus                 N0  N1  N2
  1Q GAIN MUTATED    52  30  30
  1Q GAIN WILD-TYPE 294 120  85
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              52               294
  N1              30               120
  N2              30                85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    76  23
  1Q GAIN WILD-TYPE 377  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     76   23
  1Q GAIN WILD-TYPE  377   65
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              76               377
  1              23                65
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    50  63
  1Q GAIN WILD-TYPE 239 262
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     50   63
  1Q GAIN WILD-TYPE  239  262
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              50               239
  MALE                63               262
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    89   9
  1Q GAIN WILD-TYPE 393  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     89    9
  1Q GAIN WILD-TYPE  393   20
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               89               393
  YES               9                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q GAIN MUTATED                     72                             6
  1Q GAIN WILD-TYPE                  310                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1Q GAIN MUTATED                      28                              4
  1Q GAIN WILD-TYPE                   118                              9
D2V10, multiclass
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        72               310
  COLON MUCINOUS ADENOCARCINOMA                6                56
  RECTAL ADENOCARCINOMA                       28               118
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[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                 R0  R1  R2  RX
  1Q GAIN MUTATED    79   1   9   5
  1Q GAIN WILD-TYPE 367   5  28  24
D2V11, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              79               367
  R1               1                 5
  R2               9                28
  RX               5                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"
D2V12, continuous
D2V13, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     1  70
  1Q GAIN WILD-TYPE   4 282
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1   70
  1Q GAIN WILD-TYPE    4  282
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              70               282
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    91  27
  2P GAIN WILD-TYPE 375 101
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              118               476 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               27               101 
$`2P GAIN MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3562 TCGA-AA-3867 
       14.53        24.16         1.02        34.03        19.99        24.03 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-G4-6310 TCGA-G4-6628 TCGA-NH-A8F7 
       38.04        21.37        15.52        63.62        79.69        17.85 
TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-5M-AAT4 
       31.00        21.24        18.28        55.76        15.62         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 
       39.45        43.76        37.02        34.65        36.53        30.44 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3519 TCGA-AA-3532 
       32.71        29.16        24.69        23.87         9.07        29.00 
TCGA-AA-3534 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 
       29.00        50.04        15.02        37.05        10.06        35.05 
TCGA-AA-3851 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X 
       33.07         2.01        16.08        31.00         1.02        26.01 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 
        5.79        22.42        27.42        16.44        16.31         0.20 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6718 
       18.84         5.13         3.19        12.59        12.20        10.06 
TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 
       85.45        21.99         8.02        29.06         5.03        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-D5-5537 TCGA-D5-5541 
       15.02        14.04        29.03        21.99        45.40        55.92 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1DA TCGA-DM-A280 
        4.80        17.13        14.30        13.41         7.50         7.76 
TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6627 TCGA-NH-A50T 
       35.97         8.61         8.35        74.56        74.79        18.18 
TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 
       12.79        29.46        32.98        38.70        60.13        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 
       39.48        17.23        16.83        86.63        65.98        36.03 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 
       46.03        34.03        34.03        19.99        19.99         1.02 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A032 TCGA-AH-6897 TCGA-CI-6621 TCGA-CL-5917 
        1.02        46.03        38.04        26.43        13.78        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        7.17        21.01        31.00        12.00        31.00        51.98 
TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 
       25.05       129.27        51.48        20.55        16.31        13.64 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6864 TCGA-G5-6572 
        9.96        49.51        12.46        47.08 

$`2P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        19.07         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 
       24.00        19.07        21.99        39.06        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       91.79        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6641 
       17.03        25.97        15.95        36.03        51.98        26.43 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        4.80        12.66         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       37.25        32.75        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3542 
       38.99         1.02        19.07         0.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       14.01        47.05        47.01        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       12.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 
       40.96        12.16        83.24        24.53        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.65        32.94        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
       12.76        14.30        17.56       148.01        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        16.04        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        54.61        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       56.09        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27        15.12        17.85        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        46.75        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       15.65        16.80        42.77         8.42        31.30        21.90 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       11.90        70.03        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N 
       37.74        29.98        24.36        20.02        24.59        11.84 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       17.95        36.95        13.02        35.01        14.01        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        3.98        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.56         2.50        43.20        27.55 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       19.46         6.05        33.17        44.78        47.44        48.20 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       25.05        26.04        13.97        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        12.62       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         3.48         4.18        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       11.51        10.78        17.46        11.97         8.45        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 
       38.14        11.87 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              0.2               0.0 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           129.27            148.01 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           23.145            21.990 
[1] "0.2 - 129.3 (23.1)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    83  40
  2P GAIN WILD-TYPE 365 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     83   40
  2P GAIN WILD-TYPE  365  122
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON               83               365
  RECTUM              40               122
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2P GAIN MUTATED        16        0        8        31         1         1
  2P GAIN WILD-TYPE      88        1       29       141        11         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P GAIN MUTATED           5          2         21         14       12
  2P GAIN WILD-TYPE        19         13         63         41       51
                   vv
clus                STAGE IVA STAGE IVB
  2P GAIN MUTATED           7         1
  2P GAIN WILD-TYPE        17         1
D3V4, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 16                88
  STAGE IA                 0                 1
  STAGE II                 8                29
  STAGE IIA               31               141
  STAGE IIB                1                11
  STAGE IIC                1                 1
  STAGE III                5                19
  STAGE IIIA               2                13
  STAGE IIIB              21                63
  STAGE IIIC              14                41
  STAGE IV                12                51
  STAGE IVA                7                17
  STAGE IVB                1                 1
[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     2  18  91  11
  2P GAIN WILD-TYPE  18  87 326  58
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               2                18
  T2              18                87
  T3              91               326
  T4              11                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"
                   vv
clus                 N0  N1  N2
  2P GAIN MUTATED    61  29  32
  2P GAIN WILD-TYPE 285 121  83
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              61               285
  N1              29               121
  N2              32                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    82  20
  2P GAIN WILD-TYPE 371  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     82   20
  2P GAIN WILD-TYPE  371   68
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              82               371
  1              20                68
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    63  60
  2P GAIN WILD-TYPE 226 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     63   60
  2P GAIN WILD-TYPE  226  265
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              63               226
  MALE                60               265
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    97   8
  2P GAIN WILD-TYPE 385  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     97    8
  2P GAIN WILD-TYPE  385   21
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               97               385
  YES               8                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P GAIN MUTATED                     75                             8
  2P GAIN WILD-TYPE                  307                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2P GAIN MUTATED                      40                              0
  2P GAIN WILD-TYPE                   106                             13
D3V10, multiclass
                                clus
vv                               2P GAIN MUTATED 2P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        75               307
  COLON MUCINOUS ADENOCARCINOMA                8                54
  RECTAL ADENOCARCINOMA                       40               106
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  2P GAIN MUTATED    86   3   5  10
  2P GAIN WILD-TYPE 360   3  32  19
D3V11, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              86               360
  R1               3                 3
  R2               5                32
  RX              10                19
[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, continuous
D3V13, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  83
  2P GAIN WILD-TYPE   3 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   83
  2P GAIN WILD-TYPE    3  269
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              83               269
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    89  28
  2Q GAIN WILD-TYPE 377 100
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              117               477 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               28               100 
$`2Q GAIN MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3562 TCGA-AA-3867 
       14.53        24.16         1.02        34.03        19.99        24.03 
TCGA-AD-6548 TCGA-AD-6888 TCGA-G4-6310 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       21.37        15.52        63.62        79.69        17.85        10.39 
TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-3L-AA1B TCGA-5M-AAT4 TCGA-5M-AATE 
       31.00        21.24        18.28        15.62         1.61        39.45 
TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 
       43.76        34.65        36.53        30.44        32.71        29.16 
TCGA-A6-6652 TCGA-A6-6654 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3673 
       24.69        23.87         9.07        29.00        29.00        50.04 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3851 
       15.02        37.05         5.03        10.06        35.05        33.07 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AD-6899 
        2.01        16.08        31.00         1.02        26.01         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4616 
       22.42        27.42        16.44        16.31        18.84         5.13 
TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4750 
        3.19        12.59        12.20        85.45        21.99         8.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       29.06         5.03        15.02        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 TCGA-D5-6538 TCGA-DM-A1DA 
       14.99        45.40        55.92         4.80        17.13         7.50 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6295 TCGA-G4-6299 
        7.76        14.04        35.97         8.61         8.35        74.56 
TCGA-G4-6311 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX 
       39.42        74.79        18.18        12.79        29.46        32.98 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-5654 
       38.70        60.13        46.92        39.48        17.23        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3591 
       24.36        86.63        65.98        36.03        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4007 
       34.03        19.99        19.99         1.02        48.03         1.02 
TCGA-AG-4022 TCGA-AG-A032 TCGA-AH-6897 TCGA-CI-6621 TCGA-CL-5917 TCGA-CL-5918 
       46.03        38.04        26.43        13.78        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
       31.00        12.00        31.00        51.98        25.05       129.27 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 
        4.18        20.55        16.31        13.64         9.96        49.51 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

$`2Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        19.07         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 
       24.00        19.07        38.04        21.99        39.06        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       26.17        91.79         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6235 
       17.03        25.97        15.95        36.03        51.98        55.76 
TCGA-G5-6641 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       26.43         4.80        12.66         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        37.02        32.75        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         1.02        19.07         0.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       54.02         2.01        14.01        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.98        26.99         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       21.99        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04         1.02        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 
       18.05        40.96        12.16        83.24        24.53        26.47 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
      109.28        58.39         1.41         5.65        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      148.01        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04        27.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       32.02        15.02        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        54.61        19.59        56.09        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A 
      140.38        44.32       131.51       135.65       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 
        0.53        47.41        35.31       133.18        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50U 
       36.00        26.43        26.04        13.78        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 
        8.42        31.30        21.90        11.90        70.03        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 
       13.55        37.97        34.49        37.74        29.98        20.02 
TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.59        11.84        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         3.98        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       27.55        19.46         6.05        33.17        44.78        47.44 
TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
       48.20        21.01        25.05        26.04        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         3.48        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       19.66        37.18        38.14 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.02              0.00 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           129.27            148.01 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            22.42             21.99 
[1] "1.0 - 129.3 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    80  42
  2Q GAIN WILD-TYPE 368 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     80   42
  2Q GAIN WILD-TYPE  368  120
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON               80               368
  RECTUM              42               120
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2Q GAIN MUTATED        16        0        8        29         1         1
  2Q GAIN WILD-TYPE      88        1       29       143        11         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q GAIN MUTATED           6          2         21         15       13
  2Q GAIN WILD-TYPE        18         13         63         40       50
                   vv
clus                STAGE IVA STAGE IVB
  2Q GAIN MUTATED           5         1
  2Q GAIN WILD-TYPE        19         1
D4V4, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 16                88
  STAGE IA                 0                 1
  STAGE II                 8                29
  STAGE IIA               29               143
  STAGE IIB                1                11
  STAGE IIC                1                 1
  STAGE III                6                18
  STAGE IIIA               2                13
  STAGE IIIB              21                63
  STAGE IIIC              15                40
  STAGE IV                13                50
  STAGE IVA                5                19
  STAGE IVB                1                 1
[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     2  18  90  11
  2Q GAIN WILD-TYPE  18  87 327  58
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               2                18
  T2              18                87
  T3              90               327
  T4              11                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"
                   vv
clus                 N0  N1  N2
  2Q GAIN MUTATED    59  29  33
  2Q GAIN WILD-TYPE 287 121  82
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              59               287
  N1              29               121
  N2              33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    82  19
  2Q GAIN WILD-TYPE 371  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     82   19
  2Q GAIN WILD-TYPE  371   69
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              82               371
  1              19                69
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    63  59
  2Q GAIN WILD-TYPE 226 266
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     63   59
  2Q GAIN WILD-TYPE  226  266
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              63               226
  MALE                59               266
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    96   9
  2Q GAIN WILD-TYPE 386  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     96    9
  2Q GAIN WILD-TYPE  386   20
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               96               386
  YES               9                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q GAIN MUTATED                     72                             8
  2Q GAIN WILD-TYPE                  310                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2Q GAIN MUTATED                      42                              0
  2Q GAIN WILD-TYPE                   104                             13
D4V10, multiclass
                                clus
vv                               2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        72               310
  COLON MUCINOUS ADENOCARCINOMA                8                54
  RECTAL ADENOCARCINOMA                       42               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  2Q GAIN MUTATED    85   2   6   9
  2Q GAIN WILD-TYPE 361   4  31  20
D4V11, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              85               361
  R1               2                 4
  R2               6                31
  RX               9                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"
D4V12, continuous
D4V13, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     2  81
  2Q GAIN WILD-TYPE   3 271
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2   81
  2Q GAIN WILD-TYPE    3  271
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              81               271
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    59  13
  3P GAIN WILD-TYPE 407 115
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               72               522 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13               115 
$`3P GAIN MUTATED`
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3867 TCGA-AA-3976 TCGA-AZ-6608 TCGA-G4-6314 
       19.99        19.99        24.03        26.01         1.94        35.93 
TCGA-AG-3611 TCGA-AG-3612 TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-3810 
       13.94        19.99        12.66        43.76        37.02        36.53 
TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6650 TCGA-A6-6782 TCGA-AA-3666 TCGA-AA-3667 
       29.16        24.13        20.61        20.28         2.01        14.01 
TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3971 TCGA-AA-A00F TCGA-AA-A01Q TCGA-AA-A01T 
       37.05        37.02        16.08        34.03         1.02        33.04 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-A69D 
       41.00         5.79        22.42        26.47         0.95        17.85 
TCGA-AZ-6603 TCGA-CA-5254 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6675 
       29.56        12.69        17.03        15.02        29.03        13.05 
TCGA-CM-6679 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A288 TCGA-F4-6704 
       10.06        15.12        12.49        14.30        14.04         1.55 
TCGA-G4-6303 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC TCGA-QL-A97D TCGA-AF-6655 
       65.85        13.78        46.75        12.79        21.90        20.02 
TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3725 TCGA-AG-3726 
       24.59        34.03        34.03        34.03        20.98         7.99 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A020 TCGA-CI-6623 
        1.02        36.03        14.04         9.07         1.02        47.44 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC 
       21.01        31.00        31.00        25.97        25.05        41.36 
TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
      129.27         4.18        18.28        11.97        28.57        32.19 

$`3P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       17.85        10.39         8.02        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 
       55.76        26.43        15.62         4.80         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       39.45        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       44.91        35.11        16.57        37.05        37.25        34.65 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       36.95         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        31.00        38.07        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09        16.31        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74         3.19        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6163 
       15.02         5.03        15.02        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        26.43        26.04        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.36        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        28.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       20.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
        7.17        25.05        26.04        12.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       10.98        44.02        25.05        12.62       126.44        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
        8.45         9.96        49.51        42.35         0.39        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.95              0.00 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           129.27            148.01 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           20.795            22.075 
[1] "0.9 - 129.3 (20.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    46  28
  3P GAIN WILD-TYPE 402 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     46   28
  3P GAIN WILD-TYPE  402  134
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON               46               402
  RECTUM              28               134
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3P GAIN MUTATED         9        1        2        21         1         0
  3P GAIN WILD-TYPE      95        0       35       151        11         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P GAIN MUTATED           5          4          6          7        9
  3P GAIN WILD-TYPE        19         11         78         48       54
                   vv
clus                STAGE IVA STAGE IVB
  3P GAIN MUTATED           4         2
  3P GAIN WILD-TYPE        20         0
D5V4, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  9                95
  STAGE IA                 1                 0
  STAGE II                 2                35
  STAGE IIA               21               151
  STAGE IIB                1                11
  STAGE IIC                0                 2
  STAGE III                5                19
  STAGE IIIA               4                11
  STAGE IIIB               6                78
  STAGE IIIC               7                48
  STAGE IV                 9                54
  STAGE IVA                4                20
  STAGE IVB                2                 0
[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     2  13  51   8
  3P GAIN WILD-TYPE  18  92 366  61
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                18
  T2              13                92
  T3              51               366
  T4               8                61
[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
  3P GAIN MUTATED    37  20  18
  3P GAIN WILD-TYPE 309 130  97
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              37               309
  N1              20               130
  N2              18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    47  14
  3P GAIN WILD-TYPE 406  74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     47   14
  3P GAIN WILD-TYPE  406   74
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              47               406
  1              14                74
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    39  36
  3P GAIN WILD-TYPE 250 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     39   36
  3P GAIN WILD-TYPE  250  289
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              39               250
  MALE                36               289
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    60   3
  3P GAIN WILD-TYPE 422  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     60    3
  3P GAIN WILD-TYPE  422   26
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               60               422
  YES               3                26
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P GAIN MUTATED                     41                             5
  3P GAIN WILD-TYPE                  341                            57
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3P GAIN MUTATED                      27                              1
  3P GAIN WILD-TYPE                   119                             12
D5V10, multiclass
                                clus
vv                               3P GAIN MUTATED 3P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        41               341
  COLON MUCINOUS ADENOCARCINOMA                5                57
  RECTAL ADENOCARCINOMA                       27               119
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  3P GAIN MUTATED    54   1   3   3
  3P GAIN WILD-TYPE 392   5  34  26
D5V11, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              54               392
  R1               1                 5
  R2               3                34
  RX               3                26
[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, continuous
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     0  45
  3P GAIN WILD-TYPE   5 307
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0   45
  3P GAIN WILD-TYPE    5  307
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              45               307
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED    73  21
  3Q GAIN WILD-TYPE 393 107
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               94               500 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               21               107 
$`3Q GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3867 TCGA-AA-3976 TCGA-AA-3979 
       13.02        19.99        19.99        24.03        26.01        24.00 
TCGA-AD-6888 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6314 TCGA-AF-3913 
       15.52         1.94         5.88        28.21        35.93        10.39 
TCGA-AG-3611 TCGA-AG-3612 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2686 
       13.94        19.99        12.66         1.61        43.76        37.02 
TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       36.53        29.16        27.09        25.08        20.61        21.76 
TCGA-A6-6782 TCGA-AA-3532 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3685 
       20.28        29.00        78.08         2.01        14.01        37.05 
TCGA-AA-3842 TCGA-AA-3866 TCGA-AA-3971 TCGA-AA-A00F TCGA-AA-A01Q TCGA-AA-A01T 
       37.02        17.03        16.08        34.03         1.02        33.04 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 
       41.00         5.79        22.42        26.47        14.50         0.95 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CM-4750 TCGA-CM-5868 
       17.85         5.65        29.56        12.69         8.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6675 TCGA-CM-6679 TCGA-D5-6535 
       15.02        14.04        29.03        13.05        10.06        15.12 
TCGA-D5-6539 TCGA-D5-6924 TCGA-DM-A288 TCGA-F4-6704 TCGA-G4-6303 TCGA-G4-6311 
       12.49        14.30        14.04         1.55        65.85        39.42 
TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC TCGA-QL-A97D TCGA-AF-3911 TCGA-AF-6655 
       13.78        46.75        12.79        21.90        37.74        20.02 
TCGA-AF-6672 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3725 TCGA-AG-3726 
       24.59        34.03        34.03        34.03        20.98         7.99 
TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A020 
       17.95         1.02        36.03        14.04         9.07         1.02 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6681 
       47.44        78.12        21.01        31.00        31.00        25.97 
TCGA-DC-6682 TCGA-DY-A1DC TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
       25.05        41.36         4.18        18.28        16.31        11.97 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
       28.57         0.39        32.19        11.87 

$`3Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 
       19.07        34.03         0.99        17.95        23.01         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       50.99        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 
       25.08        10.88        75.95       106.75       100.01        49.08 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       23.51        63.62        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       79.69        17.85         8.02        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE 
       55.76        26.43        15.62         4.80         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        34.65        32.75 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        25.18        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       61.02         6.97        54.02        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        31.00        38.07        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        27.09        16.31        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 
       13.02        15.02        14.04        11.01        12.95        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       25.48        43.27        17.85         4.80        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T 
       61.91        36.00        26.43        26.04        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       60.13        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.36        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A025 
       13.94         6.02        23.01        37.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 
       33.17        13.78        44.78        48.20         7.17        25.05 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       26.04        12.00        13.97        51.98        10.98        44.02 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05        12.62       126.44        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         3.48        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       49.51        42.35        36.49        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.39              0.00 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            78.12            148.01 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           20.005            22.750 
[1] "0.4 - 78.1 (20.0)"  "0.0 - 148.0 (22.8)"
[1] "hr=" "1.4"
D6V2, continuous
D6V3, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    63  34
  3Q GAIN WILD-TYPE 385 128
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     63   34
  3Q GAIN WILD-TYPE  385  128
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON               63               385
  RECTUM              34               128
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3Q GAIN MUTATED        11        1        4        23         1         0
  3Q GAIN WILD-TYPE      93        0       33       149        11         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q GAIN MUTATED           6          5         11         10       13
  3Q GAIN WILD-TYPE        18         10         73         45       50
                   vv
clus                STAGE IVA STAGE IVB
  3Q GAIN MUTATED           6         2
  3Q GAIN WILD-TYPE        18         0
D6V4, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 11                93
  STAGE IA                 1                 0
  STAGE II                 4                33
  STAGE IIA               23               149
  STAGE IIB                1                11
  STAGE IIC                0                 2
  STAGE III                6                18
  STAGE IIIA               5                10
  STAGE IIIB              11                73
  STAGE IIIC              10                45
  STAGE IV                13                50
  STAGE IVA                6                18
  STAGE IVB                2                 0
[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     4  14  68  10
  3Q GAIN WILD-TYPE  16  91 349  59
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               4                16
  T2              14                91
  T3              68               349
  T4              10                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"
                   vv
clus                 N0  N1  N2
  3Q GAIN MUTATED    44  31  22
  3Q GAIN WILD-TYPE 302 119  93
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              44               302
  N1              31               119
  N2              22                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    59  20
  3Q GAIN WILD-TYPE 394  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     59   20
  3Q GAIN WILD-TYPE  394   68
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              59               394
  1              20                68
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    50  48
  3Q GAIN WILD-TYPE 239 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     50   48
  3Q GAIN WILD-TYPE  239  277
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              50               239
  MALE                48               277
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    79   5
  3Q GAIN WILD-TYPE 403  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     79    5
  3Q GAIN WILD-TYPE  403   24
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               79               403
  YES               5                24
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q GAIN MUTATED                     57                             6
  3Q GAIN WILD-TYPE                  325                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3Q GAIN MUTATED                      33                              1
  3Q GAIN WILD-TYPE                   113                             12
D6V10, multiclass
                                clus
vv                               3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        57               325
  COLON MUCINOUS ADENOCARCINOMA                6                56
  RECTAL ADENOCARCINOMA                       33               113
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  3Q GAIN MUTATED    73   1   3   4
  3Q GAIN WILD-TYPE 373   5  34  25
D6V11, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              73               373
  R1               1                 5
  R2               3                34
  RX               4                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"
D6V12, continuous
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     1  60
  3Q GAIN WILD-TYPE   4 292
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1   60
  3Q GAIN WILD-TYPE    4  292
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              60               292
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    16   4
  4P GAIN WILD-TYPE 450 124
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               20               574 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4               124 
$`4P GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3560 TCGA-AG-3890 TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-A56B 
       45.60        19.99        17.03        15.62        43.76        56.25 
TCGA-AA-3982 TCGA-AD-A5EK TCGA-AY-A8YK TCGA-CM-5862 TCGA-G4-6307 TCGA-RU-A8FL 
       27.02        16.44        18.84         5.03        55.04        38.70 
TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A011 TCGA-CI-6621 TCGA-DC-4749 TCGA-DC-6682 
       32.02        46.03        37.02        13.78        25.05        25.05 
TCGA-DY-A1DG TCGA-EI-6510 
       51.48        18.28 

$`4P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       26.43         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       26.47         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       74.56        67.30        65.85        53.62        44.68        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 
        3.98        20.98        13.94         6.02        23.01         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46         6.05        33.17        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       48.20        78.12         7.17        21.01        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             5.03              0.00 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            56.25            148.01 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           26.035            21.990 
[1] "5.0 - 56.2 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D7V2, continuous
D7V3, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    11   9
  4P GAIN WILD-TYPE 437 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     11    9
  4P GAIN WILD-TYPE  437  153
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON               11               437
  RECTUM               9               153
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4P GAIN MUTATED         4        0        1         4         0         0
  4P GAIN WILD-TYPE     100        1       36       168        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P GAIN MUTATED           0          0          5          1        1
  4P GAIN WILD-TYPE        24         15         79         54       62
                   vv
clus                STAGE IVA STAGE IVB
  4P GAIN MUTATED           3         0
  4P GAIN WILD-TYPE        21         2
D7V4, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  4               100
  STAGE IA                 0                 1
  STAGE II                 1                36
  STAGE IIA                4               168
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                0                24
  STAGE IIIA               0                15
  STAGE IIIB               5                79
  STAGE IIIC               1                54
  STAGE IV                 1                62
  STAGE IVA                3                21
  STAGE IVB                0                 2
[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     0   5  15   0
  4P GAIN WILD-TYPE  20 100 402  69
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                20
  T2               5               100
  T3              15               402
  T4               0                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"
                   vv
clus                 N0  N1  N2
  4P GAIN MUTATED    10   6   4
  4P GAIN WILD-TYPE 336 144 111
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              10               336
  N1               6               144
  N2               4               111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    12   4
  4P GAIN WILD-TYPE 441  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     12    4
  4P GAIN WILD-TYPE  441   84
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              12               441
  1               4                84
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     6  14
  4P GAIN WILD-TYPE 283 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      6   14
  4P GAIN WILD-TYPE  283  311
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               6               283
  MALE                14               311
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    17   1
  4P GAIN WILD-TYPE 465  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     17    1
  4P GAIN WILD-TYPE  465   28
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               17               465
  YES               1                28
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P GAIN MUTATED                     11                             0
  4P GAIN WILD-TYPE                  371                            62
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4P GAIN MUTATED                       9                              0
  4P GAIN WILD-TYPE                   137                             13
D7V10, multiclass
                                clus
vv                               4P GAIN MUTATED 4P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        11               371
  COLON MUCINOUS ADENOCARCINOMA                0                62
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  4P GAIN MUTATED    17   0   0   0
  4P GAIN WILD-TYPE 429   6  37  29
D7V11, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0              17               429
  R1               0                 6
  R2               0                37
  RX               0                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"
D7V12, continuous
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0  14
  4P GAIN WILD-TYPE   5 338
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0   14
  4P GAIN WILD-TYPE    5  338
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              14               338
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    13   7
  4Q GAIN WILD-TYPE 453 121
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               20               574 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7               121 
$`4Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3560 TCGA-AA-3867 TCGA-AA-3939 TCGA-AG-3890 
       24.33        45.60        19.99        24.03        12.99        17.03 
TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-A56B TCGA-AA-3982 TCGA-AD-A5EK TCGA-AY-A8YK 
       43.76        37.02        56.25        27.02        16.44        18.84 
TCGA-AZ-4614 TCGA-AZ-6607 TCGA-G4-6307 TCGA-RU-A8FL TCGA-AG-3893 TCGA-AG-3902 
        5.65         3.19        55.04        38.70        35.01        32.02 
TCGA-DC-6682 TCGA-DY-A1DG 
       25.05        51.48 

$`4Q GAIN WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        29.98        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        39.45        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.05        37.25        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        5.79        22.42        27.42        26.47         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       60.13        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        24.36        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.95        36.95        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             3.19              0.00 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            56.25            148.01 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           26.035            21.990 
[1] "3.2 - 56.2 (26.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.6"
D8V2, continuous
D8V3, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16   5
  4Q GAIN WILD-TYPE 432 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16    5
  4Q GAIN WILD-TYPE  432  157
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON               16               432
  RECTUM               5               157
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4Q GAIN MUTATED         2        0        0         5         0         0
  4Q GAIN WILD-TYPE     102        1       37       167        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q GAIN MUTATED           0          0          5          2        4
  4Q GAIN WILD-TYPE        24         15         79         53       59
                   vv
clus                STAGE IVA STAGE IVB
  4Q GAIN MUTATED           3         0
  4Q GAIN WILD-TYPE        21         2
D8V4, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  2               102
  STAGE IA                 0                 1
  STAGE II                 0                37
  STAGE IIA                5               167
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                0                24
  STAGE IIIA               0                15
  STAGE IIIB               5                79
  STAGE IIIC               2                53
  STAGE IV                 4                59
  STAGE IVA                3                21
  STAGE IVB                0                 2
[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     0   2  16   3
  4Q GAIN WILD-TYPE  20 103 401  66
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                20
  T2               2               103
  T3              16               401
  T4               3                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"
                   vv
clus                 N0  N1  N2
  4Q GAIN MUTATED     7   7   7
  4Q GAIN WILD-TYPE 339 143 108
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               7               339
  N1               7               143
  N2               7               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    12   7
  4Q GAIN WILD-TYPE 441  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     12    7
  4Q GAIN WILD-TYPE  441   81
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              12               441
  1               7                81
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     7  14
  4Q GAIN WILD-TYPE 282 311
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      7   14
  4Q GAIN WILD-TYPE  282  311
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               7               282
  MALE                14               311
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    19   0
  4Q GAIN WILD-TYPE 463  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     19    0
  4Q GAIN WILD-TYPE  463   29
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               19               463
  YES               0                29
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q GAIN MUTATED                     16                             0
  4Q GAIN WILD-TYPE                  366                            62
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4Q GAIN MUTATED                       5                              0
  4Q GAIN WILD-TYPE                   141                             13
D8V10, multiclass
                                clus
vv                               4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        16               366
  COLON MUCINOUS ADENOCARCINOMA                0                62
  RECTAL ADENOCARCINOMA                        5               141
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  4Q GAIN MUTATED    16   0   2   0
  4Q GAIN WILD-TYPE 430   6  35  29
D8V11, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0              16               430
  R1               0                 6
  R2               2                35
  RX               0                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"
D8V12, continuous
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0  13
  4Q GAIN WILD-TYPE   5 339
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0   13
  4Q GAIN WILD-TYPE    5  339
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              13               339
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    80  23
  5P GAIN WILD-TYPE 386 105
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              103               491 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               23               105 
$`5P GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3844 
       45.60        13.02        19.99        19.00        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3976 TCGA-AZ-6608 TCGA-DM-A285 TCGA-AG-3890 
       24.03        12.99        26.01         1.94         5.88        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-3L-AA1B TCGA-A6-2679 
       25.97        36.03        31.00        21.24        15.62        44.91 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-6650 TCGA-A6-6651 
       37.25        37.02        34.65        32.45        20.61        21.76 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3842 
       12.99        24.00         2.01        47.01         5.98        37.02 
TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3968 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A03J 
        0.99        17.03        21.99        51.98         2.96        40.96 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A8YK 
        5.79        16.44         0.92        33.01         0.20        18.84 
TCGA-AZ-6598 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5860 
       49.41        29.56        12.69        25.02        13.02        32.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 
       15.02        14.04        14.99        13.02        11.01        19.59 
TCGA-D5-6531 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6931 TCGA-DM-A1D8 TCGA-DM-A1DA 
       17.75        14.30        13.41        12.00        12.59         7.50 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6297 
       98.24        95.18        31.96         1.55        47.41        82.39 
TCGA-G4-6307 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL 
       55.04        46.75        74.79        12.79         8.42        38.70 
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 
       37.74        20.02        24.59        86.63        65.98        36.03 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3609 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-4001 
       46.03        34.03        19.99         1.02        17.95        36.03 
TCGA-AG-4007 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 
        1.02         1.94        38.96        41.00        38.04        43.20 
TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6683 TCGA-EF-5831 
       27.55        31.00        31.00        10.98        25.05         4.18 
TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6814 
       16.31        11.51         9.96        28.57        32.19        37.18 
TCGA-F5-6863 
       11.87 

$`5P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       34.03         0.99        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3870 
        0.92        36.00        85.05        19.04        31.07        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        50.99        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 
       75.95       106.75       100.01        49.08        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       17.03        15.95        51.98        18.28        55.76        26.43 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.76        43.43        42.90        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       16.57        37.05        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.08        25.18        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.05        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       33.01        26.01        20.98        34.03         2.01        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F 
        1.02        33.04         1.02        26.01        37.02        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       18.05        12.16        83.24        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       26.47         0.46        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       65.00        62.79        88.21         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 
       37.02        26.04         8.02        27.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       17.03        12.00        29.03        16.04        21.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
      117.07         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 
        0.53        35.31       133.18         8.35        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       65.85        53.62        44.68        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        26.43        26.04        13.78        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       29.46        32.98        31.30        21.90        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N 
       37.97        34.49        29.98        16.83        24.36        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       19.99        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        28.04        14.04 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
       37.02         9.07         1.02         1.02        49.97        61.97 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       38.56         2.50        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
       21.01        25.05        26.04        12.00        13.97        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46        11.97         8.45        49.51        42.35         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        38.14        12.46        47.08 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              0.2               0.0 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            98.24            148.01 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            21.24             22.06 
[1] "0.2 - 98.2 (21.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D9V2, continuous
D9V3, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    69  37
  5P GAIN WILD-TYPE 379 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     69   37
  5P GAIN WILD-TYPE  379  125
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON               69               379
  RECTUM              37               125
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5P GAIN MUTATED        14        0        4        26         1         1
  5P GAIN WILD-TYPE      90        1       33       146        11         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P GAIN MUTATED           3          5         13         16       13
  5P GAIN WILD-TYPE        21         10         71         39       50
                   vv
clus                STAGE IVA STAGE IVB
  5P GAIN MUTATED           6         1
  5P GAIN WILD-TYPE        18         1
D9V4, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 14                90
  STAGE IA                 0                 1
  STAGE II                 4                33
  STAGE IIA               26               146
  STAGE IIB                1                11
  STAGE IIC                1                 1
  STAGE III                3                21
  STAGE IIIA               5                10
  STAGE IIIB              13                71
  STAGE IIIC              16                39
  STAGE IV                13                50
  STAGE IVA                6                18
  STAGE IVB                1                 1
[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     2  20  71  13
  5P GAIN WILD-TYPE  18  85 346  56
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               2                18
  T2              20                85
  T3              71               346
  T4              13                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"
                   vv
clus                 N0  N1  N2
  5P GAIN MUTATED    47  32  26
  5P GAIN WILD-TYPE 299 118  89
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              47               299
  N1              32               118
  N2              26                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    72  19
  5P GAIN WILD-TYPE 381  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     72   19
  5P GAIN WILD-TYPE  381   69
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              72               381
  1              19                69
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    49  57
  5P GAIN WILD-TYPE 240 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     49   57
  5P GAIN WILD-TYPE  240  268
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              49               240
  MALE                57               268
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    80   8
  5P GAIN WILD-TYPE 402  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     80    8
  5P GAIN WILD-TYPE  402   21
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               80               402
  YES               8                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P GAIN MUTATED                     61                             8
  5P GAIN WILD-TYPE                  321                            54
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5P GAIN MUTATED                      37                              0
  5P GAIN WILD-TYPE                   109                             13
D9V10, multiclass
                                clus
vv                               5P GAIN MUTATED 5P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        61               321
  COLON MUCINOUS ADENOCARCINOMA                8                54
  RECTAL ADENOCARCINOMA                       37               109
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  5P GAIN MUTATED    79   1   9   2
  5P GAIN WILD-TYPE 367   5  28  27
D9V11, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              79               367
  R1               1                 5
  R2               9                28
  RX               2                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"
D9V12, continuous
D9V13, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     0  63
  5P GAIN WILD-TYPE   5 289
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      0   63
  5P GAIN WILD-TYPE    5  289
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              63               289
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED    51  12
  5Q GAIN WILD-TYPE 415 116
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               63               531 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12               116 
$`5Q GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3976 
       45.60        19.00        19.04        14.93        12.99        26.01 
TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A01N TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2685 
       17.03        25.97        31.00        15.62        44.91        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-6650 TCGA-AA-3666 TCGA-AA-3681 TCGA-AA-3842 
       34.65        32.45        20.61         2.01         5.98        37.02 
TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6899 
        0.99        17.03        51.98         2.96        40.96         5.79 
TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CM-4752 
       16.44        33.01        49.41        29.56        11.74        13.02 
TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6167 TCGA-CM-6678 TCGA-D5-5539 
       32.02        15.02        14.04        14.99        11.01        19.59 
TCGA-D5-6531 TCGA-DM-A1D8 TCGA-DM-A28M TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC 
       17.75        12.59        95.18        46.75        74.79        12.79 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3609 
       20.02        24.59        65.98        36.03        34.03        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-4007 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 
        1.02        17.95         1.02        41.00        38.04        43.20 
TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6683 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 
       27.55        31.00        25.05        16.31        11.51        11.97 
TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 
        9.96        32.19        37.18 

$`5Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       19.99         6.05         0.92        36.00        85.05        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        24.00         2.01        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       26.43         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 
       35.11        16.57        37.05        37.02        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.97        54.02        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 
       39.98        18.05        12.16        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       88.21         6.77        12.10         5.23         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 
       12.00        29.03        16.04        21.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       55.92        20.19        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.04        13.78        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.04        19.99        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       38.56         2.50        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       21.01        25.05        26.04        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
        8.61        10.78        13.64        17.46         8.45        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       42.35        28.57         0.39        36.49        19.66        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.99              0.00 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            95.18            148.01 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            20.02             22.03 
[1] "1.0 - 95.2 (20.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    40  25
  5Q GAIN WILD-TYPE 408 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     40   25
  5Q GAIN WILD-TYPE  408  137
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON               40               408
  RECTUM              25               137
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5Q GAIN MUTATED         9        0        3        16         1         1
  5Q GAIN WILD-TYPE      95        1       34       156        11         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q GAIN MUTATED           2          4          6          8        9
  5Q GAIN WILD-TYPE        22         11         78         47       54
                   vv
clus                STAGE IVA STAGE IVB
  5Q GAIN MUTATED           2         1
  5Q GAIN WILD-TYPE        22         1
D10V4, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  9                95
  STAGE IA                 0                 1
  STAGE II                 3                34
  STAGE IIA               16               156
  STAGE IIB                1                11
  STAGE IIC                1                 1
  STAGE III                2                22
  STAGE IIIA               4                11
  STAGE IIIB               6                78
  STAGE IIIC               8                47
  STAGE IV                 9                54
  STAGE IVA                2                22
  STAGE IVB                1                 1
[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     1  13  43   8
  5Q GAIN WILD-TYPE  19  92 374  61
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               1                19
  T2              13                92
  T3              43               374
  T4               8                61
[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
  5Q GAIN MUTATED    31  20  13
  5Q GAIN WILD-TYPE 315 130 102
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0              31               315
  N1              20               130
  N2              13               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    46  11
  5Q GAIN WILD-TYPE 407  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     46   11
  5Q GAIN WILD-TYPE  407   77
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              46               407
  1              11                77
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    30  35
  5Q GAIN WILD-TYPE 259 290
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     30   35
  5Q GAIN WILD-TYPE  259  290
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              30               259
  MALE                35               290
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    49   6
  5Q GAIN WILD-TYPE 433  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     49    6
  5Q GAIN WILD-TYPE  433   23
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               49               433
  YES               6                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q GAIN MUTATED                     36                             4
  5Q GAIN WILD-TYPE                  346                            58
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5Q GAIN MUTATED                      25                              0
  5Q GAIN WILD-TYPE                   121                             13
D10V10, multiclass
                                clus
vv                               5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        36               346
  COLON MUCINOUS ADENOCARCINOMA                4                58
  RECTAL ADENOCARCINOMA                       25               121
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  5Q GAIN MUTATED    48   0   6   1
  5Q GAIN WILD-TYPE 398   6  31  28
D10V11, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              48               398
  R1               0                 6
  R2               6                31
  RX               1                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"
D10V12, continuous
D10V13, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  35
  5Q GAIN WILD-TYPE   5 317
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   35
  5Q GAIN WILD-TYPE    5  317
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              35               317
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    95  21
  6P GAIN WILD-TYPE 371 107
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              116               478 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               107 
$`6P GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3697 TCGA-G4-6310 TCGA-G4-6625 TCGA-AF-3913 
       13.02        19.99        85.05        63.62        91.79        10.39 
TCGA-AG-3612 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 
       19.99        36.03        31.00        21.24        18.28        26.43 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       43.43        42.90        44.91        36.53        32.45        30.44 
TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-A56B TCGA-AA-3532 TCGA-AA-3534 
       29.19        25.08        20.61        56.25        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 
       12.99        24.00        15.02        37.05        10.06        35.05 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 
       37.02        17.03        27.02         2.01        20.98        21.99 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A02E 
       27.02         7.96        34.03        31.00        35.01         2.96 
TCGA-AA-A03J TCGA-AD-6901 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L 
       40.96        22.42        14.50         0.95         0.20        17.26 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 
       22.36        65.00        14.30        15.62        21.99         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        30.08        32.02         5.03        15.02 
TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 
       13.02        15.02        19.59        55.92        25.48        17.13 
TCGA-D5-6539 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A288 
       12.49         9.04        13.41        11.38         7.50        14.04 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
      117.07        98.24        95.18         8.61        31.96        35.74 
TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC 
        1.55        82.39        39.42        46.75        10.98        12.79 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 
       29.46        21.90        38.70        46.92        43.04        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3725 TCGA-AG-3728 
       29.98        24.36        65.98        46.03        20.98        29.98 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 
        1.02         1.02        14.04         1.02        46.03         9.07 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       27.55         6.05        47.44        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 
       51.98       129.27        20.55        15.85        17.69        49.51 
TCGA-F5-6702 TCGA-F5-6810 
       28.57         0.39 

$`6P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 
       79.69        17.85         8.02        13.94        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A023 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T 
       25.97        15.95        51.98        55.76        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       43.76        42.28        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       37.02        34.65        32.75        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13         8.38        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 
       38.99         1.02         9.07        19.07         0.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       50.04        47.05        47.01        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       38.99        36.95         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       17.03        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
       16.44         0.46         0.92        27.09        16.31        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 
       58.39         1.41         5.65        32.94         5.13        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.59        12.59        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      148.01        85.45        70.16        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5863 
       26.04        27.02        22.03        22.98        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        54.61        56.09        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       18.25        43.27        15.12        17.85         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        26.47        81.37       119.93        35.97        60.79 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18         8.35        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        85.48        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       26.04        13.78        74.79        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        15.65        16.80        42.77        32.98         8.42 
TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       31.30        60.13        11.90        70.03        39.48        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       13.55        37.97        34.49        16.83        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       19.99        28.04        36.03         3.98        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        23.01        37.02         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 
        2.50        43.20        26.43        19.46        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       44.78        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       26.04        13.97        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        12.62       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         3.48         4.18        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        42.35        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
              0.2               0.0 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           129.27            148.01 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           24.720            21.405 
[1] "0.2 - 129.3 (24.7)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.3"
D11V2, continuous
D11V3, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    83  37
  6P GAIN WILD-TYPE 365 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     83   37
  6P GAIN WILD-TYPE  365  125
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON               83               365
  RECTUM              37               125
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6P GAIN MUTATED        18        0        4        23         2         0
  6P GAIN WILD-TYPE      86        1       33       149        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P GAIN MUTATED           4          5         20         16       14
  6P GAIN WILD-TYPE        20         10         64         39       49
                   vv
clus                STAGE IVA STAGE IVB
  6P GAIN MUTATED           9         1
  6P GAIN WILD-TYPE        15         1
D11V4, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 18                86
  STAGE IA                 0                 1
  STAGE II                 4                33
  STAGE IIA               23               149
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                4                20
  STAGE IIIA               5                10
  STAGE IIIB              20                64
  STAGE IIIC              16                39
  STAGE IV                14                49
  STAGE IVA                9                15
  STAGE IVB                1                 1
[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     6  18  83  14
  6P GAIN WILD-TYPE  14  87 334  55
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               6                14
  T2              18                87
  T3              83               334
  T4              14                55
[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
  6P GAIN MUTATED    53  30  37
  6P GAIN WILD-TYPE 293 120  78
D11V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              53               293
  N1              30               120
  N2              37                78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    81  23
  6P GAIN WILD-TYPE 372  65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     81   23
  6P GAIN WILD-TYPE  372   65
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              81               372
  1              23                65
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    52  70
  6P GAIN WILD-TYPE 237 255
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     52   70
  6P GAIN WILD-TYPE  237  255
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              52               237
  MALE                70               255
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    90   9
  6P GAIN WILD-TYPE 392  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     90    9
  6P GAIN WILD-TYPE  392   20
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               90               392
  YES               9                20
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P GAIN MUTATED                     73                            10
  6P GAIN WILD-TYPE                  309                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6P GAIN MUTATED                      36                              1
  6P GAIN WILD-TYPE                   110                             12
D11V10, multiclass
                                clus
vv                               6P GAIN MUTATED 6P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        73               309
  COLON MUCINOUS ADENOCARCINOMA               10                52
  RECTAL ADENOCARCINOMA                       36               110
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  6P GAIN MUTATED    90   0  10   4
  6P GAIN WILD-TYPE 356   6  27  25
D11V11, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              90               356
  R1               0                 6
  R2              10                27
  RX               4                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"
D11V12, continuous
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0  75
  6P GAIN WILD-TYPE   5 277
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   75
  6P GAIN WILD-TYPE    5  277
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              75               277
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    87  19
  6Q GAIN WILD-TYPE 379 109
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              106               488 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               19               109 
$`6Q GAIN MUTATED`
TCGA-AA-3562 TCGA-AA-3697 TCGA-G4-6310 TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3612 
       19.99        85.05        63.62        91.79        10.39        19.99 
TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
       36.03        31.00        21.24        43.43        42.90        44.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6650 TCGA-AA-3532 TCGA-AA-3534 
       30.44        29.19        25.08        20.61        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 
       26.01        12.99        24.00        15.02        37.05        10.06 
TCGA-AA-3812 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 
       35.05        37.02        17.03        27.02         2.01        20.98 
TCGA-AA-A00F TCGA-AA-A01I TCGA-AA-A01R TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 
       34.03        31.00        35.01         2.96        40.96        22.42 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 
       14.50         0.95         0.20        17.26         5.65        22.36 
TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 
       65.00        14.30        15.62        21.99         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 
       29.06        32.02         5.03        15.02        13.02        15.02 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6926 
       19.59        55.92        25.48        17.13        12.49         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K 
       13.41        11.38         7.50        14.04       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-G4-6297 TCGA-G4-6299 
       95.18         8.61        31.96        35.74        82.39        74.56 
TCGA-G4-6311 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL 
       39.42        10.98        12.79        29.46        21.90        38.70 
TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3592 
       46.92        37.74        29.98        24.36        65.98        34.03 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4021 
       20.98        29.98         1.02         1.02         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A016 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 
       46.03         9.07        27.55         6.05        47.44        31.00 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 
       12.00        31.00        51.98        51.48        20.55        15.85 
TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       17.69        49.51        28.57         0.39 

$`6Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 
       19.99         6.05         0.92        19.00        36.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 
       26.17        79.69        17.85         8.02        13.94        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       17.03        25.97        15.95        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2680 
       39.45        43.76        46.65        43.76        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       36.53        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3544 
       38.99         1.02         9.07        19.07         0.00        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        47.01        11.01         5.98         5.03        26.99 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       36.95         0.00        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 
       18.05        31.00        24.00        33.01        26.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       39.98        18.05        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       27.42        26.47        16.44         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X 
       16.31        33.01        21.44        17.82        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5916 
       17.56       148.01        85.45        70.16        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       25.02        26.04        27.02        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       29.03        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 
       10.06        12.03        45.40        54.61        56.09        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       35.97        60.79        11.11        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6302 
        0.53        47.41        35.31       133.18         8.35        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       18.18        19.33        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H 
       42.77        32.98         8.42        31.30        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       34.49        16.83        20.02        24.59        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 
       24.00         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       36.03        14.04        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       26.43        19.46        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 
       78.12         7.17        21.01        25.05        26.04        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        3.48         4.18        19.96        20.91        17.00        18.28 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       13.64        17.46        11.97         8.45         9.96        42.35 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
              0.2               0.0 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           117.07            148.01 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           24.180            21.875 
[1] "0.2 - 117.1 (24.2)" "0.0 - 148.0 (21.9)"
[1] "hr=" "1.3"
D12V2, continuous
D12V3, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    76  33
  6Q GAIN WILD-TYPE 372 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     76   33
  6Q GAIN WILD-TYPE  372  129
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON               76               372
  RECTUM              33               129
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6Q GAIN MUTATED        16        0        4        20         2         0
  6Q GAIN WILD-TYPE      88        1       33       152        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q GAIN MUTATED           4          4         17         14       13
  6Q GAIN WILD-TYPE        20         11         67         41       50
                   vv
clus                STAGE IVA STAGE IVB
  6Q GAIN MUTATED          11         1
  6Q GAIN WILD-TYPE        13         1
D12V4, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 16                88
  STAGE IA                 0                 1
  STAGE II                 4                33
  STAGE IIA               20               152
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                4                20
  STAGE IIIA               4                11
  STAGE IIIB              17                67
  STAGE IIIC              14                41
  STAGE IV                13                50
  STAGE IVA               11                13
  STAGE IVB                1                 1
[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     4  17  74  15
  6Q GAIN WILD-TYPE  16  88 343  54
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               4                16
  T2              17                88
  T3              74               343
  T4              15                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"
                   vv
clus                 N0  N1  N2
  6Q GAIN MUTATED    48  28  33
  6Q GAIN WILD-TYPE 298 122  82
D12V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              48               298
  N1              28               122
  N2              33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    71  24
  6Q GAIN WILD-TYPE 382  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     71   24
  6Q GAIN WILD-TYPE  382   64
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              71               382
  1              24                64
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    49  62
  6Q GAIN WILD-TYPE 240 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     49   62
  6Q GAIN WILD-TYPE  240  263
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              49               240
  MALE                62               263
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    82   8
  6Q GAIN WILD-TYPE 400  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     82    8
  6Q GAIN WILD-TYPE  400   21
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO               82               400
  YES               8                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q GAIN MUTATED                     67                             9
  6Q GAIN WILD-TYPE                  315                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6Q GAIN MUTATED                      33                              0
  6Q GAIN WILD-TYPE                   113                             13
D12V10, multiclass
                                clus
vv                               6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        67               315
  COLON MUCINOUS ADENOCARCINOMA                9                53
  RECTAL ADENOCARCINOMA                       33               113
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  6Q GAIN MUTATED    80   0  10   4
  6Q GAIN WILD-TYPE 366   6  27  25
D12V11, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              80               366
  R1               0                 6
  R2              10                27
  RX               4                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"
D12V12, continuous
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  68
  6Q GAIN WILD-TYPE   5 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   68
  6Q GAIN WILD-TYPE    5  284
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              68               284
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   262  74
  7P GAIN WILD-TYPE 204  54
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              336               258 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               74                54 
$`7P GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3524 
       45.60        13.94        24.16         1.02        58.03        36.03 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       13.02        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 
       85.05        14.93        24.03        29.98        24.00        26.01 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6608 
       38.04        21.37        15.52        75.95       106.75         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
        5.88        28.21        23.51        63.62        35.93        91.79 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       17.85        10.39        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 
       25.97        15.95        36.03        31.00        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       55.76        26.43        15.62         4.80        12.66         1.61 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2685 
       43.76        43.76        43.43        44.91        35.11        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       30.44        29.19        29.16        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 
       25.18        20.61        24.69        23.87        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       24.92        56.25         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3529 
       37.05        35.01         6.97        38.99         9.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        33.99        24.00 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 
       61.02        78.08        54.02         2.01        14.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 
        0.99        36.95        37.02         0.00        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       31.07        17.03        27.02        18.05        31.00        24.00 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3994 
       20.98        21.99        16.08        34.06        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C 
       13.94        19.00        34.03        42.02        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
       32.02        33.04        26.01        51.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.92        39.98        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        26.47        16.44        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
       33.01         0.20        17.82        17.26        18.84       109.28 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       22.36        65.00        62.79        88.21        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       29.56         5.23         3.19        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 
       12.59        14.30        17.56       148.01        85.45        21.99 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        25.02         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       17.03        15.02        14.04        29.03        16.04        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       12.99        15.02        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 
       10.06        19.59        55.92        17.75        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       15.12         4.80        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD 
       12.43        14.30         9.04        13.41        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       38.20        92.75        49.91        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
      131.51         7.76        14.04        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6854 
        8.61        31.96        35.74         1.55        33.67         0.53 
TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       47.41       133.18        82.39        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 
       55.04        39.42        61.91        36.00        26.43        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        74.79        18.18         9.93        15.65        12.79 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
        8.42        21.90        38.70        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       17.23        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 
       86.63        65.98         7.07        36.03        24.00        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       19.99        20.98        29.98         0.99         0.99        19.99 
TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       17.95        35.01         1.02        48.03        19.99        36.03 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G 
        1.02        46.03         9.07         1.02         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       38.04        38.56        43.20        27.55        26.43         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       31.00        12.00        31.00        51.98        10.98        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
       24.13         3.48         4.18        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.31        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       32.19        36.49        19.66        11.87        12.46        47.08 

$`7P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       24.33        14.53        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3672 
       19.07        34.03         0.99        17.95        23.01         0.92 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       19.04        19.04        31.07        12.99         2.01        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 
       24.00        19.07        21.99        39.06        25.08        10.88 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
      100.01        49.08        22.09        35.80        26.17        79.69 
TCGA-AG-3580 TCGA-AG-A023 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 
        8.02        51.98         9.53        39.45        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5662 
       42.28        16.57        37.05        32.75        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 
       22.09        22.06        32.71        27.09         8.38        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A567 TCGA-AA-3492 TCGA-AA-3510 
       24.39        20.12        19.66        61.84         3.02        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3549 TCGA-AA-3555 
        1.02         1.02        19.07        29.00        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       20.98        13.94         6.97        50.04        47.05        47.01 
TCGA-AA-3710 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       26.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
        0.00        17.03        10.06         0.00        33.07        36.03 
TCGA-AA-3864 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
       53.00         2.01        33.01        26.01        34.03         2.01 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       13.05        25.02         7.96        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       34.98        10.98        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A02E 
        1.02        35.01         1.02         1.02        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       39.98        22.03        41.00        18.05        12.16        83.24 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X 
        0.46         0.92        27.09        21.44        17.85        19.33 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 
       58.39         1.41         5.65        32.94         5.13         6.77 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       11.74        12.69        12.59        12.20        12.76        10.06 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 TCGA-CM-5861 
      124.27        23.05        37.02        26.04        30.08        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        21.99        13.02        14.04        12.95        13.05 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        54.61        56.09        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       18.25        17.85        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 
       11.64        13.35        12.00        11.38       119.70       130.65 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
       13.32       140.38       135.65       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 
      119.93        60.79        98.24        11.11        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 
       47.87        34.42        41.42        43.04        13.25        35.31 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6322 TCGA-NH-A50U 
        8.35        67.30        53.62        85.48        26.04        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        19.33        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       31.30        60.13        11.90        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       34.49        24.59        11.84        36.03        12.00        32.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3726 
       20.05         1.02        34.03         2.01        50.04         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 
        0.99        37.02        32.98        19.04         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       13.02        14.01        25.02        32.02        28.04        14.04 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        3.98        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 
        1.02        49.97        61.97        41.00         2.50        19.46 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 
       33.17        13.78        44.78        26.04        13.97        44.02 
TCGA-DC-6681 TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       25.97        51.48        32.61        20.55        19.96        17.00 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       16.41         8.61        17.46        49.51        37.18        38.14 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 0 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           148.01            140.38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           22.195            21.990 
[1] "0.0 - 148.0 (22.2)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.1"
D13V2, continuous
D13V3, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   244 102
  7P GAIN WILD-TYPE 204  60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    244  102
  7P GAIN WILD-TYPE  204   60
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON              244               204
  RECTUM             102                60
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7P GAIN MUTATED        57        1       19        72         3         1
  7P GAIN WILD-TYPE      47        0       18       100         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P GAIN MUTATED          13         11         60         37       42
  7P GAIN WILD-TYPE        11          4         24         18       21
                   vv
clus                STAGE IVA STAGE IVB
  7P GAIN MUTATED          16         1
  7P GAIN WILD-TYPE         8         1
D13V4, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 57                47
  STAGE IA                 1                 0
  STAGE II                19                18
  STAGE IIA               72               100
  STAGE IIB                3                 9
  STAGE IIC                1                 1
  STAGE III               13                11
  STAGE IIIA              11                 4
  STAGE IIIB              60                24
  STAGE IIIC              37                18
  STAGE IV                42                21
  STAGE IVA               16                 8
  STAGE IVB                1                 1
[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    13  60 234  38
  7P GAIN WILD-TYPE   7  45 183  31
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1              13                 7
  T2              60                45
  T3             234               183
  T4              38                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
  7P GAIN MUTATED   167 103  75
  7P GAIN WILD-TYPE 179  47  40
D13V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             167               179
  N1             103                47
  N2              75                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   242  59
  7P GAIN WILD-TYPE 211  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    242   59
  7P GAIN WILD-TYPE  211   29
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             242               211
  1              59                29
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   160 188
  7P GAIN WILD-TYPE 129 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    160  188
  7P GAIN WILD-TYPE  129  137
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE             160               129
  MALE               188               137
[1] 2 2
[1] FALSE
D13V9, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   272  18
  7P GAIN WILD-TYPE 210  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    272   18
  7P GAIN WILD-TYPE  210   11
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              272               210
  YES              18                11
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7P GAIN MUTATED                    218                            25
  7P GAIN WILD-TYPE                  164                            37
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7P GAIN MUTATED                      98                              3
  7P GAIN WILD-TYPE                    48                             10
D13V10, multiclass
                                clus
vv                               7P GAIN MUTATED 7P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       218               164
  COLON MUCINOUS ADENOCARCINOMA               25                37
  RECTAL ADENOCARCINOMA                       98                48
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  7P GAIN MUTATED   250   5  24  14
  7P GAIN WILD-TYPE 196   1  13  15
D13V11, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0             250               196
  R1               5                 1
  R2              24                13
  RX              14                15
[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, continuous
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED     2 210
  7P GAIN WILD-TYPE   3 142
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2  210
  7P GAIN WILD-TYPE    3  142
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             210               142
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   236  64
  7Q GAIN WILD-TYPE 230  64
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              300               294 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               64                64 
$`7Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3524 
       45.60        13.94        24.16         1.02        58.03        36.03 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 
       13.02        19.99        19.99         6.05        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AD-6888 
       14.93        24.03        29.98        24.00         2.01        15.52 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       75.95       106.75         5.88        23.51        63.62        35.93 
TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       91.79        17.85        10.39        13.94        19.99        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        21.24        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2675 
       26.43        15.62        12.66         1.61        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       44.91        35.11        37.25        37.02        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       31.63        30.44        29.19        29.16        22.52        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       16.24        24.92         9.63         5.03         7.04         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3534 
       37.05        35.01         6.97        38.99         9.07        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3655 
       26.01        12.99        14.01        33.99        24.00        61.02 
TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       78.08         2.01        14.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 
       37.05         5.03        35.05         0.99        36.95        37.02 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3875 
        0.00        32.05         0.99        31.07        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       31.00        24.00        20.98        21.99        16.08        34.06 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       27.02        27.02        13.94        19.00        34.03        42.02 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 
       15.02        15.02        32.02        33.04        26.01        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6890 
        2.01         5.03         0.92        39.98        40.96        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       22.42        27.42        26.47        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31         0.95         0.20        17.82        17.26        18.84 
TCGA-AZ-4308 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
      109.28        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       12.10         5.23         3.19        12.36        12.46        12.39 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 
       14.30        17.56       148.01        85.45        21.99        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       25.02         8.02        27.02        13.02        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       14.04        29.03        16.04        14.99        12.99        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5539 
       11.01        11.08        11.08        11.01        10.06        19.59 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       55.92        17.75        25.48        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       17.13        12.49         7.53        10.13        12.43        14.30 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       13.41        10.26        38.20        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 
       12.59         7.50        44.32       131.51         7.76        14.04 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 
       95.18         8.61        31.96        35.74         1.55        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41       133.18        82.39        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        39.42        61.91        36.00        26.43 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB 
       13.78        46.75        74.79        18.18         9.93        15.65 
TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       12.79         8.42        21.90        38.70        70.03        46.92 
TCGA-AF-2689 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       39.48        29.98        16.83        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3592 
       65.98         7.07        36.03        24.00        46.03        34.03 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 
       12.03         0.99        15.95        19.99        20.98        29.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 
        0.99         0.99        19.99        17.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 
       48.03        19.99        28.04         1.02        46.03         9.07 
TCGA-AG-A01J TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.02        38.96        38.04        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       26.43         6.05        47.44        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       25.05        31.00        12.00        31.00        51.98        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        25.05        12.62        41.36        57.24        24.13 
TCGA-EF-5830 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        3.48        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       16.31        11.51        11.97         9.96        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.39        32.19        19.66        11.87        12.46        47.08 

$`7Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       24.33        14.53        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3672 
       19.07        34.03         0.99        17.95        23.01         0.92 
TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3972 
       19.00        19.04        19.04        31.07        12.99        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       21.37        25.08        10.88       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 
       28.21        22.09        35.80        26.17        79.69         8.02 
TCGA-AG-4008 TCGA-AG-A023 TCGA-G5-6233 TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE 
       17.03        51.98        18.28         4.80         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 
       46.65        43.76        42.90        42.28        16.57        37.05 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       34.65        32.75        36.53        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 
       22.06        32.71        27.09         8.38        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3510 
       20.12        19.66        61.84        56.25         3.02        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3549 
        1.02         1.02        19.07         0.00        29.00        21.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3673 
       29.95        20.98        13.94         6.97        54.02        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 
       47.05        47.01        26.99        10.06        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3930 
        0.00        33.07        36.03        53.00        17.03         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 
       33.01        26.01        34.03         2.01        13.05        25.02 
TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
        7.96        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D 
       27.02         0.99        17.03        14.99        34.98        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02R 
        1.02         1.02        37.02         2.96        39.98        22.03 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AM-5821 
       41.00        18.05        12.16        83.24         5.79         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
       27.09        33.01        21.44        17.85        19.33        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 TCGA-AZ-6603 
        1.41         5.65        32.94         5.13         6.77        29.56 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       11.74        12.69        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       10.06        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5341 
        2.01       124.27        23.05        37.02        26.04        29.06 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 
       30.08        15.02        12.00        21.99        13.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       12.95        13.05        12.03        45.40        54.61        56.09 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 
       20.19        20.42        18.25        17.85        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1HB 
       11.38       119.70        24.43       130.65       140.38       135.65 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
      117.07        98.24        11.11        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 
       34.42        41.42        43.04        13.25        35.31         8.35 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A50V 
       67.30        53.62        85.48        26.04        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       19.33        16.80        42.77        29.46        32.98        31.30 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       60.13        11.90        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       34.49        37.74        24.59        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 
       32.02        20.05         1.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       50.04         6.05         7.99         0.99        37.02        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 
       19.04         1.02        36.95        13.02        14.01        25.02 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       32.02        36.03        14.04         3.98        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        6.02        23.01        37.02         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 
       61.97        41.00         2.50        19.46        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 
       44.78        48.20        26.04        13.97        44.02        25.97 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
      126.44       129.27        51.48        32.61         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       19.96        17.00        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       17.46         8.45        49.51        36.49        37.18        38.14 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 0 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           148.01            140.38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           21.990            22.045 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   223  86
  7Q GAIN WILD-TYPE 225  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    223   86
  7Q GAIN WILD-TYPE  225   76
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON              223               225
  RECTUM              86                76
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7Q GAIN MUTATED        54        1       17        61         3         1
  7Q GAIN WILD-TYPE      50        0       20       111         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q GAIN MUTATED          12          7         56         32       38
  7Q GAIN WILD-TYPE        12          8         28         23       25
                   vv
clus                STAGE IVA STAGE IVB
  7Q GAIN MUTATED          16         1
  7Q GAIN WILD-TYPE         8         1
D14V4, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 54                50
  STAGE IA                 1                 0
  STAGE II                17                20
  STAGE IIA               61               111
  STAGE IIB                3                 9
  STAGE IIC                1                 1
  STAGE III               12                12
  STAGE IIIA               7                 8
  STAGE IIIB              56                28
  STAGE IIIC              32                23
  STAGE IV                38                25
  STAGE IVA               16                 8
  STAGE IVB                1                 1
[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    13  53 208  34
  7Q GAIN WILD-TYPE   7  52 209  35
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1              13                 7
  T2              53                52
  T3             208               209
  T4              34                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
  7Q GAIN MUTATED   151  90  67
  7Q GAIN WILD-TYPE 195  60  48
D14V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             151               195
  N1              90                60
  N2              67                48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   212  55
  7Q GAIN WILD-TYPE 241  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    212   55
  7Q GAIN WILD-TYPE  241   33
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             212               241
  1              55                33
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   143 168
  7Q GAIN WILD-TYPE 146 157
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    143  168
  7Q GAIN WILD-TYPE  146  157
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE             143               146
  MALE               168               157
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   245  14
  7Q GAIN WILD-TYPE 237  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    245   14
  7Q GAIN WILD-TYPE  237   15
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              245               237
  YES              14                15
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q GAIN MUTATED                    198                            23
  7Q GAIN WILD-TYPE                  184                            39
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7Q GAIN MUTATED                      83                              2
  7Q GAIN WILD-TYPE                    63                             11
D14V10, multiclass
                                clus
vv                               7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       198               184
  COLON MUCINOUS ADENOCARCINOMA               23                39
  RECTAL ADENOCARCINOMA                       83                63
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
[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                 R0  R1  R2  RX
  7Q GAIN MUTATED   224   4  23  14
  7Q GAIN WILD-TYPE 222   2  14  15
D14V11, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0             224               222
  R1               4                 2
  R2              23                14
  RX              14                15
[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, continuous
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED     2 185
  7Q GAIN WILD-TYPE   3 167
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      2  185
  7Q GAIN WILD-TYPE    3  167
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO             185               167
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED   125  35
  8P GAIN WILD-TYPE 341  93
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              160               434 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               35                93 
$`8P GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3524 TCGA-AA-3662 TCGA-AA-3713 
       24.33        13.94        24.16        36.03         6.05        19.04 
TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-A00Z TCGA-G4-6310 TCGA-AG-A01N 
       19.04        29.98        12.99        21.99        63.62        31.00 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 
       15.62        12.66        39.45        37.02        32.45        31.63 
TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3502 
       29.19        32.71        29.16         9.63         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        6.97         1.02        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 
       12.99        14.01        20.98         6.97        14.01        50.04 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3875 
        5.03        10.06        17.03         0.00        31.07        18.05 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D 
       34.03         2.01        18.05         0.99        17.03        10.98 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AD-5900 
       37.02        51.98         2.96         5.03         0.92        12.16 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L 
        5.79        27.42        16.44        27.09        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
       18.84        32.94         5.13        22.36        65.00        88.21 
TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       49.41         5.23         3.19        12.69        12.36        12.46 
TCGA-CA-6715 TCGA-CK-4948 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
       12.59       148.01        51.32         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       25.02         8.02        27.02        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6677 
       17.03        15.02        29.03        14.99        12.99        11.08 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 
       55.92        20.19        17.75        25.48         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6924 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA 
       16.14        14.30        10.26       119.70        38.20         7.50 
TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6569 
       44.32        35.97       117.07        98.24         8.61        35.74 
TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        6.18        43.04         8.35        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB 
       44.68        39.42        46.75        74.79        18.18        15.65 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-A56L 
       29.46        32.98         8.42        70.03        34.49        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3598 TCGA-AG-3881 TCGA-AG-3887 
       36.03        32.02        34.03        50.04        19.04        36.95 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
        1.02        48.03        32.02         1.02         3.98        46.03 
TCGA-AG-A016 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
        9.07        38.04        38.56        43.20        27.55         6.05 
TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6682 TCGA-DY-A1DC 
       13.78        47.44         7.17        31.00        25.05        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6883 
       57.24        24.13         3.48        17.00        16.31        11.51 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6572 
       49.51         0.39        11.87        47.08 

$`8P GAIN WILD-TYPE`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       45.60        14.53         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99        19.99         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3950 
       36.00        85.05        14.93        31.07        24.03        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
      106.75       100.01         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       23.51        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 
       17.03        17.03        25.97        15.95        36.03        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       21.24        18.28        55.76        26.43         4.80         1.61 
TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        9.53        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5661 
       34.65        32.75        36.53        32.91        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        22.06        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84        56.25         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 
       37.05        63.98        38.99         1.02         9.07         0.00 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        24.00        29.95        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       78.08        54.02         2.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98        37.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
       37.02         0.00        10.06         0.00        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 
       32.05         0.99        53.00        17.03        27.02        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3968 
        2.01        24.00        33.01        26.01        20.98        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 
       18.05         4.01        27.02        42.02        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       26.01        39.98         2.01        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 
       18.05        40.96        83.24        24.53        22.42        26.47 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
        0.20        17.82        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
        1.41         5.65        62.79         6.77        12.10        29.56 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       11.74        12.39        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5914 
       14.30        17.56        85.45        70.16        15.62        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4752 
       21.14        82.95       124.27        23.05        26.04        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       12.00        14.04        16.04        21.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.42        18.25        43.27        15.12        17.85        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
      140.38       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 
       26.47        81.37       119.93        60.79        95.18        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       11.11        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       82.39        74.56        55.04        85.48        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.43        26.04        13.78        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D 
        9.93        12.79        16.80        42.77        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       38.70        60.13        11.90        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 
       24.36        20.02        24.59        86.63        11.84        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03        34.03         2.01        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3909 
       17.95        13.02        35.01        14.01        25.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       38.96        61.97        41.00         2.50        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       33.17        44.78        48.20        78.12        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       26.04        31.00        12.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       44.02        25.97        25.05        12.62       126.44       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         4.18        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       42.35        28.57        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6864 
       38.14        12.46 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 0 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           148.01            140.38 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           20.585            22.075 
[1] "0.0 - 148.0 (20.6)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1.1"
D15V2, continuous
D15V3, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   130  39
  8P GAIN WILD-TYPE 318 123
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    130   39
  8P GAIN WILD-TYPE  318  123
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON              130               318
  RECTUM              39               123
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8P GAIN MUTATED        26        0       15        48         3         2
  8P GAIN WILD-TYPE      78        1       22       124         9         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P GAIN MUTATED           4          1         22         16       19
  8P GAIN WILD-TYPE        20         14         62         39       44
                   vv
clus                STAGE IVA STAGE IVB
  8P GAIN MUTATED           6         0
  8P GAIN WILD-TYPE        18         2
D15V4, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 26                78
  STAGE IA                 0                 1
  STAGE II                15                22
  STAGE IIA               48               124
  STAGE IIB                3                 9
  STAGE IIC                2                 0
  STAGE III                4                20
  STAGE IIIA               1                14
  STAGE IIIB              22                62
  STAGE IIIC              16                39
  STAGE IV                19                44
  STAGE IVA                6                18
  STAGE IVB                0                 2
[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     4  25 121  17
  8P GAIN WILD-TYPE  16  80 296  52
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               4                16
  T2              25                80
  T3             121               296
  T4              17                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"
                   vv
clus                 N0  N1  N2
  8P GAIN MUTATED   102  32  32
  8P GAIN WILD-TYPE 244 118  83
D15V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0             102               244
  N1              32               118
  N2              32                83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   119  26
  8P GAIN WILD-TYPE 334  62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    119   26
  8P GAIN WILD-TYPE  334   62
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0             119               334
  1              26                62
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    80  89
  8P GAIN WILD-TYPE 209 236
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     80   89
  8P GAIN WILD-TYPE  209  236
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              80               209
  MALE                89               236
[1] 2 2
[1] FALSE
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED   126   8
  8P GAIN WILD-TYPE 356  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED    126    8
  8P GAIN WILD-TYPE  356   21
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO              126               356
  YES               8                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P GAIN MUTATED                    115                            14
  8P GAIN WILD-TYPE                  267                            48
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8P GAIN MUTATED                      35                              3
  8P GAIN WILD-TYPE                   111                             10
D15V10, multiclass
                                clus
vv                               8P GAIN MUTATED 8P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       115               267
  COLON MUCINOUS ADENOCARCINOMA               14                48
  RECTAL ADENOCARCINOMA                       35               111
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  8P GAIN MUTATED   114   0  13  12
  8P GAIN WILD-TYPE 332   6  24  17
D15V11, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0             114               332
  R1               0                 6
  R2              13                24
  RX              12                17
[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, continuous
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1 100
  8P GAIN WILD-TYPE   4 252
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1  100
  8P GAIN WILD-TYPE    4  252
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO             100               252
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED   230  72
  8Q GAIN WILD-TYPE 236  56
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              302               292 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               72                56 
$`8Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3524 
       24.33        45.60        13.94        24.16         1.02        36.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3713 
       13.02        23.01        19.99         6.05        36.00        19.04 
TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3976 TCGA-AA-3979 
       19.04        24.03        29.98        12.99        26.01        24.00 
TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 
       21.99        15.52       106.75         5.88        23.51        63.62 
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N 
       10.39        19.99        17.03        25.97        15.95        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       51.98        21.24        18.28        55.76        26.43        15.62 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-2680 
       12.66         1.61         9.53        39.45        43.43        35.11 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       16.57        37.25        37.02        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       31.63        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        20.61        24.69        23.87 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 
        9.63         5.03         1.02        37.05        35.01         6.97 
TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3660 
       12.99        14.01        33.99        24.00        20.98        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 
        5.98        37.05         5.03        10.06        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       17.03         0.00         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
       18.05         2.01        34.03         2.01        16.08        34.06 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A01D 
       13.94        19.00        18.05         0.99        17.03        10.98 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       12.00        31.00         1.02        37.02        51.98         2.96 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 
        5.03         0.92        41.00        12.16         5.79        27.42 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L 
       16.44         0.92        27.09        16.31        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       18.84       109.28        32.94         5.13        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6718 
        3.19        12.69        12.36        12.46        12.59        10.06 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
       14.30       148.01        15.62        51.32         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       17.03        15.02        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       13.02        11.08        54.61        56.09        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       17.75        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.04        13.41        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28G 
      130.65       140.38         7.50        44.32        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24         8.61        31.96        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 
        6.18        34.42        43.04         8.35        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 
       65.85        53.62        44.68        55.04        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       26.43        46.75        74.79        18.18        10.98         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       15.65        16.80        29.46        32.98         8.42        38.70 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 
       34.49        37.74        20.02        24.59        65.98        36.03 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       32.02        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 
       34.03        50.04         6.05         7.99        32.98        19.04 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       36.95         1.02        48.03        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        1.02         3.98        46.03        37.02         9.07         1.02 
TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.04        38.56         2.50        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        13.78        47.44        48.20        78.12         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       31.00        13.97        31.00        10.98        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         3.48 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.00        16.34        16.31        11.51        10.78        13.64 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
        9.96        49.51        28.57         0.39        32.19        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`8Q GAIN WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       14.53        58.03        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 
       19.07        34.03         0.99        17.95        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 
       19.00        85.05        14.93        31.07        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       50.99        19.07        38.04        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 
       10.88        75.95       100.01         1.94        49.08        28.21 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A015 TCGA-4N-A93T 
       17.85         8.02        13.94        17.03        36.03         4.80 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       43.76        46.65        43.76        42.90        42.28        44.91 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       37.05        34.65        32.75        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
       22.06        22.52         8.38        21.76        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        7.04         3.02        63.98        38.99         1.02         9.07 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3675 
       21.01        29.95        13.94        61.02         2.01        47.05 
TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       11.01        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       17.98        15.95        38.99         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 
       33.07        36.03        32.05        53.00        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 
       33.01        26.01        20.98        21.99        13.05        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
       27.02         7.96        27.02        38.04        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 
       18.05         4.01        27.02        42.02        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        15.02        32.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02H 
       35.01        33.04         1.02        26.01        39.98         2.01 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 
       22.03        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
       22.42        26.47         0.46        14.50         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        17.82        17.85        19.33        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        5.65        62.79         6.77        12.39        12.59        12.20 
TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 
       12.76        17.56        85.45        70.16        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5860 
       82.95       124.27        23.05        26.04        22.03        32.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       12.00        14.04        16.04        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 
       45.40        19.59        20.42        18.25        17.85        12.49 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD 
       12.39         9.44        11.64        13.35        12.00        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        47.87         1.55        41.42        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
       13.25         0.53        47.41        35.31       133.18        82.39 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50V TCGA-NH-A5IV 
       85.48        61.91        26.04        13.78        19.33        19.33 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       12.79        42.77        31.30        21.90        60.13        11.90 
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N 
       37.97        29.98        16.83        24.36        86.63        11.84 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
       12.00         7.07        20.05        34.03         2.01        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99        20.98         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-4001 
       13.02        35.01        14.01        25.02        19.99        36.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A020 TCGA-AG-A025 
       20.98        13.94         6.02        23.01         1.02        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       38.96        61.97        41.00        26.43        19.46        33.17 
TCGA-CI-6622 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6157 
       44.78        21.01        25.05        26.04        12.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 
       44.02        25.97        12.62       129.27        51.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       16.41         8.61        17.46        11.97         8.45        42.35 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       36.49        19.66        37.18        38.14 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 0 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           148.01            139.17 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           22.995            21.945 
[1] "0.0 - 148.0 (23.0)" "0.0 - 139.2 (21.9)"
[1] "hr=" "1.3"
D16V2, continuous
D16V3, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   227  87
  8Q GAIN WILD-TYPE 221  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    227   87
  8Q GAIN WILD-TYPE  221   75
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON              227               221
  RECTUM              87                75
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8Q GAIN MUTATED        45        0       21        84         3         2
  8Q GAIN WILD-TYPE      59        1       16        88         9         0
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q GAIN MUTATED          10         10         42         33       42
  8Q GAIN WILD-TYPE        14          5         42         22       21
                   vv
clus                STAGE IVA STAGE IVB
  8Q GAIN MUTATED          13         0
  8Q GAIN WILD-TYPE        11         2
D16V4, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 45                59
  STAGE IA                 0                 1
  STAGE II                21                16
  STAGE IIA               84                88
  STAGE IIB                3                 9
  STAGE IIC                2                 0
  STAGE III               10                14
  STAGE IIIA              10                 5
  STAGE IIIB              42                42
  STAGE IIIC              33                22
  STAGE IV                42                21
  STAGE IVA               13                11
  STAGE IVB                0                 2
[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     6  51 222  34
  8Q GAIN WILD-TYPE  14  54 195  35
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               6                14
  T2              51                54
  T3             222               195
  T4              34                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
  8Q GAIN MUTATED   169  73  70
  8Q GAIN WILD-TYPE 177  77  45
D16V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0             169               177
  N1              73                77
  N2              70                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   221  55
  8Q GAIN WILD-TYPE 232  33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    221   55
  8Q GAIN WILD-TYPE  232   33
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0             221               232
  1              55                33
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   146 169
  8Q GAIN WILD-TYPE 143 156
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    146  169
  8Q GAIN WILD-TYPE  143  156
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE             146               143
  MALE               169               156
[1] 2 2
[1] FALSE
D16V9, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED   242  16
  8Q GAIN WILD-TYPE 240  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED    242   16
  8Q GAIN WILD-TYPE  240   13
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO              242               240
  YES              16                13
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q GAIN MUTATED                    203                            22
  8Q GAIN WILD-TYPE                  179                            40
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8Q GAIN MUTATED                      81                              4
  8Q GAIN WILD-TYPE                    65                              9
D16V10, multiclass
                                clus
vv                               8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                       203               179
  COLON MUCINOUS ADENOCARCINOMA               22                40
  RECTAL ADENOCARCINOMA                       81                65
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[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                 R0  R1  R2  RX
  8Q GAIN MUTATED   217   3  25  17
  8Q GAIN WILD-TYPE 229   3  12  12
D16V11, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0             217               229
  R1               3                 3
  R2              25                12
  RX              17                12
[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, continuous
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     3 188
  8Q GAIN WILD-TYPE   2 164
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3  188
  8Q GAIN WILD-TYPE    2  164
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             188               164
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    84  36
  9P GAIN WILD-TYPE 382  92
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
              120               474 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               36                92 
$`9P GAIN MUTATED`
TCGA-A6-2682 TCGA-AA-3520 TCGA-AA-3844 TCGA-AA-3976 TCGA-AA-A00Z TCGA-AZ-4313 
       13.94        24.03        14.93        26.01        21.99        75.95 
TCGA-DM-A285 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
        5.88        91.79        17.85        13.94        19.99        17.03 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6641 TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2679 
       51.98        18.28        26.43         1.61        43.76        44.91 
TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-6142 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A56B 
       37.02        31.63        25.08        20.28        16.24        56.25 
TCGA-AA-3488 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3558 
        5.03        29.00        29.00        14.01        33.99        20.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3848 TCGA-AA-3852 
       78.08         6.97         2.01        50.04        10.06         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00Q 
       36.03         0.99        27.02        27.02        13.94        42.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       15.02        10.98        51.98         5.79        22.42        16.44 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5796 
       33.01         0.20        17.26        12.10        29.56        12.39 
TCGA-CK-5914 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       21.99        13.02        22.03         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6539 
       14.04        29.03        14.99        19.59        17.75        12.49 
TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28A 
       11.64        13.41        12.59         7.50        14.04        26.47 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6704 
       98.24        95.18         8.61        31.96         6.18         1.55 
TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QL-A97D 
       13.78        46.75        10.98        12.79        42.77        21.90 
TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-6655 
       60.13        70.03        39.48        17.23        34.49        20.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
       46.03        34.03        34.03         2.01        50.04         0.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3896 TCGA-AG-3902 
       20.98         7.99         0.99        19.04         1.02        32.02 
TCGA-AG-4001 TCGA-AG-A020 TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-4745 
       36.03         1.02        38.04        43.20        27.55        21.01 
TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 
       51.98       129.27         4.18        11.51        10.78         8.45 
TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
        9.96        28.57         0.39        19.66        38.14        12.46 

$`9P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
        2.01        50.99        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94        49.08        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 
       22.09        35.80        26.17        79.69        10.39         8.02 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 
       17.03        25.97        15.95        36.03        31.00        21.24 
TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE 
       55.76        15.62         4.80        12.66         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.76        43.43        42.90        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A566 TCGA-A6-A567 
       24.39        23.87        20.12        19.66        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        9.63         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3553 
       19.07         0.00        26.01        12.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 
       29.95        13.94        61.02        54.02        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       17.03         0.00        33.07        32.05        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00A 
       13.05        34.06        25.02        27.02         7.96        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31         0.95        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       49.41         6.77         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       15.02        15.02        12.00        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       54.61        56.09        55.92        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       14.30         9.04         9.44        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32       140.38        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        7.76       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6805 
      117.07        11.11        35.74        35.74        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T 
       61.91        36.00        26.43        26.04        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33         9.93        15.65        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 
       32.98         8.42        31.30        38.70        11.90        46.92 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       24.36        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
        1.02        34.03        12.03         6.05        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
        0.99        29.98        37.02        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        25.02        19.99        28.04        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       61.97        41.00        38.56         2.50        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        31.00        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        12.62       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         3.48        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       16.41         8.61        13.64        17.46        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6572 
       42.35        32.19        36.49        37.18        11.87        47.08 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                 0 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           129.27            148.01 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           19.625            23.280 
[1] "0.0 - 129.3 (19.6)" "0.0 - 148.0 (23.3)"
[1] "hr=" "1.7"
D17V2, continuous
D17V3, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    82  42
  9P GAIN WILD-TYPE 366 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     82   42
  9P GAIN WILD-TYPE  366  120
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON               82               366
  RECTUM              42               120
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9P GAIN MUTATED        15        1        7        32         3         1
  9P GAIN WILD-TYPE      89        0       30       140         9         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P GAIN MUTATED           3          6         12         17       12
  9P GAIN WILD-TYPE        21          9         72         38       51
                   vv
clus                STAGE IVA STAGE IVB
  9P GAIN MUTATED           6         1
  9P GAIN WILD-TYPE        18         1
D17V4, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 15                89
  STAGE IA                 1                 0
  STAGE II                 7                30
  STAGE IIA               32               140
  STAGE IIB                3                 9
  STAGE IIC                1                 1
  STAGE III                3                21
  STAGE IIIA               6                 9
  STAGE IIIB              12                72
  STAGE IIIC              17                38
  STAGE IV                12                51
  STAGE IVA                6                18
  STAGE IVB                1                 1
[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     3  17  85  17
  9P GAIN WILD-TYPE  17  88 332  52
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               3                17
  T2              17                88
  T3              85               332
  T4              17                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"
                   vv
clus                 N0  N1  N2
  9P GAIN MUTATED    63  31  28
  9P GAIN WILD-TYPE 283 119  87
D17V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              63               283
  N1              31               119
  N2              28                87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    86  19
  9P GAIN WILD-TYPE 367  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     86   19
  9P GAIN WILD-TYPE  367   69
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              86               367
  1              19                69
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    60  64
  9P GAIN WILD-TYPE 229 261
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     60   64
  9P GAIN WILD-TYPE  229  261
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              60               229
  MALE                64               261
[1] 2 2
[1] FALSE
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    94   6
  9P GAIN WILD-TYPE 388  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     94    6
  9P GAIN WILD-TYPE  388   23
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               94               388
  YES               6                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P GAIN MUTATED                     64                            18
  9P GAIN WILD-TYPE                  318                            44
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9P GAIN MUTATED                      36                              5
  9P GAIN WILD-TYPE                   110                              8
D17V10, multiclass
                                clus
vv                               9P GAIN MUTATED 9P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        64               318
  COLON MUCINOUS ADENOCARCINOMA               18                44
  RECTAL ADENOCARCINOMA                       36               110
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[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                 R0  R1  R2  RX
  9P GAIN MUTATED    97   0   6   3
  9P GAIN WILD-TYPE 349   6  31  26
D17V11, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              97               349
  R1               0                 6
  R2               6                31
  RX               3                26
[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, continuous
D17V13, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  67
  9P GAIN WILD-TYPE   3 285
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   67
  9P GAIN WILD-TYPE    3  285
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              67               285
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    70  30
  9Q GAIN WILD-TYPE 396  98
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              100               494 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               30                98 
$`9Q GAIN MUTATED`
TCGA-A6-2682 TCGA-AA-3844 TCGA-AA-A00Z TCGA-AZ-4313 TCGA-DM-A285 TCGA-G4-6625 
       13.94        14.93        21.99        75.95         5.88        91.79 
TCGA-NH-A8F7 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6641 
       17.85        13.94        17.03        51.98        18.28        26.43 
TCGA-A6-2671 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-A565 TCGA-A6-A56B 
       43.76        44.91        37.02        31.63        16.24        56.25 
TCGA-AA-3488 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3558 
        5.03        29.00        29.00        14.01        33.99        20.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3848 TCGA-AA-3852 
       78.08         6.97         2.01        50.04        10.06         0.00 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00Q 
       36.03         0.99        27.02        27.02        13.94        42.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A029 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       15.02        10.98        51.98         5.79        22.42        16.44 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-6600 TCGA-CA-5796 TCGA-CK-5914 
       33.01         0.20        17.26        12.10        12.39        21.99 
TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       13.02         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6167 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6928 TCGA-D5-6929 TCGA-DM-A1D8 
       14.99        17.75        12.49        11.64        13.41        12.59 
TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 
        7.50        14.04        26.47        98.24        95.18        31.96 
TCGA-F4-6570 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QL-A97D 
        6.18        13.78        46.75        10.98        12.79        21.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3591 TCGA-AG-3592 
       70.03        39.48        34.49        20.02        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3878 TCGA-AG-3881 
        2.01        50.04         0.99        20.98         0.99        19.04 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-A020 TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 
        1.02        32.02         1.02        38.04        27.55        21.01 
TCGA-DC-6157 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6464 
       51.98       129.27         4.18        11.51        10.78         9.96 
TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
        0.39        19.66        38.14        12.46 

$`9Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       38.04        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94        49.08        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       63.62        35.93        22.09        35.80        26.17        79.69 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T 
       36.03        31.00        21.24        55.76        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        39.45        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.90        42.28        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        32.75        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        20.28        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        9.63         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3553 
       19.07         0.00        26.01        12.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 
       29.95        13.94        61.02        54.02        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       17.03         0.00        33.07        32.05        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00A 
       13.05        34.06        25.02        27.02         7.96        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31         0.95        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.46        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       32.02        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       44.32       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6461 
      119.93        35.97        60.79       117.07         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       36.00        26.43        26.04        74.79        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       46.92        17.23        43.04        13.55        37.97        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       29.98        16.83        24.36        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 
       20.05        24.00         1.02        46.03        34.03        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02        32.98         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        9.07         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.56         2.50        43.20        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        31.00        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        12.62       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         3.48        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       16.41         8.61        13.64        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       49.51        42.35        28.57        32.19        36.49        37.18 
TCGA-F5-6863 TCGA-G5-6572 
       11.87        47.08 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 0 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           129.27            148.01 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            17.80             23.28 
[1] "0.0 - 129.3 (17.8)" "0.0 - 148.0 (23.3)"
[1] "hr=" "1.7"
D18V2, continuous
D18V3, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    70  33
  9Q GAIN WILD-TYPE 378 129
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     70   33
  9Q GAIN WILD-TYPE  378  129
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON               70               378
  RECTUM              33               129
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9Q GAIN MUTATED        13        1        5        31         1         1
  9Q GAIN WILD-TYPE      91        0       32       141        11         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q GAIN MUTATED           3          4          9         13       11
  9Q GAIN WILD-TYPE        21         11         75         42       52
                   vv
clus                STAGE IVA STAGE IVB
  9Q GAIN MUTATED           4         1
  9Q GAIN WILD-TYPE        20         1
D18V4, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 13                91
  STAGE IA                 1                 0
  STAGE II                 5                32
  STAGE IIA               31               141
  STAGE IIB                1                11
  STAGE IIC                1                 1
  STAGE III                3                21
  STAGE IIIA               4                11
  STAGE IIIB               9                75
  STAGE IIIC              13                42
  STAGE IV                11                52
  STAGE IVA                4                20
  STAGE IVB                1                 1
[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     3  13  72  13
  9Q GAIN WILD-TYPE  17  92 345  56
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               3                17
  T2              13                92
  T3              72               345
  T4              13                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"
                   vv
clus                 N0  N1  N2
  9Q GAIN MUTATED    55  23  23
  9Q GAIN WILD-TYPE 291 127  92
D18V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              55               291
  N1              23               127
  N2              23                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    72  16
  9Q GAIN WILD-TYPE 381  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     72   16
  9Q GAIN WILD-TYPE  381   72
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              72               381
  1              16                72
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    47  56
  9Q GAIN WILD-TYPE 242 269
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     47   56
  9Q GAIN WILD-TYPE  242  269
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              47               242
  MALE                56               269
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    76   5
  9Q GAIN WILD-TYPE 406  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     76    5
  9Q GAIN WILD-TYPE  406   24
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               76               406
  YES               5                24
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q GAIN MUTATED                     54                            16
  9Q GAIN WILD-TYPE                  328                            46
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9Q GAIN MUTATED                      28                              4
  9Q GAIN WILD-TYPE                   118                              9
D18V10, multiclass
                                clus
vv                               9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        54               328
  COLON MUCINOUS ADENOCARCINOMA               16                46
  RECTAL ADENOCARCINOMA                       28               118
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[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                 R0  R1  R2  RX
  9Q GAIN MUTATED    79   0   6   3
  9Q GAIN WILD-TYPE 367   6  31  26
D18V11, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              79               367
  R1               0                 6
  R2               6                31
  RX               3                26
[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, continuous
D18V13, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     0  56
  9Q GAIN WILD-TYPE   5 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0   56
  9Q GAIN WILD-TYPE    5  296
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              56               296
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    30  14
  10P GAIN WILD-TYPE 436 114
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                44                550 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                114 
$`10P GAIN MUTATED`
TCGA-A6-6649 TCGA-AA-3952 TCGA-G4-6625 TCGA-AG-A014 TCGA-BM-6198 TCGA-4T-AA8H 
       24.16         2.01        91.79        15.95        21.24        12.66 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-6650 
        1.61        39.45        43.76        37.02        32.45        20.61 
TCGA-A6-6782 TCGA-AA-3548 TCGA-AA-3666 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3869 
       20.28        33.99         2.01         0.00        33.07        27.02 
TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A8YK TCGA-CA-5254 TCGA-CM-5860 TCGA-CM-5862 
       16.31        17.26        18.84        12.69        32.02         5.03 
TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6534 TCGA-D5-6924 
       14.04        11.01        19.59        56.09        43.27        14.30 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 
       12.59         7.50         8.61         1.55        74.56        36.00 
TCGA-QL-A97D TCGA-AF-2689 TCGA-AG-3902 TCGA-AG-A016 TCGA-DC-4745 TCGA-DY-A1DF 
       21.90        39.48        32.02         9.07        21.01        24.13 
TCGA-F5-6571 TCGA-F5-6812 
       42.35        36.49 

$`10P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       35.80        26.17        79.69        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 
       13.94        19.99        17.03        17.03        25.97        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       31.00        51.98        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        4.80         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 
        0.99        31.07        53.00        17.03        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       27.42        26.47        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        54.61        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       39.42        61.91        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        38.70        60.13        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.92        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        25.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       20.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       48.20        78.12         7.17        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       49.51        28.57         0.39        32.19        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                  0 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             91.79             148.01 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            20.810             22.075 
[1] "0.0 - 91.8 (20.8)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.8"
D19V2, continuous
D19V3, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    38  11
  10P GAIN WILD-TYPE 410 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     38   11
  10P GAIN WILD-TYPE  410  151
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON                38                410
  RECTUM               11                151
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10P GAIN MUTATED         5        0        1        16         1         0
  10P GAIN WILD-TYPE      99        1       36       156        11         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P GAIN MUTATED           2          1          5          8        6
  10P GAIN WILD-TYPE        22         14         79         47       57
                    vv
clus                 STAGE IVA STAGE IVB
  10P GAIN MUTATED           3         0
  10P GAIN WILD-TYPE        21         2
D19V4, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   5                 99
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                16                156
  STAGE IIB                 1                 11
  STAGE IIC                 0                  2
  STAGE III                 2                 22
  STAGE IIIA                1                 14
  STAGE IIIB                5                 79
  STAGE IIIC                8                 47
  STAGE IV                  6                 57
  STAGE IVA                 3                 21
  STAGE IVB                 0                  2
[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     1   4  40   4
  10P GAIN WILD-TYPE  19 101 377  65
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                1                 19
  T2                4                101
  T3               40                377
  T4                4                 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"
                    vv
clus                  N0  N1  N2
  10P GAIN MUTATED    24   9  16
  10P GAIN WILD-TYPE 322 141  99
D19V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0               24                322
  N1                9                141
  N2               16                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    32   9
  10P GAIN WILD-TYPE 421  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     32    9
  10P GAIN WILD-TYPE  421   79
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               32                421
  1                9                 79
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    23  26
  10P GAIN WILD-TYPE 266 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     23   26
  10P GAIN WILD-TYPE  266  299
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               23                266
  MALE                 26                299
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    36   0
  10P GAIN WILD-TYPE 446  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     36    0
  10P GAIN WILD-TYPE  446   29
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                36                446
  YES                0                 29
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P GAIN MUTATED                     34                             4
  10P GAIN WILD-TYPE                  348                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10P GAIN MUTATED                      11                              0
  10P GAIN WILD-TYPE                   135                             13
D19V10, multiclass
                                clus
vv                               10P GAIN MUTATED 10P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         34                348
  COLON MUCINOUS ADENOCARCINOMA                 4                 58
  RECTAL ADENOCARCINOMA                        11                135
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  10P GAIN MUTATED    36   1   3   2
  10P GAIN WILD-TYPE 410   5  34  27
D19V11, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               36                410
  R1                1                  5
  R2                3                 34
  RX                2                 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"
D19V12, continuous
D19V13, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     2  32
  10P GAIN WILD-TYPE   3 320
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2   32
  10P GAIN WILD-TYPE    3  320
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               32                320
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    20   6
  10Q GAIN WILD-TYPE 446 122
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                568 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                122 
$`10Q GAIN MUTATED`
TCGA-BM-6198 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-4107 TCGA-AA-3666 
       21.24        12.66         1.61        39.45        32.45         2.01 
TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3982 TCGA-AA-A01R TCGA-AY-A54L TCGA-AY-A8YK 
       33.07        27.02        27.02        35.01        17.26        18.84 
TCGA-CA-5254 TCGA-CM-5860 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6924 TCGA-DM-A1D8 
       12.69        32.02        11.01        19.59        14.30        12.59 
TCGA-DM-A1DA TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QL-A97D TCGA-AF-2689 
        7.50         1.55        74.56        36.00        21.90        39.48 
TCGA-AG-3999 TCGA-DC-4745 
       28.04        21.01 

$`10Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 
       18.28        55.76        26.43        15.62         4.80         9.53 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        17.03        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S 
       12.00        31.00        31.00        38.07         1.02         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
        0.20        21.44        17.82        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74         3.19        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        82.39        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        39.42        61.91        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       11.90        70.03        46.92        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1.55               0.00 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             74.56             148.01 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            21.125             22.045 
[1] "1.6 - 74.6 (21.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D20V2, continuous
D20V3, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    23   6
  10Q GAIN WILD-TYPE 425 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     23    6
  10Q GAIN WILD-TYPE  425  156
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON                23                425
  RECTUM                6                156
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10Q GAIN MUTATED         3        0        1         7         0         0
  10Q GAIN WILD-TYPE     101        1       36       165        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q GAIN MUTATED           2          1          4          5        3
  10Q GAIN WILD-TYPE        22         14         80         50       60
                    vv
clus                 STAGE IVA STAGE IVB
  10Q GAIN MUTATED           2         0
  10Q GAIN WILD-TYPE        22         2
D20V4, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                 7                165
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 2                 22
  STAGE IIIA                1                 14
  STAGE IIIB                4                 80
  STAGE IIIC                5                 50
  STAGE IV                  3                 60
  STAGE IVA                 2                 22
  STAGE IVB                 0                  2
[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     0   3  24   2
  10Q GAIN WILD-TYPE  20 102 393  67
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                 20
  T2                3                102
  T3               24                393
  T4                2                 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"
                    vv
clus                  N0  N1  N2
  10Q GAIN MUTATED    12   8   9
  10Q GAIN WILD-TYPE 334 142 106
D20V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0               12                334
  N1                8                142
  N2                9                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    17   5
  10Q GAIN WILD-TYPE 436  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     17    5
  10Q GAIN WILD-TYPE  436   83
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               17                436
  1                5                 83
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    14  15
  10Q GAIN WILD-TYPE 275 310
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     14   15
  10Q GAIN WILD-TYPE  275  310
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               14                275
  MALE                 15                310
[1] 2 2
[1] FALSE
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    21   1
  10Q GAIN WILD-TYPE 461  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     21    1
  10Q GAIN WILD-TYPE  461   28
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                21                461
  YES                1                 28
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q GAIN MUTATED                     19                             4
  10Q GAIN WILD-TYPE                  363                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10Q GAIN MUTATED                       6                              0
  10Q GAIN WILD-TYPE                   140                             13
D20V10, multiclass
                                clus
vv                               10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         19                363
  COLON MUCINOUS ADENOCARCINOMA                 4                 58
  RECTAL ADENOCARCINOMA                         6                140
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  10Q GAIN MUTATED    22   0   1   2
  10Q GAIN WILD-TYPE 424   6  36  27
D20V11, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0               22                424
  R1                0                  6
  R2                1                 36
  RX                2                 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"
D20V12, continuous
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     2  17
  10Q GAIN WILD-TYPE   3 335
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2   17
  10Q GAIN WILD-TYPE    3  335
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               17                335
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    67  17
  11P GAIN WILD-TYPE 399 111
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                84                510 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                17                111 
$`11P GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3867 TCGA-AD-6888 TCGA-AZ-6608 TCGA-G4-6310 
       13.02        19.99        24.03        15.52         1.94        63.62 
TCGA-G4-6314 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A01N 
       35.93        10.39        13.94        19.99        25.97        31.00 
TCGA-BM-6198 TCGA-G5-6233 TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 
       21.24        18.28         1.61        43.76        43.43        44.91 
TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 
       29.19        25.08        25.18        23.87        56.25         5.03 
TCGA-AA-3494 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3842 TCGA-AA-3846 
        1.02        12.99        24.00        50.04        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 TCGA-AA-A00F 
       33.07         0.99        18.05        20.98        27.02        34.03 
TCGA-AA-A02F TCGA-AD-6901 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK TCGA-AZ-4684 
       39.98        22.42        16.31         0.95        18.84        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6164 
       62.79        29.56       148.01         8.02        17.03        29.03 
TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       21.99        11.08        25.48        43.27        17.85         7.53 
TCGA-D5-6929 TCGA-DM-A28F TCGA-G4-6303 TCGA-G4-6307 TCGA-QG-A5YW TCGA-RU-A8FL 
       13.41        35.97        65.85        55.04        29.46        38.70 
TCGA-AF-2690 TCGA-AF-6655 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3591 
       17.23        20.02        65.98        12.00        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-4001 TCGA-AG-4007 TCGA-AH-6897 TCGA-CI-6623 
       34.03        19.99        36.03         1.02        26.43        47.44 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 
       48.20        25.05        31.00        12.00        51.98        44.02 
TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 
      126.44         4.18        16.31        13.64         0.39        32.19 

$`11P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       21.99        39.06        21.37        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 
        8.02        17.03        17.03        15.95        36.03        51.98 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       55.76        26.43        15.62         4.80        12.66         9.53 
TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
       39.45        46.65        43.76        42.90        42.28        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       36.53        32.45        32.91        31.63        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13         8.38        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
       61.84         9.63         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
       19.07         0.00        29.00        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3848 
       17.98        15.95        38.99        36.95         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       17.03        27.02        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        25.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 
       12.16        83.24        24.53         5.79        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
       16.44         0.46         0.92        14.50        27.09        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        14.04        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.42        17.75        18.25        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
        8.35        82.39        74.56        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        46.92        39.48        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       34.49        37.74        29.98        16.83        24.36        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       86.63        11.84        36.03        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04        14.04         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       38.04        38.56         2.50        43.20        27.55        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17        13.78        44.78        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       21.01        26.04        13.97        31.00        10.98        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        25.05        12.62        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 
        8.45         9.96        49.51        42.35        28.57        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.00 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            148.01             140.38 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            25.065             21.600 
[1] "0.4 - 148.0 (25.1)" "0.0 - 140.4 (21.6)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    53  31
  11P GAIN WILD-TYPE 395 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     53   31
  11P GAIN WILD-TYPE  395  131
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON                53                395
  RECTUM               31                131
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11P GAIN MUTATED        13        0        3        17         1         0
  11P GAIN WILD-TYPE      91        1       34       155        11         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P GAIN MUTATED           1          4         12         10       13
  11P GAIN WILD-TYPE        23         11         72         45       50
                    vv
clus                 STAGE IVA STAGE IVB
  11P GAIN MUTATED           6         0
  11P GAIN WILD-TYPE        18         2
D21V4, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  13                 91
  STAGE IA                  0                  1
  STAGE II                  3                 34
  STAGE IIA                17                155
  STAGE IIB                 1                 11
  STAGE IIC                 0                  2
  STAGE III                 1                 23
  STAGE IIIA                4                 11
  STAGE IIIB               12                 72
  STAGE IIIC               10                 45
  STAGE IV                 13                 50
  STAGE IVA                 6                 18
  STAGE IVB                 0                  2
[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     4  16  60   4
  11P GAIN WILD-TYPE  16  89 357  65
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                4                 16
  T2               16                 89
  T3               60                357
  T4                4                 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"
                    vv
clus                  N0  N1  N2
  11P GAIN MUTATED    40  23  21
  11P GAIN WILD-TYPE 306 127  94
D21V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               40                306
  N1               23                127
  N2               21                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    55  19
  11P GAIN WILD-TYPE 398  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     55   19
  11P GAIN WILD-TYPE  398   69
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               55                398
  1               19                 69
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    40  45
  11P GAIN WILD-TYPE 249 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     40   45
  11P GAIN WILD-TYPE  249  280
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               40                249
  MALE                 45                280
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    71   4
  11P GAIN WILD-TYPE 411  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     71    4
  11P GAIN WILD-TYPE  411   25
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                71                411
  YES                4                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P GAIN MUTATED                     51                             2
  11P GAIN WILD-TYPE                  331                            60
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11P GAIN MUTATED                      31                              0
  11P GAIN WILD-TYPE                   115                             13
D21V10, multiclass
                                clus
vv                               11P GAIN MUTATED 11P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         51                331
  COLON MUCINOUS ADENOCARCINOMA                 2                 60
  RECTAL ADENOCARCINOMA                        31                115
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  11P GAIN MUTATED    61   1   6   2
  11P GAIN WILD-TYPE 385   5  31  27
D21V11, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               61                385
  R1                1                  5
  R2                6                 31
  RX                2                 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"
D21V12, continuous
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  54
  11P GAIN WILD-TYPE   4 298
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   54
  11P GAIN WILD-TYPE    4  298
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               54                298
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    64  13
  11Q GAIN WILD-TYPE 402 115
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                77                517 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                13                115 
$`11Q GAIN MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3867 TCGA-AZ-6608 TCGA-G4-6310 TCGA-G4-6314 
       13.02        19.99        24.03         1.94        63.62        35.93 
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A01N TCGA-5M-AAT4 TCGA-A6-2675 
       10.39        19.99        25.97        31.00         1.61        43.43 
TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-A56B 
       44.91        29.19        29.16        25.08        25.18        56.25 
TCGA-AA-3494 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3685 
        1.02        29.00        12.99        24.00        50.04        37.05 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       37.02        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3955 TCGA-AA-3982 TCGA-AA-A00F TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-4684 
       20.98        27.02        34.03        16.31        18.84        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6164 
       62.79        29.56       148.01         8.02        17.03        29.03 
TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6898 
       21.99        11.08        55.92        25.48        43.27         7.53 
TCGA-D5-6929 TCGA-DM-A1D8 TCGA-DM-A28F TCGA-G4-6303 TCGA-G4-6307 TCGA-QG-A5YW 
       13.41        12.59        35.97        65.85        55.04        29.46 
TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3592 
       38.70        17.23        65.98        12.00        46.03        34.03 
TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-4007 TCGA-AH-6897 TCGA-CI-6623 TCGA-CI-6624 
        1.02        36.03         1.02        26.43        47.44        48.20 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A0XA 
       25.05        31.00        12.00        31.00        51.98       126.44 
TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       16.31        13.64         0.39        32.19        36.49 

$`11Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       75.95       106.75       100.01        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       23.51        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       17.85         8.02        13.94        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       36.03        51.98        21.24        18.28        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
       46.65        43.76        42.90        42.28        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
        9.63         5.03         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
       19.07         0.00        29.00        26.01        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02         2.01        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       38.99        36.95         0.00         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        25.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02        25.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        14.04        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       45.40        54.61        19.59        56.09        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       82.39        74.56        67.30        53.62        44.68        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        9.93        15.65        12.79        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        60.13        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.92        39.48        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       86.63        11.84        36.03        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        28.04        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5917 
       19.46         6.05        33.17        13.78        44.78        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.17        21.01        26.04        13.97        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05        12.62        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       28.57        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.00 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            148.01             140.38 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             29.00              21.01 
[1] "0.4 - 148.0 (29.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.5"
D22V2, continuous
D22V3, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    52  26
  11Q GAIN WILD-TYPE 396 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     52   26
  11Q GAIN WILD-TYPE  396  136
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON                52                396
  RECTUM               26                136
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11Q GAIN MUTATED        12        0        4        15         1         0
  11Q GAIN WILD-TYPE      92        1       33       157        11         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q GAIN MUTATED           1          3         11         10       10
  11Q GAIN WILD-TYPE        23         12         73         45       53
                    vv
clus                 STAGE IVA STAGE IVB
  11Q GAIN MUTATED           7         0
  11Q GAIN WILD-TYPE        17         2
D22V4, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  12                 92
  STAGE IA                  0                  1
  STAGE II                  4                 33
  STAGE IIA                15                157
  STAGE IIB                 1                 11
  STAGE IIC                 0                  2
  STAGE III                 1                 23
  STAGE IIIA                3                 12
  STAGE IIIB               11                 73
  STAGE IIIC               10                 45
  STAGE IV                 10                 53
  STAGE IVA                 7                 17
  STAGE IVB                 0                  2
[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     2  16  54   5
  11Q GAIN WILD-TYPE  18  89 363  64
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 18
  T2               16                 89
  T3               54                363
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  11Q GAIN MUTATED    37  21  19
  11Q GAIN WILD-TYPE 309 129  96
D22V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               37                309
  N1               21                129
  N2               19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    51  17
  11Q GAIN WILD-TYPE 402  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     51   17
  11Q GAIN WILD-TYPE  402   71
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               51                402
  1               17                 71
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    37  41
  11Q GAIN WILD-TYPE 252 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     37   41
  11Q GAIN WILD-TYPE  252  284
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               37                252
  MALE                 41                284
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    64   3
  11Q GAIN WILD-TYPE 418  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     64    3
  11Q GAIN WILD-TYPE  418   26
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                64                418
  YES                3                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q GAIN MUTATED                     50                             2
  11Q GAIN WILD-TYPE                  332                            60
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11Q GAIN MUTATED                      26                              0
  11Q GAIN WILD-TYPE                   120                             13
D22V10, multiclass
                                clus
vv                               11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         50                332
  COLON MUCINOUS ADENOCARCINOMA                 2                 60
  RECTAL ADENOCARCINOMA                        26                120
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  11Q GAIN MUTATED    57   1   4   2
  11Q GAIN WILD-TYPE 389   5  33  27
D22V11, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               57                389
  R1                1                  5
  R2                4                 33
  RX                2                 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"
D22V12, continuous
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     1  49
  11Q GAIN WILD-TYPE   4 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1   49
  11Q GAIN WILD-TYPE    4  303
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               49                303
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED    93  28
  12P GAIN WILD-TYPE 373 100
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               121                473 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                28                100 
$`12P GAIN MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3715 
       13.94        14.53        58.03        19.99         0.92        19.04 
TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AZ-6608 TCGA-AG-3611 TCGA-AG-A014 
       14.93        12.99        24.00         1.94        13.94        15.95 
TCGA-AG-A015 TCGA-G5-6233 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2686 
       36.03        18.28        15.62        12.66        44.91        37.02 
TCGA-A6-3809 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-6780 
       32.75        22.09        25.08        20.61        23.87        20.12 
TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
       24.92         1.02         0.00        29.00        29.00        12.99 
TCGA-AA-3660 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       78.08        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 
       35.05         0.99        37.02         0.00        33.07         0.00 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A029 
       24.00        26.01        18.05        12.00        31.00        51.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6963 
        0.92        22.03        39.98        40.96        12.16        27.42 
TCGA-AM-5821 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-6598 TCGA-AZ-6599 
        0.92         0.20        18.84         1.41        49.41         6.77 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 
        3.19        12.69        12.36       148.01        85.45        15.62 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 
       20.02        25.02        32.02        15.02        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 
       14.04        11.01        20.19        17.75         4.80        14.30 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.41        12.00        10.26       119.70        24.43 
TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 TCGA-G4-6306 TCGA-G4-6323 
       44.32        95.18         8.61        47.87        44.68        13.78 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       74.79        10.98        15.65        34.49        37.74        16.83 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 
       24.59        36.03        46.03         2.01         6.05        19.99 
TCGA-AG-3726 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 
        7.99        19.04         1.02        36.95         1.02        36.03 
TCGA-AG-A02G TCGA-AG-A02N TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       38.96        61.97        78.12        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
      126.44        32.61        19.96        18.28        17.69        13.64 
TCGA-EI-7002 
       11.97 

$`12P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        17.95        23.01        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        85.05        19.04        31.07        24.03        29.98 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       75.95       106.75       100.01        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 
       91.79        79.69        17.85        10.39         8.02        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       17.03        17.03        25.97        31.00        51.98        21.24 
TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       55.76        26.43         4.80         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 
       35.11        16.57        37.05        37.25        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        21.76        24.69        24.39 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        20.28        16.24        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        5.03         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       26.01        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        61.02         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3811 
       14.01        50.04        47.05        47.01        15.02        10.06 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03        10.06         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
        2.01        33.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        26.01        37.02         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
        5.03        41.00        18.05        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 
       22.42        26.47        16.44         0.46        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       17.85        19.33       109.28        58.39         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
        5.13        22.36        65.00        62.79        88.21        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23        11.74        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
      124.27        23.05        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        54.61        19.59        56.09        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25        25.48        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF 
       12.43         9.04         9.44        13.35        11.38        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       74.56        67.30        65.85        53.62        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6626 
       39.42        61.91        36.00        26.43        26.04        46.75 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       18.18        19.33        19.33         9.93        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       38.70        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 
       17.23        43.04        13.55        37.97        29.98        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       20.02        86.63        65.98        11.84        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 
        7.07        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        17.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       44.78        47.44        48.20         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.98        44.02        25.97        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         3.48         4.18        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  0 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            148.01             140.38 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             19.04              23.01 
[1] "0.0 - 148.0 (19.0)" "0.0 - 140.4 (23.0)"
[1] "hr=" "1.2"
D23V2, continuous
D23V3, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    95  33
  12P GAIN WILD-TYPE 353 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     95   33
  12P GAIN WILD-TYPE  353  129
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON                95                353
  RECTUM               33                129
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12P GAIN MUTATED        19        1       11        44         2         0
  12P GAIN WILD-TYPE      85        0       26       128        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P GAIN MUTATED           4          3         10         13       11
  12P GAIN WILD-TYPE        20         12         74         42       52
                    vv
clus                 STAGE IVA STAGE IVB
  12P GAIN MUTATED           6         0
  12P GAIN WILD-TYPE        18         2
D23V4, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  19                 85
  STAGE IA                  1                  0
  STAGE II                 11                 26
  STAGE IIA                44                128
  STAGE IIB                 2                 10
  STAGE IIC                 0                  2
  STAGE III                 4                 20
  STAGE IIIA                3                 12
  STAGE IIIB               10                 74
  STAGE IIIC               13                 42
  STAGE IV                 11                 52
  STAGE IVA                 6                 18
  STAGE IVB                 0                  2
[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     1  24  86  16
  12P GAIN WILD-TYPE  19  81 331  53
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                 19
  T2               24                 81
  T3               86                331
  T4               16                 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"
                    vv
clus                  N0  N1  N2
  12P GAIN MUTATED    82  24  22
  12P GAIN WILD-TYPE 264 126  93
D23V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               82                264
  N1               24                126
  N2               22                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    95  16
  12P GAIN WILD-TYPE 358  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     95   16
  12P GAIN WILD-TYPE  358   72
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               95                358
  1               16                 72
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    60  68
  12P GAIN WILD-TYPE 229 257
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     60   68
  12P GAIN WILD-TYPE  229  257
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               60                229
  MALE                 68                257
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    91   9
  12P GAIN WILD-TYPE 391  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     91    9
  12P GAIN WILD-TYPE  391   20
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                91                391
  YES                9                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P GAIN MUTATED                     79                            16
  12P GAIN WILD-TYPE                  303                            46
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12P GAIN MUTATED                      28                              4
  12P GAIN WILD-TYPE                   118                              9
D23V10, multiclass
                                clus
vv                               12P GAIN MUTATED 12P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         79                303
  COLON MUCINOUS ADENOCARCINOMA                16                 46
  RECTAL ADENOCARCINOMA                        28                118
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[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                  R0  R1  R2  RX
  12P GAIN MUTATED    95   1   5   6
  12P GAIN WILD-TYPE 351   5  32  23
D23V11, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               95                351
  R1                1                  5
  R2                5                 32
  RX                6                 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"
D23V12, continuous
D23V13, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     0  71
  12P GAIN WILD-TYPE   5 281
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      0   71
  12P GAIN WILD-TYPE    5  281
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               71                281
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED    85  24
  12Q GAIN WILD-TYPE 381 104
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               109                485 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                24                104 
$`12Q GAIN MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3715 
       13.94        14.53        58.03        19.99         0.92        19.04 
TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AZ-6608 TCGA-AG-A015 
       14.93        12.99        24.00        26.01         1.94        36.03 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5664 
       15.62        12.66        44.91        37.02        32.75        22.09 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-A566 TCGA-AA-3494 
       25.08        20.61        23.87        20.12        24.92         1.02 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3660 TCGA-AA-3681 
        0.00        29.00        29.00        12.99        78.08         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 
       37.05         5.03        26.99        35.05         0.99        37.02 
TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-A00J 
        0.00        33.07         0.00        24.00        26.01        18.05 
TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R 
       18.05        12.00        31.00        51.98         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4323 
       39.98        40.96        12.16         0.92        18.84         1.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5254 TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 
       49.41         6.77        12.69        12.36       148.01        85.45 
TCGA-CK-4952 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6166 TCGA-CM-6169 
       15.62        25.02        32.02        15.02        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6924 
       14.04        11.01        20.19        17.75         4.80        14.30 
TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DB 
       11.64        12.00        10.26       119.70        24.43        44.32 
TCGA-DM-A28M TCGA-F4-6463 TCGA-F4-6703 TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6627 
       95.18        35.74        47.87        44.68        13.78        74.79 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-QL-A97D TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
       10.98        15.65        21.90        34.49        16.83        36.03 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-3883 
       46.03        34.03         2.01        19.99        19.04         1.02 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A02G TCGA-AG-A02N TCGA-DC-6682 TCGA-DC-6683 
        1.02        36.03        38.96        61.97        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
      126.44        32.61        19.96        18.28        17.69        13.64 
TCGA-EI-7002 
       11.97 

$`12Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        17.95        23.01        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       36.00        85.05        19.04        31.07        24.03        29.98 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        25.97        15.95        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       21.24        18.28        55.76        26.43         4.80         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        23.61        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 
       27.09        22.52        24.13         8.38        25.18        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 
       24.69        24.39        19.66        20.28        16.24        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
        9.07        19.07        26.01        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       15.02        11.01        10.06        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        36.95        17.03        10.06         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 
       27.02        18.05        31.00         2.01        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
        1.02        33.04         1.02        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6889 
       39.98         2.01         5.03        41.00        18.05        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        88.21        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4951 
       12.20        12.76        10.06        14.30        17.56        70.16 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       23.05        20.02        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        14.99        12.99        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       45.40        54.61        19.59        56.09        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       18.25        25.48        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
       12.43         9.04         9.44        13.41        13.35        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        98.24         8.61        31.96        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       82.39        74.56        67.30        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       46.75        18.18        19.33        19.33         9.93        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       38.70        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       17.23        43.04        13.55        37.97        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03        34.03        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       37.02        32.98         0.99         0.99        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        28.04        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X 
        9.07         1.02         1.02        49.97         1.94        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       44.02        25.97        12.62        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         3.48         4.18        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  0 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            148.01             140.38 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             20.12              22.42 
[1] "0.0 - 148.0 (20.1)" "0.0 - 140.4 (22.4)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    90  24
  12Q GAIN WILD-TYPE 358 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     90   24
  12Q GAIN WILD-TYPE  358  138
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON                90                358
  RECTUM               24                138
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12Q GAIN MUTATED        17        1        9        44         2         0
  12Q GAIN WILD-TYPE      87        0       28       128        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q GAIN MUTATED           3          4         10          9        7
  12Q GAIN WILD-TYPE        21         11         74         46       56
                    vv
clus                 STAGE IVA STAGE IVB
  12Q GAIN MUTATED           6         0
  12Q GAIN WILD-TYPE        18         2
D24V4, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  17                 87
  STAGE IA                  1                  0
  STAGE II                  9                 28
  STAGE IIA                44                128
  STAGE IIB                 2                 10
  STAGE IIC                 0                  2
  STAGE III                 3                 21
  STAGE IIIA                4                 11
  STAGE IIIB               10                 74
  STAGE IIIC                9                 46
  STAGE IV                  7                 56
  STAGE IVA                 6                 18
  STAGE IVB                 0                  2
[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     1  23  75  14
  12Q GAIN WILD-TYPE  19  82 342  55
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                 19
  T2               23                 82
  T3               75                342
  T4               14                 55
[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
  12Q GAIN MUTATED    77  25  12
  12Q GAIN WILD-TYPE 269 125 103
D24V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               77                269
  N1               25                125
  N2               12                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    88  13
  12Q GAIN WILD-TYPE 365  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     88   13
  12Q GAIN WILD-TYPE  365   75
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               88                365
  1               13                 75
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    57  57
  12Q GAIN WILD-TYPE 232 268
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     57   57
  12Q GAIN WILD-TYPE  232  268
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               57                232
  MALE                 57                268
[1] 2 2
[1] FALSE
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    85   5
  12Q GAIN WILD-TYPE 397  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     85    5
  12Q GAIN WILD-TYPE  397   24
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                85                397
  YES                5                 24
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                     73                            17
  12Q GAIN WILD-TYPE                  309                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q GAIN MUTATED                      21                              2
  12Q GAIN WILD-TYPE                   125                             11
D24V10, multiclass
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         73                309
  COLON MUCINOUS ADENOCARCINOMA                17                 45
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[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                  R0  R1  R2  RX
  12Q GAIN MUTATED    87   1   4   4
  12Q GAIN WILD-TYPE 359   5  33  25
D24V11, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               87                359
  R1                1                  5
  R2                4                 33
  RX                4                 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"
D24V12, continuous
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     0  62
  12Q GAIN WILD-TYPE   5 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0   62
  12Q GAIN WILD-TYPE    5  290
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               62                290
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED   284  74
  13Q GAIN WILD-TYPE 182  54
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               358                236 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                74                 54 
$`13Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 
       24.03        36.03        34.03         0.99        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
       19.99         6.05        19.00        85.05        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 
       24.03        29.98        12.99        50.99        26.01        19.07 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AZ-4313 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       38.04        21.37        75.95         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A8F7 
       28.21        23.51        63.62        35.80        91.79        17.85 
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       15.95        36.03        51.98        18.28        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.76        43.43        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       16.57        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        33.53        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       24.69        23.87        20.28        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 
        7.04        37.05         6.97        38.99         9.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       24.00        20.98        13.94        78.08         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 
       50.04        15.02         5.98        37.05        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 
        0.99        36.95        37.02        17.03        10.06        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 
        0.99        31.07        17.03        27.02         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       34.03        42.02        14.99        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       12.00        31.00        33.04         2.96        39.98         2.01 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        39.98        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47        16.44        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 
       21.44        17.26        18.84       109.28         1.41         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 
        5.23        11.74        12.69        12.36        12.59        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 
       17.56       148.01         2.01        20.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        32.02         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.80        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
        7.50       131.51         7.76        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.97        31.96         6.18        41.42        43.04        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
        0.53        47.41       133.18         8.35        82.39        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 
       65.85        44.68        39.42        36.00        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       74.79        18.18        19.33        15.65        16.80        42.77 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 
       29.46        21.90        38.70        60.13        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       17.23        43.04        13.55        37.97        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
        7.07        36.03        20.05         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 
       34.03         0.99        19.99        20.98         0.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        17.95        36.95        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 
        1.02        46.03         6.02         9.07        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.96        38.04        38.56        43.20        27.55        26.43 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.05        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       31.00        51.98        10.98        44.02        25.05        25.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        3.48        20.55        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 
       16.34        16.31        16.41        11.51        10.78        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
       36.49        19.66        11.87        47.08 

$`13Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 
       24.33        13.02        37.05         8.05        19.07        17.95 
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3950 
       23.01         0.92        36.00        19.04        31.07        24.00 
TCGA-AA-3952 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 
        2.01        24.00        21.99        39.06        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6588 
       10.88       106.75       100.01        35.93        22.09        26.17 
TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A01N TCGA-BM-6198 TCGA-5M-AAT4 TCGA-A6-2676 
       79.69         8.02        31.00        21.24         1.61        42.90 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5664 
       37.05        37.25        37.02        32.75        31.63        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       24.92        56.25         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3655 
        1.02         1.02        19.07         0.00        29.95        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3696 
        6.97        54.02        47.05        47.01        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       26.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
        0.00         0.00        33.07         0.00        36.03        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A 
       18.05        31.00        33.01         2.01        25.02        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       17.03        34.98        10.98        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02         1.02        26.01        37.02        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        5.03         0.92        22.03        18.05        12.16        83.24 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 
        0.46         0.92        14.50        27.09         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 
       17.85        19.33        58.39         5.65        32.94        88.21 
TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        6.77         3.19        12.46        12.39        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       12.76        10.06        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.99        21.14        82.95       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       25.02        26.04        27.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       21.99        14.04        12.95        13.05        12.03        45.40 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.19        20.42        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.64        13.35        24.43        38.20        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       135.65       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6302 
       47.87         1.55        34.42        13.25        35.31        67.30 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       53.62        55.04        85.48        61.91        26.04        13.78 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 
       10.98        19.33         9.93        12.79        32.98         8.42 
TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
       31.30        11.90        70.03        34.49        16.83        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3598 
       12.00        32.02        24.00        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 
       12.03         6.05        15.95         7.99        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-3901 
        0.99        19.04         1.02        13.02        48.03        25.02 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
        3.98        20.98        13.94        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 
        1.02        61.97        41.00         2.50        19.46        33.17 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6507 
       13.97        25.97        12.62       126.44         4.18        19.96 
TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 
       20.91         8.61        13.64        17.46         8.45        37.18 
TCGA-F5-6861 TCGA-F5-6864 
       38.14        12.46 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.39               0.00 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            148.01             140.38 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             22.75              21.19 
[1] "0.4 - 148.0 (22.8)" "0.0 - 140.4 (21.2)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   257 111
  13Q GAIN WILD-TYPE 191  51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    257  111
  13Q GAIN WILD-TYPE  191   51
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON               257                191
  RECTUM              111                 51
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  13Q GAIN MUTATED        62        0       19        85         5         2
  13Q GAIN WILD-TYPE      42        1       18        87         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q GAIN MUTATED          14         13         55         38       48
  13Q GAIN WILD-TYPE        10          2         29         17       15
                    vv
clus                 STAGE IVA STAGE IVB
  13Q GAIN MUTATED          17         0
  13Q GAIN WILD-TYPE         7         2
D25V4, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  62                 42
  STAGE IA                  0                  1
  STAGE II                 19                 18
  STAGE IIA                85                 87
  STAGE IIB                 5                  7
  STAGE IIC                 2                  0
  STAGE III                14                 10
  STAGE IIIA               13                  2
  STAGE IIIB               55                 29
  STAGE IIIC               38                 17
  STAGE IV                 48                 15
  STAGE IVA                17                  7
  STAGE IVB                 0                  2
[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    14  63 249  44
  13Q GAIN WILD-TYPE   6  42 168  25
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               14                  6
  T2               63                 42
  T3              249                168
  T4               44                 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
  13Q GAIN MUTATED   184 104  81
  13Q GAIN WILD-TYPE 162  46  34
D25V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0              184                162
  N1              104                 46
  N2               81                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   264  64
  13Q GAIN WILD-TYPE 189  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    264   64
  13Q GAIN WILD-TYPE  189   24
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0              264                189
  1               64                 24
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   168 204
  13Q GAIN WILD-TYPE 121 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    168  204
  13Q GAIN WILD-TYPE  121  121
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE              168                121
  MALE                204                121
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   296  22
  13Q GAIN WILD-TYPE 186   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    296   22
  13Q GAIN WILD-TYPE  186    7
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO               296                186
  YES               22                  7
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q GAIN MUTATED                    239                            17
  13Q GAIN WILD-TYPE                  143                            45
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  13Q GAIN MUTATED                     107                              3
  13Q GAIN WILD-TYPE                    39                             10
D25V10, multiclass
                                clus
vv                               13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        239                143
  COLON MUCINOUS ADENOCARCINOMA                17                 45
  RECTAL ADENOCARCINOMA                       107                 39
  RECTAL MUCINOUS ADENOCARCINOMA                3                 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                  R0  R1  R2  RX
  13Q GAIN MUTATED   261   4  27  12
  13Q GAIN WILD-TYPE 185   2  10  17
D25V11, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0              261                185
  R1                4                  2
  R2               27                 10
  RX               12                 17
[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, continuous
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4 219
  13Q GAIN WILD-TYPE   1 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4  219
  13Q GAIN WILD-TYPE    1  133
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              219                133
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    34   6
  14Q GAIN WILD-TYPE 432 122
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                40                554 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 6                122 
$`14Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-DM-A285 TCGA-AG-3611 TCGA-AG-A014 TCGA-A6-2674 
       45.60        24.16         5.88        13.94        15.95        43.76 
TCGA-A6-2686 TCGA-A6-5667 TCGA-A6-6648 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3558 
       37.02        29.16        25.18        26.01        12.99        20.98 
TCGA-AA-3660 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00D 
       78.08        33.07         0.00        24.00         2.01        19.00 
TCGA-AA-A01D TCGA-AA-A02O TCGA-AD-6890 TCGA-AD-6965 TCGA-AZ-6607 TCGA-CA-5254 
       10.98         0.92        24.53        26.47         3.19        12.69 
TCGA-CA-6719 TCGA-CM-5864 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6538 TCGA-DM-A28M 
       14.30        15.02        11.01        19.59        17.13        95.18 
TCGA-F4-6704 TCGA-G4-6307 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5YW 
        1.55        55.04        46.75        74.79        12.79        29.46 
TCGA-AF-6136 TCGA-AG-3999 TCGA-EI-6512 TCGA-EI-6885 
       24.36        28.04        17.69        13.64 

$`14Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N 
       19.99        17.03        17.03        25.97        36.03        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       51.98        21.24        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       29.00        29.00        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       29.95        13.94        61.02         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       83.24         5.79        22.42        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5255 
        6.77        12.10        29.56         5.23        11.74        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.43        26.04        13.78        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       19.33         9.93        15.65        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                  0 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             95.18             148.01 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            20.285             22.030 
[1] "0.0 - 95.2 (20.3)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D26V2, continuous
D26V3, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    35   8
  14Q GAIN WILD-TYPE 413 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     35    8
  14Q GAIN WILD-TYPE  413  154
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON                35                413
  RECTUM                8                154
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  14Q GAIN MUTATED         6        0        3        11         0         0
  14Q GAIN WILD-TYPE      98        1       34       161        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q GAIN MUTATED           0          1          7          6        4
  14Q GAIN WILD-TYPE        24         14         77         49       59
                    vv
clus                 STAGE IVA STAGE IVB
  14Q GAIN MUTATED           3         1
  14Q GAIN WILD-TYPE        21         1
D26V4, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   6                 98
  STAGE IA                  0                  1
  STAGE II                  3                 34
  STAGE IIA                11                161
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 0                 24
  STAGE IIIA                1                 14
  STAGE IIIB                7                 77
  STAGE IIIC                6                 49
  STAGE IV                  4                 59
  STAGE IVA                 3                 21
  STAGE IVB                 1                  1
[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     1   6  31   5
  14Q GAIN WILD-TYPE  19  99 386  64
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                1                 19
  T2                6                 99
  T3               31                386
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  14Q GAIN MUTATED    22  11  10
  14Q GAIN WILD-TYPE 324 139 105
D26V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               22                324
  N1               11                139
  N2               10                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    29   8
  14Q GAIN WILD-TYPE 424  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     29    8
  14Q GAIN WILD-TYPE  424   80
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               29                424
  1                8                 80
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    20  23
  14Q GAIN WILD-TYPE 269 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     20   23
  14Q GAIN WILD-TYPE  269  302
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               20                269
  MALE                 23                302
[1] 2 2
[1] FALSE
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    32   1
  14Q GAIN WILD-TYPE 450  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     32    1
  14Q GAIN WILD-TYPE  450   28
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                32                450
  YES                1                 28
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q GAIN MUTATED                     26                             9
  14Q GAIN WILD-TYPE                  356                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  14Q GAIN MUTATED                       8                              0
  14Q GAIN WILD-TYPE                   138                             13
D26V10, multiclass
                                clus
vv                               14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         26                356
  COLON MUCINOUS ADENOCARCINOMA                 9                 53
  RECTAL ADENOCARCINOMA                         8                138
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  14Q GAIN MUTATED    30   1   1   3
  14Q GAIN WILD-TYPE 416   5  36  26
D26V11, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0               30                416
  R1                1                  5
  R2                1                 36
  RX                3                 26
[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, continuous
D26V13, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     0  26
  14Q GAIN WILD-TYPE   5 326
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      0   26
  14Q GAIN WILD-TYPE    5  326
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               26                326
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    10   3
  15Q GAIN WILD-TYPE 456 125
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                581 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                125 
$`15Q GAIN MUTATED`
TCGA-A6-6649 TCGA-3L-AA1B TCGA-AA-3534 TCGA-AA-3941 TCGA-AZ-4614 TCGA-CA-5254 
       24.16        15.62        29.00        24.00         5.65        12.69 
TCGA-CM-6161 TCGA-D5-6531 TCGA-DM-A1DB TCGA-G4-6297 TCGA-AF-3400 TCGA-EI-7004 
       15.02        17.75        44.32        82.39        34.49         8.45 
TCGA-F5-6464 
        9.96 

$`15Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       18.28        55.76        26.43         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.25        37.02        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       12.10        29.56         5.23        11.74         3.19        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       60.13        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       11.51        10.78        13.64        17.46        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              5.65               0.00 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             82.39             148.01 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             17.75              22.03 
[1] "5.7 - 82.4 (17.8)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D27V2, continuous
D27V3, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 437 158
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  437  158
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON                11                437
  RECTUM                4                158
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  15Q GAIN MUTATED         2        0        1         5         0         0
  15Q GAIN WILD-TYPE     102        1       36       167        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q GAIN MUTATED           0          0          1          1        2
  15Q GAIN WILD-TYPE        24         15         83         54       61
                    vv
clus                 STAGE IVA STAGE IVB
  15Q GAIN MUTATED           2         0
  15Q GAIN WILD-TYPE        22         2
D27V4, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   2                102
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                 5                167
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 0                 24
  STAGE IIIA                0                 15
  STAGE IIIB                1                 83
  STAGE IIIC                1                 54
  STAGE IV                  2                 61
  STAGE IVA                 2                 22
  STAGE IVB                 0                  2
[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     0   2   8   5
  15Q GAIN WILD-TYPE  20 103 409  64
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                 20
  T2                2                103
  T3                8                409
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  15Q GAIN MUTATED     8   3   4
  15Q GAIN WILD-TYPE 338 147 111
D27V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                8                338
  N1                3                147
  N2                4                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 442  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  442   84
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               11                442
  1                4                 84
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   4
  15Q GAIN WILD-TYPE 278 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    4
  15Q GAIN WILD-TYPE  278  321
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               11                278
  MALE                  4                321
[1] 2 2
[1] FALSE
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    11   1
  15Q GAIN WILD-TYPE 471  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     11    1
  15Q GAIN WILD-TYPE  471   28
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                11                471
  YES                1                 28
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q GAIN MUTATED                     10                             1
  15Q GAIN WILD-TYPE                  372                            61
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  15Q GAIN MUTATED                       2                              2
  15Q GAIN WILD-TYPE                   144                             11
D27V10, multiclass
                                clus
vv                               15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         10                372
  COLON MUCINOUS ADENOCARCINOMA                 1                 61
  RECTAL ADENOCARCINOMA                         2                144
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[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                  R0  R1  R2  RX
  15Q GAIN MUTATED    11   0   1   1
  15Q GAIN WILD-TYPE 435   6  36  28
D27V11, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0               11                435
  R1                0                  6
  R2                1                 36
  RX                1                 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"
D27V12, continuous
D27V13, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0  11
  15Q GAIN WILD-TYPE   5 341
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0   11
  15Q GAIN WILD-TYPE    5  341
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               11                341
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   118  23
  16P GAIN WILD-TYPE 348 105
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               141                453 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                105 
$`16P GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       24.33        45.60        13.02        19.99        19.99        19.00 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3976 
       14.93        24.03        29.98        12.99         2.01        26.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A014 
        1.94        49.08        63.62        13.94        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 
       36.03        31.00        21.24        39.45        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 
       44.91        35.11        16.57        37.25        32.45        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 
       29.19        29.16        24.13        23.87        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       12.99        33.99        24.00        50.04        47.01        15.02 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 
       36.95        37.02        17.03        33.07         0.99        17.03 
TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 
       27.02        24.00        20.98        34.03        16.08        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A03J 
       34.03        42.02        15.02        12.00        33.04        40.96 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
       22.42        27.42        26.47         0.95        33.01        17.26 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 
       18.84         5.13        62.79        29.56         5.23        12.69 
TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 
       12.59        14.30       148.01        21.99        20.02         8.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       13.02        22.98        32.02        17.03        14.04        29.03 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 
       14.99        15.02        10.06        19.59        18.25        25.48 
TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-F4-6460 
       15.12        12.49        13.41        11.38        38.20        31.96 
TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 
        1.55        82.39        65.85        44.68        55.04        39.42 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D 
       26.43        13.78        46.75        15.65        12.79        21.90 
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       39.48        37.74        24.36        20.02        86.63        65.98 
TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3885 TCGA-AG-3909 
       34.03         6.05        20.98         7.99        17.95        19.99 
TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 
       36.03        46.03         9.07        38.96        38.04        27.55 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       44.78        47.44        78.12        25.05        31.00        12.00 
TCGA-DC-6683 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
       25.05        24.13         3.48        17.69        16.31        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
       28.57         0.39        11.87 

$`16P GAIN WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 
        0.99        17.95        23.01         6.05         0.92        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3972 
       85.05        19.04        19.04        31.07        24.00        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       19.99        17.03        25.97        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2686 
       46.65        43.76        42.90        42.28        37.05        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        32.75        36.53        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       14.01        21.01        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       38.99         0.00        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       32.05        31.07        53.00        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       33.01        26.01         2.01        21.99        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK 
       18.05        12.16        83.24        24.53         5.79        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 
        0.46         0.92        14.50        27.09        16.31         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       21.44        17.82        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        1.41         5.65        32.94        22.36        65.00        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       49.41         6.77        12.10        11.74         3.19        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.46        12.39        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56        85.45        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        23.05        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 
       26.04        27.02        29.06        22.03        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       43.27        17.85         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
      133.18         8.35        74.56        67.30        53.62        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       61.91        36.00        26.04        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        19.33         9.93        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        46.92        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 
       34.49        29.98        16.83        24.59        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 
       12.03         0.99        15.95        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        25.02        32.02        28.04        14.04         1.02 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        3.98        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
        1.02         1.02        49.97         1.94        61.97        41.00 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       38.56         2.50        43.20        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
       33.17        13.78        48.20         7.17        21.01        26.04 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        42.35        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       38.14        12.46        47.08 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.39               0.00 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            148.01             140.38 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             24.13              21.01 
[1] "0.4 - 148.0 (24.1)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   106  41
  16P GAIN WILD-TYPE 342 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    106   41
  16P GAIN WILD-TYPE  342  121
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON               106                342
  RECTUM               41                121
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16P GAIN MUTATED        18        1        4        31         3         0
  16P GAIN WILD-TYPE      86        0       33       141         9         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P GAIN MUTATED           8          7         24         20       17
  16P GAIN WILD-TYPE        16          8         60         35       46
                    vv
clus                 STAGE IVA STAGE IVB
  16P GAIN MUTATED           6         1
  16P GAIN WILD-TYPE        18         1
D28V4, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  18                 86
  STAGE IA                  1                  0
  STAGE II                  4                 33
  STAGE IIA                31                141
  STAGE IIB                 3                  9
  STAGE IIC                 0                  2
  STAGE III                 8                 16
  STAGE IIIA                7                  8
  STAGE IIIB               24                 60
  STAGE IIIC               20                 35
  STAGE IV                 17                 46
  STAGE IVA                 6                 18
  STAGE IVB                 1                  1
[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     5  25 100  16
  16P GAIN WILD-TYPE  15  80 317  53
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                5                 15
  T2               25                 80
  T3              100                317
  T4               16                 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"
                    vv
clus                  N0  N1  N2
  16P GAIN MUTATED    64  46  36
  16P GAIN WILD-TYPE 282 104  79
D28V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               64                282
  N1               46                104
  N2               36                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   101  24
  16P GAIN WILD-TYPE 352  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    101   24
  16P GAIN WILD-TYPE  352   64
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0              101                352
  1               24                 64
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    70  78
  16P GAIN WILD-TYPE 219 247
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     70   78
  16P GAIN WILD-TYPE  219  247
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               70                219
  MALE                 78                247
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   122   9
  16P GAIN WILD-TYPE 360  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    122    9
  16P GAIN WILD-TYPE  360   20
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               122                360
  YES                9                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P GAIN MUTATED                    100                             5
  16P GAIN WILD-TYPE                  282                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16P GAIN MUTATED                      41                              0
  16P GAIN WILD-TYPE                   105                             13
D28V10, multiclass
                                clus
vv                               16P GAIN MUTATED 16P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        100                282
  COLON MUCINOUS ADENOCARCINOMA                 5                 57
  RECTAL ADENOCARCINOMA                        41                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  16P GAIN MUTATED   111   1  10   7
  16P GAIN WILD-TYPE 335   5  27  22
D28V11, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0              111                335
  R1                1                  5
  R2               10                 27
  RX                7                 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"
D28V12, continuous
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     1  82
  16P GAIN WILD-TYPE   4 270
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1   82
  16P GAIN WILD-TYPE    4  270
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               82                270
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   114  25
  16Q GAIN WILD-TYPE 352 103
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               139                455 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                25                103 
$`16Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3844 
       24.33        45.60        13.02        19.99        19.00        14.93 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3976 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 
       24.03        12.99        26.01         1.94        49.08        63.62 
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       10.39        13.94        17.03        15.95        36.03        31.00 
TCGA-BM-6198 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 
       21.24        39.45        43.76        43.43        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 TCGA-A6-6140 
       16.57        37.25        32.45        30.44        29.16        24.13 
TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3553 
       23.87        29.00        26.01        12.99        33.99        24.00 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       50.04        47.01        15.02        36.95        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3955 
       33.07         0.99        17.03        27.02        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C 
       34.03        16.08        27.02        34.03        42.02        15.02 
TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.00        33.04        40.96        22.42        27.42        26.47 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 
        0.95        33.01        17.26        18.84         5.13        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5914 
       29.56         5.23        12.69        12.59       148.01        21.99 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 
       20.02         8.02        13.02        22.98        32.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6679 TCGA-D5-5539 
       14.04        29.03        14.99        15.02        10.06        19.59 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 
       18.25        25.48        15.12        17.13        12.49        10.13 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 
       13.41        11.38        38.20        35.97         8.61        31.96 
TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6320 
        1.55        82.39        44.68        55.04        39.42        26.43 
TCGA-G4-6323 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-3911 
       13.78        15.65        12.79        21.90        39.48        37.74 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3592 TCGA-AG-3725 
       24.36        20.02        86.63        65.98        34.03        20.98 
TCGA-AG-3885 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A02G 
       17.95        19.99        36.03        46.03         9.07        38.96 
TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 
       38.04        27.55        47.44        78.12        25.05        31.00 
TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 
       12.00        25.05        24.13        51.48         3.48        17.69 
TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       16.31        49.51        28.57         0.39        36.49        19.66 
TCGA-F5-6863 
       11.87 

$`16Q GAIN WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
        0.99        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 
       36.00        85.05        19.04        19.04        31.07        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        50.99        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
       75.95       106.75       100.01         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 
       17.85         8.02        19.99        17.03        25.97        51.98 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       18.28        55.76        26.43        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        1.61         9.53        46.65        43.76        42.90        42.28 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       37.05        37.02        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        22.52         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3555 
       19.07         0.00        29.00        14.01        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01        47.05        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 
        1.02        17.98        15.95        38.99         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       18.05        31.00         2.01        33.01        26.01         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       21.99        13.05        34.06        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       22.03        41.00        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       24.53         5.79        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31         0.20        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        37.02        25.02        26.04        27.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       15.02        15.02        12.00        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        11.01        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 
       55.92        20.19        20.42        17.75        43.27        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.80        16.14        15.58         7.53        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
      119.93        60.79       117.07        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18         8.35        74.56        67.30        65.85        53.62 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 TCGA-G4-6627 
       85.48        61.91        36.00        26.04        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 
       18.18        10.98        19.33        19.33         9.93        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       60.13        11.90        70.03        46.92        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 
       13.55        37.97        34.49        29.98        16.83        24.59 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 
       32.02        28.04        14.04         1.02         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        23.01        37.02         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        61.97        41.00        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       43.20        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
       44.78        48.20         7.17        21.01        26.04        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
       12.62       126.44        41.36        57.24       129.27        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       13.64        17.46        11.97         8.45         9.96        42.35 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       32.19        37.18        38.14        12.46        47.08 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.39               0.00 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            148.01             140.38 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             24.13              21.14 
[1] "0.4 - 148.0 (24.1)" "0.0 - 140.4 (21.1)"
[1] "hr=" "1.2"
D29V2, continuous
D29V3, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   103  41
  16Q GAIN WILD-TYPE 345 121
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    103   41
  16Q GAIN WILD-TYPE  345  121
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON               103                345
  RECTUM               41                121
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16Q GAIN MUTATED        17        1        4        30         2         0
  16Q GAIN WILD-TYPE      87        0       33       142        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q GAIN MUTATED           8          8         26         17       16
  16Q GAIN WILD-TYPE        16          7         58         38       47
                    vv
clus                 STAGE IVA STAGE IVB
  16Q GAIN MUTATED           7         1
  16Q GAIN WILD-TYPE        17         1
D29V4, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  17                 87
  STAGE IA                  1                  0
  STAGE II                  4                 33
  STAGE IIA                30                142
  STAGE IIB                 2                 10
  STAGE IIC                 0                  2
  STAGE III                 8                 16
  STAGE IIIA                8                  7
  STAGE IIIB               26                 58
  STAGE IIIC               17                 38
  STAGE IV                 16                 47
  STAGE IVA                 7                 17
  STAGE IVB                 1                  1
[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     5  24  99  15
  16Q GAIN WILD-TYPE  15  81 318  54
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                5                 15
  T2               24                 81
  T3               99                318
  T4               15                 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"
                    vv
clus                  N0  N1  N2
  16Q GAIN MUTATED    61  48  34
  16Q GAIN WILD-TYPE 285 102  81
D29V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               61                285
  N1               48                102
  N2               34                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    98  24
  16Q GAIN WILD-TYPE 355  64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     98   24
  16Q GAIN WILD-TYPE  355   64
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               98                355
  1               24                 64
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    69  76
  16Q GAIN WILD-TYPE 220 249
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     69   76
  16Q GAIN WILD-TYPE  220  249
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               69                220
  MALE                 76                249
[1] 2 2
[1] FALSE
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   122   7
  16Q GAIN WILD-TYPE 360  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    122    7
  16Q GAIN WILD-TYPE  360   22
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO               122                360
  YES                7                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q GAIN MUTATED                     97                             5
  16Q GAIN WILD-TYPE                  285                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16Q GAIN MUTATED                      41                              0
  16Q GAIN WILD-TYPE                   105                             13
D29V10, multiclass
                                clus
vv                               16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         97                285
  COLON MUCINOUS ADENOCARCINOMA                 5                 57
  RECTAL ADENOCARCINOMA                        41                105
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  16Q GAIN MUTATED   110   1   9   6
  16Q GAIN WILD-TYPE 336   5  28  23
D29V11, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0              110                336
  R1                1                  5
  R2                9                 28
  RX                6                 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"
D29V12, continuous
D29V13, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     1  85
  16Q GAIN WILD-TYPE   4 267
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1   85
  16Q GAIN WILD-TYPE    4  267
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               85                267
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED    37   2
  17P GAIN WILD-TYPE 429 126
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                39                555 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                126 
$`17P GAIN MUTATED`
TCGA-AA-3506 TCGA-AA-3939 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       58.03        12.99        26.43        15.62         4.80        12.66 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6652 TCGA-AA-3812 
       37.02        36.53        29.19        25.08        24.69        35.05 
TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-CA-6715 
        1.02        17.03         2.01        13.05        34.06        12.59 
TCGA-CK-4948 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6535 TCGA-D5-6537 
      148.01        22.03        14.04        11.01        15.12         4.80 
TCGA-D5-6929 TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6317 TCGA-QG-A5YW 
       13.41        95.18         1.55        74.56        36.00        29.46 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-4007 
        7.07        46.03        15.95        19.99        19.99         1.02 
TCGA-AH-6897 TCGA-CI-6623 TCGA-DC-6682 
       26.43        47.44        25.05 

$`17P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       55.76         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       16.57        37.05        37.25        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        20.61        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       36.95        37.02         0.00        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       18.25        25.48        43.27        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        47.87        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        39.42        61.91        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        9.93        15.65        12.79        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02        36.03        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        43.20        27.55        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.02               0.00 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            148.01             140.38 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             19.99              22.03 
[1] "1.0 - 148.0 (20.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "4.2"
D30V2, continuous
D30V3, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    29  10
  17P GAIN WILD-TYPE 419 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     29   10
  17P GAIN WILD-TYPE  419  152
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON                29                419
  RECTUM               10                152
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17P GAIN MUTATED        10        0        0        10         0         0
  17P GAIN WILD-TYPE      94        1       37       162        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P GAIN MUTATED           1          1          5          6        3
  17P GAIN WILD-TYPE        23         14         79         49       60
                    vv
clus                 STAGE IVA STAGE IVB
  17P GAIN MUTATED           3         0
  17P GAIN WILD-TYPE        21         2
D30V4, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  10                 94
  STAGE IA                  0                  1
  STAGE II                  0                 37
  STAGE IIA                10                162
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 1                 23
  STAGE IIIA                1                 14
  STAGE IIIB                5                 79
  STAGE IIIC                6                 49
  STAGE IV                  3                 60
  STAGE IVA                 3                 21
  STAGE IVB                 0                  2
[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     3   8  24   4
  17P GAIN WILD-TYPE  17  97 393  65
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                3                 17
  T2                8                 97
  T3               24                393
  T4                4                 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"
                    vv
clus                  N0  N1  N2
  17P GAIN MUTATED    21  11   7
  17P GAIN WILD-TYPE 325 139 108
D30V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               21                325
  N1               11                139
  N2                7                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    26   6
  17P GAIN WILD-TYPE 427  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     26    6
  17P GAIN WILD-TYPE  427   82
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               26                427
  1                6                 82
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    18  21
  17P GAIN WILD-TYPE 271 304
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     18   21
  17P GAIN WILD-TYPE  271  304
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               18                271
  MALE                 21                304
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    33   1
  17P GAIN WILD-TYPE 449  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     33    1
  17P GAIN WILD-TYPE  449   28
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                33                449
  YES                1                 28
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P GAIN MUTATED                     24                             5
  17P GAIN WILD-TYPE                  358                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17P GAIN MUTATED                       9                              1
  17P GAIN WILD-TYPE                   137                             12
D30V10, multiclass
                                clus
vv                               17P GAIN MUTATED 17P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         24                358
  COLON MUCINOUS ADENOCARCINOMA                 5                 57
  RECTAL ADENOCARCINOMA                         9                137
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[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                  R0  R1  R2  RX
  17P GAIN MUTATED    29   0   2   2
  17P GAIN WILD-TYPE 417   6  35  27
D30V11, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0               29                417
  R1                0                  6
  R2                2                 35
  RX                2                 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"
D30V12, continuous
D30V13, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     1  24
  17P GAIN WILD-TYPE   4 328
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1   24
  17P GAIN WILD-TYPE    4  328
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               24                328
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    95  15
  17Q GAIN WILD-TYPE 371 113
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               110                484 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                113 
$`17Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3556 TCGA-AA-3692 
       24.33        14.53         1.02        58.03        23.01        36.00 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6888 
       24.03        12.99        50.99        38.04        21.99        15.52 
TCGA-DM-A285 TCGA-G4-6310 TCGA-NH-A8F7 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01N 
        5.88        63.62        17.85        17.03        15.95        31.00 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2675 
       26.43        15.62        12.66         1.61        39.45        43.43 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       37.02        36.53        30.44        29.19        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-AA-3494 TCGA-AA-3553 
       27.09        25.08        25.18        24.69         1.02        24.00 
TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3956 TCGA-AA-3966 
       35.05         1.02        17.03         0.99        34.03         2.01 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A01S TCGA-AA-A02W TCGA-AD-6890 
       13.05        34.06        27.02         1.02        41.00        24.53 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6607 
       27.42        16.44        16.31        88.21        29.56         3.19 
TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 
       12.59       148.01         8.02        29.06        22.03        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 
       14.04        29.03        21.99        14.99        13.05        11.08 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       11.01        19.59        55.92        25.48        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6307 
       17.13        13.41       130.65        95.18        74.56        55.04 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-QG-A5YW TCGA-RU-A8FL 
       39.42        36.00        26.43        46.75        29.46        38.70 
TCGA-AF-2690 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3593 
       17.23        11.84        12.00         7.07        46.03        34.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A016 
       15.95        19.99        19.99        36.03         1.02         9.07 
TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-DC-6154 TCGA-DC-6682 
       43.20        26.43         6.05        13.78        12.00        25.05 
TCGA-DC-6683 TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
       25.05        51.48        17.00        18.28        16.31        11.97 
TCGA-F5-6811 TCGA-F5-6864 
       32.19        12.46 

$`17Q GAIN WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       45.60        13.94        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       85.05        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 
       24.00         2.01        26.01        24.00        19.07        39.06 
TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       21.37        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 
        1.94        49.08        28.21        23.51        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 
       35.80        26.17        91.79        79.69        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A023 
       13.94        19.99        17.03        25.97        36.03        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 
       21.24        18.28        55.76         4.80         9.53        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.76        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       16.57        37.05        37.25        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.52        24.13         8.38        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       26.01        12.99        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
        0.99        25.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02         0.00        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       36.03        32.05        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       20.98        21.99        16.08        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6901 
       18.05        40.96        12.16        83.24         5.79        22.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       26.47         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
       32.94         5.13        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
        6.77        12.10         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.46        12.39        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 
       15.02        14.04        11.01        12.95        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 
       12.03        45.40        54.61        56.09        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       17.75        18.25        43.27        17.85        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43        38.20        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 
       67.30        65.85        53.62        44.68        85.48        61.91 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        13.78        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        46.92        39.48        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 
       24.59        86.63        65.98        36.03        32.02        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 
       20.05        24.00         1.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 
       50.04        12.03         6.05         0.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        23.01        37.02         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        2.50        27.55        19.46        33.17        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       31.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.97        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       20.91        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57         0.39        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       37.18        38.14        11.87        47.08 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.99               0.00 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            148.01             140.38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            23.505             21.945 
[1] "1.0 - 148.0 (23.5)" "0.0 - 140.4 (21.9)"
[1] "hr=" "1.6"
D31V2, continuous
D31V3, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    82  31
  17Q GAIN WILD-TYPE 366 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     82   31
  17Q GAIN WILD-TYPE  366  131
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON                82                366
  RECTUM               31                131
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17Q GAIN MUTATED        18        0        3        27         0         1
  17Q GAIN WILD-TYPE      86        1       34       145        12         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q GAIN MUTATED           4          4         17         11       15
  17Q GAIN WILD-TYPE        20         11         67         44       48
                    vv
clus                 STAGE IVA STAGE IVB
  17Q GAIN MUTATED           7         1
  17Q GAIN WILD-TYPE        17         1
D31V4, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  18                 86
  STAGE IA                  0                  1
  STAGE II                  3                 34
  STAGE IIA                27                145
  STAGE IIB                 0                 12
  STAGE IIC                 1                  1
  STAGE III                 4                 20
  STAGE IIIA                4                 11
  STAGE IIIB               17                 67
  STAGE IIIC               11                 44
  STAGE IV                 15                 48
  STAGE IVA                 7                 17
  STAGE IVB                 1                  1
[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     5  20  78  10
  17Q GAIN WILD-TYPE  15  85 339  59
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                 15
  T2               20                 85
  T3               78                339
  T4               10                 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"
                    vv
clus                  N0  N1  N2
  17Q GAIN MUTATED    58  32  23
  17Q GAIN WILD-TYPE 288 118  92
D31V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               58                288
  N1               32                118
  N2               23                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    72  23
  17Q GAIN WILD-TYPE 381  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     72   23
  17Q GAIN WILD-TYPE  381   65
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               72                381
  1               23                 65
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    51  62
  17Q GAIN WILD-TYPE 238 263
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     51   62
  17Q GAIN WILD-TYPE  238  263
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               51                238
  MALE                 62                263
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    91   6
  17Q GAIN WILD-TYPE 391  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     91    6
  17Q GAIN WILD-TYPE  391   23
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                91                391
  YES                6                 23
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q GAIN MUTATED                     74                             7
  17Q GAIN WILD-TYPE                  308                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17Q GAIN MUTATED                      30                              1
  17Q GAIN WILD-TYPE                   116                             12
D31V10, multiclass
                                clus
vv                               17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         74                308
  COLON MUCINOUS ADENOCARCINOMA                 7                 55
  RECTAL ADENOCARCINOMA                        30                116
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[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                  R0  R1  R2  RX
  17Q GAIN MUTATED    79   1  10   2
  17Q GAIN WILD-TYPE 367   5  27  27
D31V11, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               79                367
  R1                1                  5
  R2               10                 27
  RX                2                 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"
D31V12, continuous
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     3  69
  17Q GAIN WILD-TYPE   2 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3   69
  17Q GAIN WILD-TYPE    2  283
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO               69                283
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    21   8
  18P GAIN WILD-TYPE 445 120
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                29                565 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                120 
$`18P GAIN MUTATED`
TCGA-A6-6649 TCGA-DM-A285 TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3811 TCGA-AA-A01D 
       24.16         5.88        54.02         5.98        10.06        10.98 
TCGA-AA-A01Z TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CM-4751 TCGA-CM-6171 
       37.02        12.16         0.20         3.19        27.02        14.04 
TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A1DA 
       13.05        11.08        17.75        16.14        11.64         7.50 
TCGA-DM-A28K TCGA-G4-6299 TCGA-NH-A50V TCGA-NH-A6GA TCGA-AF-6672 TCGA-AG-3578 
       98.24        74.56        19.33         9.93        24.59        32.02 
TCGA-AG-3600 TCGA-AG-A02G TCGA-CI-6621 TCGA-DT-5265 TCGA-F5-6464 
        6.05        38.96        13.78        12.62         9.96 

$`18P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
       49.08        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       55.76        26.43        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.25        37.02        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 
       47.05        47.01        15.02        11.01        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       12.69        12.36        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04         8.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        12.49        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 
       10.13        12.43        14.30         9.04         9.44        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18         8.35        82.39        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       10.98        19.33        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       60.13        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        24.36        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       27.55        26.43        19.46         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        25.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               0.2                0.0 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             98.24             148.01 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             13.05              22.36 
[1] "0.2 - 98.2 (13.1)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D32V2, continuous
D32V3, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    23   8
  18P GAIN WILD-TYPE 425 154
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     23    8
  18P GAIN WILD-TYPE  425  154
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON                23                425
  RECTUM                8                154
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18P GAIN MUTATED         4        0        5         4         0         0
  18P GAIN WILD-TYPE     100        1       32       168        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P GAIN MUTATED           2          0          4          7        4
  18P GAIN WILD-TYPE        22         15         80         48       59
                    vv
clus                 STAGE IVA STAGE IVB
  18P GAIN MUTATED           0         1
  18P GAIN WILD-TYPE        24         1
D32V4, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   4                100
  STAGE IA                  0                  1
  STAGE II                  5                 32
  STAGE IIA                 4                168
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 2                 22
  STAGE IIIA                0                 15
  STAGE IIIB                4                 80
  STAGE IIIC                7                 48
  STAGE IV                  4                 59
  STAGE IVA                 0                 24
  STAGE IVB                 1                  1
[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     0   5  21   5
  18P GAIN WILD-TYPE  20 100 396  64
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                 20
  T2                5                100
  T3               21                396
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  18P GAIN MUTATED    13   5  13
  18P GAIN WILD-TYPE 333 145 102
D32V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               13                333
  N1                5                145
  N2               13                102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    22   4
  18P GAIN WILD-TYPE 431  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     22    4
  18P GAIN WILD-TYPE  431   84
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               22                431
  1                4                 84
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    11  20
  18P GAIN WILD-TYPE 278 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     11   20
  18P GAIN WILD-TYPE  278  305
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               11                278
  MALE                 20                305
[1] 2 2
[1] FALSE
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    21   3
  18P GAIN WILD-TYPE 461  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     21    3
  18P GAIN WILD-TYPE  461   26
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                21                461
  YES                3                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P GAIN MUTATED                     16                             7
  18P GAIN WILD-TYPE                  366                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18P GAIN MUTATED                       6                              2
  18P GAIN WILD-TYPE                   140                             11
D32V10, multiclass
                                clus
vv                               18P GAIN MUTATED 18P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         16                366
  COLON MUCINOUS ADENOCARCINOMA                 7                 55
  RECTAL ADENOCARCINOMA                         6                140
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[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                  R0  R1  R2  RX
  18P GAIN MUTATED    22   0   1   1
  18P GAIN WILD-TYPE 424   6  36  28
D32V11, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0               22                424
  R1                0                  6
  R2                1                 36
  RX                1                 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"
D32V12, continuous
D32V13, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     0  21
  18P GAIN WILD-TYPE   5 331
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      0   21
  18P GAIN WILD-TYPE    5  331
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               21                331
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    14   4
  18Q GAIN WILD-TYPE 452 124
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                18                576 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                124 
$`18Q GAIN MUTATED`
TCGA-AA-3664 TCGA-AA-3681 TCGA-AA-3811 TCGA-AD-5900 TCGA-AY-6196 TCGA-AZ-6607 
       54.02         5.98        10.06        12.16         0.20         3.19 
TCGA-CM-6171 TCGA-D5-6531 TCGA-D5-6540 TCGA-D5-6928 TCGA-DM-A28K TCGA-G4-6299 
       14.04        17.75        16.14        11.64        98.24        74.56 
TCGA-AF-6672 TCGA-AG-3600 TCGA-AG-A02G TCGA-CI-6621 TCGA-DT-5265 TCGA-F5-6464 
       24.59         6.05        38.96        13.78        12.62         9.96 

$`18Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 
       20.98        13.94        61.02        78.08         6.97         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        40.96        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       17.85         4.80        17.13        12.49        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79       117.07        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
        9.07         1.02         1.02        49.97         1.94        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46         6.05        33.17        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               0.2                0.0 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             98.24             148.01 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             13.20              22.09 
[1] "0.2 - 98.2 (13.2)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    13   6
  18Q GAIN WILD-TYPE 435 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     13    6
  18Q GAIN WILD-TYPE  435  156
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON                13                435
  RECTUM                6                156
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18Q GAIN MUTATED         3        0        3         3         0         0
  18Q GAIN WILD-TYPE     101        1       34       169        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q GAIN MUTATED           2          0          1          4        3
  18Q GAIN WILD-TYPE        22         15         83         51       60
                    vv
clus                 STAGE IVA STAGE IVB
  18Q GAIN MUTATED           0         0
  18Q GAIN WILD-TYPE        24         2
D33V4, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  3                 34
  STAGE IIA                 3                169
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 2                 22
  STAGE IIIA                0                 15
  STAGE IIIB                1                 83
  STAGE IIIC                4                 51
  STAGE IV                  3                 60
  STAGE IVA                 0                 24
  STAGE IVB                 0                  2
[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     0   4  11   4
  18Q GAIN WILD-TYPE  20 101 406  65
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                 20
  T2                4                101
  T3               11                406
  T4                4                 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"
                    vv
clus                  N0  N1  N2
  18Q GAIN MUTATED     9   3   7
  18Q GAIN WILD-TYPE 337 147 108
D33V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                9                337
  N1                3                147
  N2                7                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    13   2
  18Q GAIN WILD-TYPE 440  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     13    2
  18Q GAIN WILD-TYPE  440   86
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               13                440
  1                2                 86
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     6  13
  18Q GAIN WILD-TYPE 283 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      6   13
  18Q GAIN WILD-TYPE  283  312
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                6                283
  MALE                 13                312
[1] 2 2
[1] FALSE
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    12   3
  18Q GAIN WILD-TYPE 470  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     12    3
  18Q GAIN WILD-TYPE  470   26
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                12                470
  YES                3                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                      8                             5
  18Q GAIN WILD-TYPE                  374                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q GAIN MUTATED                       5                              1
  18Q GAIN WILD-TYPE                   141                             12
D33V10, multiclass
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                          8                374
  COLON MUCINOUS ADENOCARCINOMA                 5                 57
  RECTAL ADENOCARCINOMA                         5                141
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[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                  R0  R1  R2  RX
  18Q GAIN MUTATED    13   0   1   1
  18Q GAIN WILD-TYPE 433   6  36  28
D33V11, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0               13                433
  R1                0                  6
  R2                1                 36
  RX                1                 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"
D33V12, continuous
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     0  13
  18Q GAIN WILD-TYPE   5 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0   13
  18Q GAIN WILD-TYPE    5  339
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               13                339
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    82  18
  19P GAIN WILD-TYPE 384 110
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               100                494 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                18                110 
$`19P GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3972 TCGA-AA-A00Z TCGA-G4-6310 
       45.60        14.53        58.03        50.99        21.99        63.62 
TCGA-NH-A8F7 TCGA-AG-A014 TCGA-AG-A01N TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 
       17.85        15.95        31.00        15.62        12.66        43.76 
TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-6648 
       43.43        16.57        37.02        36.53        31.63        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 
       21.76        23.87        56.25        37.05        35.05         0.99 
TCGA-AA-3858 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00Q 
       31.07        13.05        27.02        13.94        18.05        42.02 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-A8YK 
       51.98         0.92         5.79        22.42        16.44        18.84 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 
       88.21        29.56        11.74        12.36        14.30        85.45 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 
       21.99         2.01        25.02        13.02        29.06        32.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02        14.04        29.03        21.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6932 
       13.02        11.08        19.59        56.09        15.12        11.38 
TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6311 
      119.70        35.97         8.61        82.39        74.56        39.42 
TCGA-G4-6320 TCGA-G4-6627 TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-2690 
       26.43        74.79        29.46        21.90        39.48        17.23 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       86.63        65.98        36.03        46.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4001 
        6.05        19.99         0.99        19.99         1.02        36.03 
TCGA-AG-4007 TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-CI-6621 TCGA-DC-4745 
        1.02         1.94        38.04         6.05        13.78        21.01 
TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 
       25.05        12.00        51.98        25.05       129.27        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
       17.69        16.31        13.64        11.87 

$`19P GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        13.94        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       14.93        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
        2.01        26.01        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       25.97        36.03        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       26.43         4.80         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 
       43.76        42.90        42.28        44.91        35.11        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       37.25        34.65        32.75        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        34.06        25.02        27.02         7.96 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        27.42        26.47         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       65.00        62.79        49.41         6.77        12.10         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.46        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 
       12.20        12.76        10.06        17.56       148.01        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14        82.95       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 
       20.02        37.02        26.04         8.02        27.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       22.98        30.08        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        54.61        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        43.27        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       13.35        12.00        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50T 
       61.91        36.00        26.04        13.78        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       16.80        42.77        32.98         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 
       60.13        11.90        70.03        46.92        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        24.59        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
        7.07        20.05        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        0.99        29.98        37.02        32.98         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        28.04        14.04 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       37.02         9.07         1.02         1.02        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43        19.46        33.17        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       78.12         7.17        26.04        31.00        13.97        31.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        4.18        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.92               0.00 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            129.27             148.01 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             21.99              22.03 
[1] "0.9 - 129.3 (22.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D34V2, continuous
D34V3, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    72  33
  19P GAIN WILD-TYPE 376 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     72   33
  19P GAIN WILD-TYPE  376  129
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON                72                376
  RECTUM               33                129
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19P GAIN MUTATED        18        0        5        31         0         0
  19P GAIN WILD-TYPE      86        1       32       141        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P GAIN MUTATED           3          2         19          7       13
  19P GAIN WILD-TYPE        21         13         65         48       50
                    vv
clus                 STAGE IVA STAGE IVB
  19P GAIN MUTATED           5         0
  19P GAIN WILD-TYPE        19         2
D34V4, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  18                 86
  STAGE IA                  0                  1
  STAGE II                  5                 32
  STAGE IIA                31                141
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 3                 21
  STAGE IIIA                2                 13
  STAGE IIIB               19                 65
  STAGE IIIC                7                 48
  STAGE IV                 13                 50
  STAGE IVA                 5                 19
  STAGE IVB                 0                  2
[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     2  19  74  10
  19P GAIN WILD-TYPE  18  86 343  59
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                2                 18
  T2               19                 86
  T3               74                343
  T4               10                 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"
                    vv
clus                  N0  N1  N2
  19P GAIN MUTATED    58  31  16
  19P GAIN WILD-TYPE 288 119  99
D34V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               58                288
  N1               31                119
  N2               16                 99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    71  18
  19P GAIN WILD-TYPE 382  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     71   18
  19P GAIN WILD-TYPE  382   70
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               71                382
  1               18                 70
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    44  61
  19P GAIN WILD-TYPE 245 264
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     44   61
  19P GAIN WILD-TYPE  245  264
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               44                245
  MALE                 61                264
[1] 2 2
[1] FALSE
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    79   7
  19P GAIN WILD-TYPE 403  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     79    7
  19P GAIN WILD-TYPE  403   22
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                79                403
  YES                7                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P GAIN MUTATED                     64                             8
  19P GAIN WILD-TYPE                  318                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19P GAIN MUTATED                      33                              0
  19P GAIN WILD-TYPE                   113                             13
D34V10, multiclass
                                clus
vv                               19P GAIN MUTATED 19P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         64                318
  COLON MUCINOUS ADENOCARCINOMA                 8                 54
  RECTAL ADENOCARCINOMA                        33                113
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  19P GAIN MUTATED    76   2   5   7
  19P GAIN WILD-TYPE 370   4  32  22
D34V11, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               76                370
  R1                2                  4
  R2                5                 32
  RX                7                 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"
D34V12, continuous
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     0  68
  19P GAIN WILD-TYPE   5 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0   68
  19P GAIN WILD-TYPE    5  284
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               68                284
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    88  18
  19Q GAIN WILD-TYPE 378 110
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
               106                488 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                18                110 
$`19Q GAIN MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3939 TCGA-AA-3972 TCGA-G4-6310 
       45.60        14.53        58.03        12.99        50.99        63.62 
TCGA-NH-A8F7 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-3L-AA1B TCGA-4T-AA8H 
       17.85        15.95        36.03        31.00        15.62        12.66 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 
       39.45        43.76        43.43        16.57        37.02        36.53 
TCGA-A6-5657 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 
       31.63        25.08        25.18        21.76        23.87        61.84 
TCGA-A6-A56B TCGA-AA-3502 TCGA-AA-3529 TCGA-AA-3542 TCGA-AA-3812 TCGA-AA-3818 
       56.25        35.01         0.00        12.99        35.05         0.99 
TCGA-AA-3854 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01G 
       36.03        13.05        18.05        27.02        42.02        12.00 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       51.98         0.92         5.79        22.42        26.47        16.44 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 
        0.20        17.85        18.84        88.21        29.56        11.74 
TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 
       12.36        14.30        85.45        21.99         2.01        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-6161 
       25.02        13.02        29.06        32.02        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        21.99        11.08        19.59        15.12 
TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F 
        4.80        11.64        12.00        11.38       119.70        35.97 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6320 
        8.61        35.74        47.41        82.39        39.42        26.43 
TCGA-G4-6627 TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-A56K TCGA-AF-A56L 
       74.79        29.46        21.90        39.48        86.63        65.98 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 
       46.03        34.03        19.99         0.99        19.99         1.02 
TCGA-AG-4007 TCGA-AG-A016 TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-CI-6621 
        1.02         9.07         1.94        38.04         6.05        13.78 
TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 
       25.05        12.00        51.98        25.05       129.27        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
       17.69        16.31        13.64        11.87 

$`19Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        13.94        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       25.97        51.98        21.24        18.28        55.76        26.43 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        4.80         1.61         9.53        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       42.28        44.91        35.11        37.05        37.25        34.65 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.45        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       22.52        24.13         8.38        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU 
       20.12        19.66        20.28        16.24        24.92         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3510 
        5.03         7.04         3.02         1.02        37.05        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        10.06        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       18.05         4.01         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        10.98        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       83.24        24.53        27.42         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.26        19.33       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
       32.94         5.13        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
        6.77        12.10         5.23         3.19        12.69        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56       148.01        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 
       82.95       124.27        23.05        20.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       27.02        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        17.03        12.00        16.04        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       25.48        43.27        17.85        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD 
        9.04         9.44        13.41        13.35        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      139.17        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        98.24        95.18        31.96        11.11        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       33.67        13.25         0.53        35.31       133.18         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       85.48        61.91        36.00        26.04        13.78        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        42.77        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 
       38.70        60.13        11.90        70.03        46.92        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 
       16.83        24.36        20.02        24.59        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 
       29.98        37.02        32.98         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       17.95        36.95        13.02        35.01        14.01        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       37.02         1.02         1.02        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       19.46        33.17        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
        7.17        21.01        26.04        31.00        13.97        31.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        4.18        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 0                  0 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            129.27             148.01 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             21.99              22.03 
[1] "0.0 - 129.3 (22.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D35V2, continuous
D35V3, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    81  32
  19Q GAIN WILD-TYPE 367 130
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     81   32
  19Q GAIN WILD-TYPE  367  130
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON                81                367
  RECTUM               32                130
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19Q GAIN MUTATED        21        0        4        33         0         0
  19Q GAIN WILD-TYPE      83        1       33       139        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q GAIN MUTATED           2          2         19         10       14
  19Q GAIN WILD-TYPE        22         13         65         45       49
                    vv
clus                 STAGE IVA STAGE IVB
  19Q GAIN MUTATED           5         0
  19Q GAIN WILD-TYPE        19         2
D35V4, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  21                 83
  STAGE IA                  0                  1
  STAGE II                  4                 33
  STAGE IIA                33                139
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 2                 22
  STAGE IIIA                2                 13
  STAGE IIIB               19                 65
  STAGE IIIC               10                 45
  STAGE IV                 14                 49
  STAGE IVA                 5                 19
  STAGE IVB                 0                  2
[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     3  21  76  13
  19Q GAIN WILD-TYPE  17  84 341  56
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                 17
  T2               21                 84
  T3               76                341
  T4               13                 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"
                    vv
clus                  N0  N1  N2
  19Q GAIN MUTATED    62  32  19
  19Q GAIN WILD-TYPE 284 118  96
D35V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               62                284
  N1               32                118
  N2               19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    76  19
  19Q GAIN WILD-TYPE 377  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     76   19
  19Q GAIN WILD-TYPE  377   69
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               76                377
  1               19                 69
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    49  64
  19Q GAIN WILD-TYPE 240 261
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     49   64
  19Q GAIN WILD-TYPE  240  261
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               49                240
  MALE                 64                261
[1] 2 2
[1] FALSE
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    86   5
  19Q GAIN WILD-TYPE 396  24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     86    5
  19Q GAIN WILD-TYPE  396   24
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                86                396
  YES                5                 24
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q GAIN MUTATED                     69                            12
  19Q GAIN WILD-TYPE                  313                            50
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19Q GAIN MUTATED                      32                              0
  19Q GAIN WILD-TYPE                   114                             13
D35V10, multiclass
                                clus
vv                               19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         69                313
  COLON MUCINOUS ADENOCARCINOMA                12                 50
  RECTAL ADENOCARCINOMA                        32                114
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  19Q GAIN MUTATED    79   3   6   7
  19Q GAIN WILD-TYPE 367   3  31  22
D35V11, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               79                367
  R1                3                  3
  R2                6                 31
  RX                7                 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"
D35V12, continuous
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     2  72
  19Q GAIN WILD-TYPE   3 280
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      2   72
  19Q GAIN WILD-TYPE    3  280
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO               72                280
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   270  74
  20P GAIN WILD-TYPE 196  54
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               344                250 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                74                 54 
$`20P GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 
       19.99         6.05        19.00        36.00        85.05        14.93 
TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       31.07        12.99        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4681 
       38.04        21.99        21.37        15.52        25.08       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 
        1.94        49.08         5.88        28.21        63.62        35.93 
TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       91.79        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       17.03        25.97        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 
       18.28        55.76        15.62         4.80        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
       43.76        43.43        44.91        35.11        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       37.02        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 
       23.61        27.09        25.08        25.18        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       23.87        20.28        61.84         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3532 
        1.02        37.05         6.97         1.02         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3561 
       29.00        12.99        14.01        21.01        20.98        13.94 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 
        2.01        14.01        50.04        47.05        15.02        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 
        5.03        10.06        35.05         0.99        25.02        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       37.02         0.00        17.03        10.06        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 
       31.07        17.03        27.02        18.05        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3982 TCGA-AA-3989 
       34.03        21.99        16.08        13.05        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C 
       13.94        18.05         4.01        17.03        14.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01T 
       10.98        32.02        12.00        31.00        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        39.98        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 
       33.01        17.26        17.85        19.33        18.84         1.41 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        5.23         3.19        12.69        12.36        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CM-4744 
       12.59        14.30        17.56       148.01        85.45        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 
       25.02         8.02        13.02        29.06        22.98         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 
       21.99        14.99        13.02        14.04        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       11.08        11.01        45.40        54.61        19.59        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       17.75        18.25        25.48        17.85        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
       12.39        10.13         9.04        11.64        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F 
       12.59         7.50       139.17        14.04       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        95.18         8.61        31.96        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 
        1.55        41.42        33.67        47.41       133.18        82.39 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       55.04        39.42        61.91        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       74.79        18.18        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QL-A97D TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       29.46        32.98        21.90        46.92        39.48        17.23 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       37.97        37.74        16.83        20.02        24.59        65.98 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
       34.03        34.03        34.03        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       19.99        20.98         0.99        29.98        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
        0.99         1.02        36.95        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A02X 
       13.94         6.02        23.01        37.02         9.07        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       19.46         6.05        13.78        44.78        47.44        48.20 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
      126.44       129.27        24.13        32.61         4.18        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.41        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       49.51         0.39        32.19        36.49        37.18        38.14 
TCGA-F5-6863 TCGA-G5-6572 
       11.87        47.08 

$`20P GAIN WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3870 
       19.99         0.92        19.04        19.04        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       24.00         2.01        39.06        10.88        75.95       100.01 
TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 
       23.51        22.09        35.80        26.17        79.69        17.85 
TCGA-AG-A014 TCGA-G5-6641 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 
       15.95        26.43        12.66         1.61         9.53        46.65 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       42.90        42.28        37.05        32.75        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       33.53        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.13         8.38        20.61        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92        56.25         3.02        35.01        63.98 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3548 
       38.99         1.02         9.07        19.07        26.01        33.99 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       24.00        29.95        61.02        78.08         6.97        54.02 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3831 
       47.01        11.01         5.98        26.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       15.95        36.95         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 
       53.00        31.00         2.01        33.01        26.01         2.01 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       34.06        25.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 
       34.03        18.05        27.02        42.02         0.99        34.98 
TCGA-AA-A017 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       15.02        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
       37.02        39.98        22.03        18.05        40.96        83.24 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       26.47         0.92        27.09         0.20        21.44        17.82 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 
      109.28        58.39         5.65        32.94        22.36        88.21 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        6.77        11.74        12.39        12.20        12.76        10.06 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
        2.01       124.27        23.05        37.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 
       22.03        30.08        32.02        15.02        12.00        29.03 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6679 TCGA-CM-6680 
       12.99        15.02        12.95        13.05        10.06        12.03 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       56.09        55.92        20.42        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       17.13        16.14        15.58        12.43        14.30         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DB 
       13.35        12.00        92.75        49.91       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G 
      131.51       135.65         7.76        26.47        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 
       98.24        11.11        35.74        47.87        34.42        43.04 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 
       13.25         0.53        35.31         8.35        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 
       65.85        53.62        44.68        85.48        36.00        26.43 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       10.98        19.33        19.33         9.93         8.42        31.30 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
       38.70        60.13        11.90        70.03        43.04        13.55 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       34.49        29.98        24.36        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
       12.00        32.02         2.01         6.05         0.99         7.99 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 
       32.98        19.04        19.99        17.95        13.02        35.01 
TCGA-AG-3902 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A01J TCGA-AG-A020 
       32.02         3.98        46.03        20.98         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6620 TCGA-CL-5917 
       49.97         1.94        38.96        61.97        33.17        78.12 
TCGA-CL-5918 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        7.17        25.05        12.62        41.36        57.24        51.48 
TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        3.48        19.96        16.34         8.61        17.46         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
       42.35        28.57        19.66        12.46 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  0 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            148.01             140.38 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            20.945             24.030 
[1] "0.0 - 148.0 (20.9)" "0.0 - 140.4 (24.0)"
[1] "hr=" "1.1"
D36V2, continuous
D36V3, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   242 108
  20P GAIN WILD-TYPE 206  54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    242  108
  20P GAIN WILD-TYPE  206   54
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON               242                206
  RECTUM              108                 54
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20P GAIN MUTATED        63        1       14        86         4         1
  20P GAIN WILD-TYPE      41        0       23        86         8         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P GAIN MUTATED          12         13         46         32       48
  20P GAIN WILD-TYPE        12          2         38         23       15
                    vv
clus                 STAGE IVA STAGE IVB
  20P GAIN MUTATED          16         1
  20P GAIN WILD-TYPE         8         1
D36V4, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  63                 41
  STAGE IA                  1                  0
  STAGE II                 14                 23
  STAGE IIA                86                 86
  STAGE IIB                 4                  8
  STAGE IIC                 1                  1
  STAGE III                12                 12
  STAGE IIIA               13                  2
  STAGE IIIB               46                 38
  STAGE IIIC               32                 23
  STAGE IV                 48                 15
  STAGE IVA                16                  8
  STAGE IVB                 1                  1
[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    12  66 236  35
  20P GAIN WILD-TYPE   8  39 181  34
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1               12                  8
  T2               66                 39
  T3              236                181
  T4               35                 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
  20P GAIN MUTATED   181  94  74
  20P GAIN WILD-TYPE 165  56  41
D36V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0              181                165
  N1               94                 56
  N2               74                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   248  65
  20P GAIN WILD-TYPE 205  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    248   65
  20P GAIN WILD-TYPE  205   23
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              248                205
  1               65                 23
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   156 196
  20P GAIN WILD-TYPE 133 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    156  196
  20P GAIN WILD-TYPE  133  129
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE              156                133
  MALE                196                129
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   279  19
  20P GAIN WILD-TYPE 203  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    279   19
  20P GAIN WILD-TYPE  203   10
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               279                203
  YES               19                 10
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                    219                            20
  20P GAIN WILD-TYPE                  163                            42
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P GAIN MUTATED                     101                              5
  20P GAIN WILD-TYPE                    45                              8
D36V10, multiclass
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        219                163
  COLON MUCINOUS ADENOCARCINOMA                20                 42
  RECTAL ADENOCARCINOMA                       101                 45
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[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                  R0  R1  R2  RX
  20P GAIN MUTATED   252   3  26  11
  20P GAIN WILD-TYPE 194   3  11  18
D36V11, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0              252                194
  R1                3                  3
  R2               26                 11
  RX               11                 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"
D36V12, continuous
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     2 200
  20P GAIN WILD-TYPE   3 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2  200
  20P GAIN WILD-TYPE    3  152
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              200                152
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   354  92
  20Q GAIN WILD-TYPE 112  36
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               446                148 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                92                 36 
$`20Q GAIN MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       63.62        35.93        91.79        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       13.94        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       26.43        15.62         4.80         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
       43.76        43.43        44.91        35.11        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       37.02        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        7.04         1.02        37.05         6.97         1.02        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       13.94        78.08         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 
       47.01        15.02        37.05         5.03        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
        0.99        25.02        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        10.06        33.07        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       17.03        27.02        18.05        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
        2.01        21.99        16.08        13.05        34.06        27.02 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
        7.96        13.94        19.00        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       27.02        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S 
       10.98        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.01         5.03         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       16.44         0.46        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
        0.20        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
       12.46        12.59        12.59        12.20        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
      148.01        85.45        21.99         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       25.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 
       12.99        13.02        15.02        14.04        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        17.75        18.25        25.48 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        17.13        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.04        11.64 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.41        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17        14.04        26.47       119.93        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        31.96        35.74        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
        0.53        47.41       133.18         8.35        82.39        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
        8.42        21.90        38.70        11.90        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       17.23        43.04        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        46.03        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
        9.07         1.02         1.02         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       48.20         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`20Q GAIN WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6298 TCGA-G4-6321 
       39.06        10.88        75.95       100.01        23.51        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       35.80        26.17        79.69        12.66         9.53        46.65 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 
       42.90        42.28        37.05        32.75        31.63        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 
       16.24        24.92         3.02        35.01        63.98         1.02 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3681 
       29.95        61.02         6.97        54.02        11.01         5.98 
TCGA-AA-3710 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 
       26.99         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       36.03        53.00        31.00         2.01        33.01        26.01 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R 
       25.02        27.02        38.04        30.02        18.05         0.99 
TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R 
       34.98        38.07         1.02        35.01         1.02        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       18.05        83.24         0.92        27.09        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 
       58.39         5.65        32.94        88.21         6.77        11.74 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       12.39        12.76        10.06        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 
       21.14        82.95       124.27        23.05        26.04        27.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 
       15.02        12.00        12.95        13.05        12.03        20.42 
TCGA-D5-6534 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       43.27        16.14        15.58         9.44        13.35        12.00 
TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
       92.75       140.38       131.51       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 
       60.79        98.24        11.11        47.87        35.31        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       53.62        85.48        10.98        19.33        19.33         9.93 
TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 
       31.30        60.13        70.03        13.55        34.49        12.00 
TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 
       32.02         2.01         6.05        32.98        19.04        13.02 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-CL-5917 TCGA-DT-5265 
        3.98        20.98        49.97        61.97        78.12        12.62 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       19.96         8.61        17.46         8.45 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  0 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            148.01             140.38 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            21.990             22.075 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D37V2, continuous
D37V3, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   315 143
  20Q GAIN WILD-TYPE 133  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    315  143
  20Q GAIN WILD-TYPE  133   19
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON               315                133
  RECTUM              143                 19
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20Q GAIN MUTATED        79        1       21       117         5         2
  20Q GAIN WILD-TYPE      25        0       16        55         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q GAIN MUTATED          17         14         66         44       56
  20Q GAIN WILD-TYPE         7          1         18         11        7
                    vv
clus                 STAGE IVA STAGE IVB
  20Q GAIN MUTATED          22         1
  20Q GAIN WILD-TYPE         2         1
D37V4, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  79                 25
  STAGE IA                  1                  0
  STAGE II                 21                 16
  STAGE IIA               117                 55
  STAGE IIB                 5                  7
  STAGE IIC                 2                  0
  STAGE III                17                  7
  STAGE IIIA               14                  1
  STAGE IIIB               66                 18
  STAGE IIIC               44                 11
  STAGE IV                 56                  7
  STAGE IVA                22                  2
  STAGE IVB                 1                  1
[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    14  84 316  44
  20Q GAIN WILD-TYPE   6  21 101  25
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1               14                  6
  T2               84                 21
  T3              316                101
  T4               44                 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
  20Q GAIN MUTATED   240 127  91
  20Q GAIN WILD-TYPE 106  23  24
D37V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0              240                106
  N1              127                 23
  N2               91                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   330  78
  20Q GAIN WILD-TYPE 123  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    330   78
  20Q GAIN WILD-TYPE  123   10
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              330                123
  1               78                 10
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   210 251
  20Q GAIN WILD-TYPE  79  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    210  251
  20Q GAIN WILD-TYPE   79   74
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE              210                 79
  MALE                251                 74
[1] 2 2
[1] FALSE
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   361  24
  20Q GAIN WILD-TYPE 121   5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    361   24
  20Q GAIN WILD-TYPE  121    5
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               361                121
  YES               24                  5
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q GAIN MUTATED                    287                            25
  20Q GAIN WILD-TYPE                   95                            37
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20Q GAIN MUTATED                     134                              7
  20Q GAIN WILD-TYPE                    12                              6
D37V10, multiclass
                                clus
vv                               20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        287                 95
  COLON MUCINOUS ADENOCARCINOMA                25                 37
  RECTAL ADENOCARCINOMA                       134                 12
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[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                  R0  R1  R2  RX
  20Q GAIN MUTATED   333   5  32  16
  20Q GAIN WILD-TYPE 113   1   5  13
D37V11, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              333                113
  R1                5                  1
  R2               32                  5
  RX               16                 13
[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, continuous
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     4 264
  20Q GAIN WILD-TYPE   1  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4  264
  20Q GAIN WILD-TYPE    1   88
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              264                 88
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    26   7
  21Q GAIN WILD-TYPE 440 121
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                33                561 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                121 
$`21Q GAIN MUTATED`
TCGA-AZ-6608 TCGA-DM-A285 TCGA-AG-3611 TCGA-AG-3612 TCGA-4T-AA8H TCGA-A6-5662 
        1.94         5.88        13.94        19.99        12.66        23.61 
TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AY-4071 TCGA-AZ-5407 
       24.00         2.01        50.04        47.01         0.95        88.21 
TCGA-CA-5255 TCGA-CM-5868 TCGA-D5-5539 TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A288 
       12.36        17.03        19.59         7.53        11.38        14.04 
TCGA-DM-A28F TCGA-DM-A28M TCGA-G4-6297 TCGA-NH-A50V TCGA-QG-A5YW TCGA-QL-A97D 
       35.97        95.18        82.39        19.33        29.46        21.90 
TCGA-RU-A8FL TCGA-AG-3732 TCGA-AG-3885 TCGA-AG-4021 TCGA-AG-A011 TCGA-AH-6644 
       38.70        32.98        17.95         3.98        37.02        27.55 
TCGA-CI-6623 TCGA-EF-5830 TCGA-EI-6885 
       47.44         3.48        13.64 

$`21Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
       49.08        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
        8.02        17.03        17.03        25.97        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       31.00        51.98        21.24        18.28        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.05        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09        16.31        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        62.79        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       29.56         5.23        11.74         3.19        12.69        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       45.40        54.61        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
      139.17        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        60.13        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        37.02         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        23.01         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       38.56         2.50        43.20        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.95               0.00 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             95.18             148.01 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             19.59              22.06 
[1] "0.9 - 95.2 (19.6)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1"  
D38V2, continuous
D38V3, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    23  10
  21Q GAIN WILD-TYPE 425 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     23   10
  21Q GAIN WILD-TYPE  425  152
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON                23                425
  RECTUM               10                152
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  21Q GAIN MUTATED         8        0        1         6         1         0
  21Q GAIN WILD-TYPE      96        1       36       166        11         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q GAIN MUTATED           2          2          5          2        4
  21Q GAIN WILD-TYPE        22         13         79         53       59
                    vv
clus                 STAGE IVA STAGE IVB
  21Q GAIN MUTATED           2         0
  21Q GAIN WILD-TYPE        22         2
D38V4, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   8                 96
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                 6                166
  STAGE IIB                 1                 11
  STAGE IIC                 0                  2
  STAGE III                 2                 22
  STAGE IIIA                2                 13
  STAGE IIIB                5                 79
  STAGE IIIC                2                 53
  STAGE IV                  4                 59
  STAGE IVA                 2                 22
  STAGE IVB                 0                  2
[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     3   7  22   2
  21Q GAIN WILD-TYPE  17  98 395  67
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                 17
  T2                7                 98
  T3               22                395
  T4                2                 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"
                    vv
clus                  N0  N1  N2
  21Q GAIN MUTATED    16   9   8
  21Q GAIN WILD-TYPE 330 141 107
D38V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               16                330
  N1                9                141
  N2                8                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    21   6
  21Q GAIN WILD-TYPE 432  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21    6
  21Q GAIN WILD-TYPE  432   82
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               21                432
  1                6                 82
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    18  16
  21Q GAIN WILD-TYPE 271 309
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18   16
  21Q GAIN WILD-TYPE  271  309
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               18                271
  MALE                 16                309
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    25   2
  21Q GAIN WILD-TYPE 457  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     25    2
  21Q GAIN WILD-TYPE  457   27
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                25                457
  YES                2                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q GAIN MUTATED                     18                             5
  21Q GAIN WILD-TYPE                  364                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  21Q GAIN MUTATED                      10                              0
  21Q GAIN WILD-TYPE                   136                             13
D38V10, multiclass
                                clus
vv                               21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         18                364
  COLON MUCINOUS ADENOCARCINOMA                 5                 57
  RECTAL ADENOCARCINOMA                        10                136
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  21Q GAIN MUTATED    21   0   1   2
  21Q GAIN WILD-TYPE 425   6  36  27
D38V11, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0               21                425
  R1                0                  6
  R2                1                 36
  RX                2                 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"
D38V12, continuous
D38V13, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  22
  21Q GAIN WILD-TYPE   5 330
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   22
  21Q GAIN WILD-TYPE    5  330
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               22                330
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    18   5
  22Q GAIN WILD-TYPE 448 123
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                23                571 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                123 
$`22Q GAIN MUTATED`
TCGA-AA-3715 TCGA-G4-6314 TCGA-AG-3612 TCGA-A6-4107 TCGA-A6-6140 TCGA-AA-3494 
       19.04        35.93        19.99        32.45        24.13         1.02 
TCGA-AA-3553 TCGA-AA-A02E TCGA-AZ-4684 TCGA-CK-4948 TCGA-CM-6163 TCGA-CM-6676 
       24.00         2.96        65.00       148.01        14.04        11.08 
TCGA-CM-6679 TCGA-RU-A8FL TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3893 
       10.06        38.70        17.23        36.03        19.99        35.01 
TCGA-AG-3999 TCGA-AG-A00Y TCGA-AH-6897 TCGA-CI-6623 TCGA-DY-A1DF 
       28.04        23.01        26.43        47.44        24.13 

$`22Q GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 
       49.08         5.88        28.21        23.51        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        22.52         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65        32.94         5.13        22.36        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        21.90        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
        3.98        46.03        20.98        13.94         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       27.55        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.02               0.00 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            148.01             140.38 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             24.13              21.99 
[1] "1.0 - 148.0 (24.1)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D39V2, continuous
D39V3, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    13  10
  22Q GAIN WILD-TYPE 435 152
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     13   10
  22Q GAIN WILD-TYPE  435  152
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON                13                435
  RECTUM               10                152
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  22Q GAIN MUTATED         5        0        1         3         0         0
  22Q GAIN WILD-TYPE      99        1       36       169        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q GAIN MUTATED           1          0          4          4        4
  22Q GAIN WILD-TYPE        23         15         80         51       59
                    vv
clus                 STAGE IVA STAGE IVB
  22Q GAIN MUTATED           1         0
  22Q GAIN WILD-TYPE        23         2
D39V4, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   5                 99
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                 3                169
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 1                 23
  STAGE IIIA                0                 15
  STAGE IIIB                4                 80
  STAGE IIIC                4                 51
  STAGE IV                  4                 59
  STAGE IVA                 1                 23
  STAGE IVB                 0                  2
[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     2   3  18   0
  22Q GAIN WILD-TYPE  18 102 399  69
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                2                 18
  T2                3                102
  T3               18                399
  T4                0                 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"
                    vv
clus                  N0  N1  N2
  22Q GAIN MUTATED    10   6   7
  22Q GAIN WILD-TYPE 336 144 108
D39V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               10                336
  N1                6                144
  N2                7                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    17   5
  22Q GAIN WILD-TYPE 436  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     17    5
  22Q GAIN WILD-TYPE  436   83
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               17                436
  1                5                 83
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    10  13
  22Q GAIN WILD-TYPE 279 312
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     10   13
  22Q GAIN WILD-TYPE  279  312
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               10                279
  MALE                 13                312
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    19   0
  22Q GAIN WILD-TYPE 463  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     19    0
  22Q GAIN WILD-TYPE  463   29
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                19                463
  YES                0                 29
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q GAIN MUTATED                     13                             0
  22Q GAIN WILD-TYPE                  369                            62
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  22Q GAIN MUTATED                      10                              0
  22Q GAIN WILD-TYPE                   136                             13
D39V10, multiclass
                                clus
vv                               22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  COLON ADENOCARCINOMA                         13                369
  COLON MUCINOUS ADENOCARCINOMA                 0                 62
  RECTAL ADENOCARCINOMA                        10                136
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  22Q GAIN MUTATED    16   0   3   0
  22Q GAIN WILD-TYPE 430   6  34  29
D39V11, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0               16                430
  R1                0                  6
  R2                3                 34
  RX                0                 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"
D39V12, continuous
D39V13, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0  13
  22Q GAIN WILD-TYPE   5 339
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0   13
  22Q GAIN WILD-TYPE    5  339
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               13                339
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    79  18
  XP GAIN WILD-TYPE 387 110
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               97               497 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               110 
$`XP GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3524 TCGA-AA-3844 TCGA-AD-6888 TCGA-AZ-6608 TCGA-G4-6310 
       45.60        36.03        14.93        15.52         1.94        63.62 
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6235 
       10.39        19.99        15.95        36.03        31.00        55.76 
TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 
       12.66        44.91        35.11        25.08        20.61        24.69 
TCGA-A6-6654 TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3664 TCGA-AA-3667 
       23.87        29.00        24.00        20.98        54.02        14.01 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3852 
       47.01         5.98         5.03        35.05         0.99         0.00 
TCGA-AA-3869 TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A01I TCGA-AA-A029 TCGA-AA-A02H 
       27.02         2.01        27.02        31.00        51.98         2.01 
TCGA-AA-A02O TCGA-AA-A02Y TCGA-AD-A5EK TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L 
        0.92        39.98        16.44        33.01         0.20        17.26 
TCGA-AY-A8YK TCGA-AZ-4682 TCGA-AZ-6598 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
       18.84        22.36        49.41        14.30        21.99         2.01 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5539 
       32.02         5.03        15.02        21.99        14.99        19.59 
TCGA-D5-5541 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-DM-A0X9 
       55.92        15.12         4.80        17.13        12.49       119.70 
TCGA-DM-A1DA TCGA-DM-A28F TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-G4-6299 
        7.50        35.97        98.24        95.18         8.61        74.56 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-QG-A5YW TCGA-QL-A97D TCGA-SS-A7HO 
       44.68        55.04        39.42        29.46        21.90        60.13 
TCGA-AF-2692 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3592 TCGA-AG-3609 
       13.55        16.83        20.02        86.63        34.03        19.99 
TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A032 
       35.01        28.04         1.02        46.03         9.07        38.04 
TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 
       27.55        47.44        78.12        21.01        12.00        31.00 
TCGA-DY-A1H8 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6810 
       32.61        18.28        17.69        13.64        49.51         0.39 
TCGA-F5-6863 
       11.87 

$`XP GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        24.03        37.05         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        31.07        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       21.99        39.06        21.37        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01        49.08         5.88        28.21        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       17.85         8.02        13.94        17.03        17.03        25.97 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       51.98        21.24        18.28        26.43        15.62         4.80 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       43.43        42.90        42.28        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        32.75        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        25.18        21.76        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       33.99        21.01        29.95        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        6.97         2.01        50.04        47.05        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       37.05        26.99        10.06        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        33.01        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
       33.04         1.02        26.01        37.02         2.96        39.98 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        5.03        22.03        41.00        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       21.44        17.82        17.85        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.65        32.94         5.13        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.20        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       30.08        15.02        15.02        15.02        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        16.04        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.85        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        11.38        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 
       26.47        81.37       119.93        60.79       117.07        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       65.85        53.62        85.48        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H 
       42.77        32.98         8.42        31.30        38.70        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       70.03        46.92        39.48        17.23        43.04        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L 
       34.49        37.74        29.98        24.36        24.59        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 
       32.02        19.99        36.03        14.04         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        23.01        37.02         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.97         1.94        38.96        61.97        41.00        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        43.20        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       13.78        44.78        48.20         7.17        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       31.00        13.97        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        8.45         9.96        42.35        28.57        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        12.46        47.08 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
                0                 0 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           119.70            148.01 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            21.99             22.03 
[1] "0.0 - 119.7 (22.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    68  31
  XP GAIN WILD-TYPE 380 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     68   31
  XP GAIN WILD-TYPE  380  131
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  COLON               68               380
  RECTUM              31               131
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XP GAIN MUTATED        14        0        8        18         2         0
  XP GAIN WILD-TYPE      90        1       29       154        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP GAIN MUTATED           3          4         20          9        9
  XP GAIN WILD-TYPE        21         11         64         46       54
                   vv
clus                STAGE IVA STAGE IVB
  XP GAIN MUTATED           8         0
  XP GAIN WILD-TYPE        16         2
D40V4, multiclass
            clus
vv           XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                 14                90
  STAGE IA                 0                 1
  STAGE II                 8                29
  STAGE IIA               18               154
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                3                21
  STAGE IIIA               4                11
  STAGE IIIB              20                64
  STAGE IIIC               9                46
  STAGE IV                 9                54
  STAGE IVA                8                16
  STAGE IVB                0                 2
[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     2  19  71   7
  XP GAIN WILD-TYPE  18  86 346  62
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1               2                18
  T2              19                86
  T3              71               346
  T4               7                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"
                   vv
clus                 N0  N1  N2
  XP GAIN MUTATED    48  32  18
  XP GAIN WILD-TYPE 298 118  97
D40V6, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              48               298
  N1              32               118
  N2              18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    67  17
  XP GAIN WILD-TYPE 386  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     67   17
  XP GAIN WILD-TYPE  386   71
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              67               386
  1              17                71
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    55  45
  XP GAIN WILD-TYPE 234 280
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     55   45
  XP GAIN WILD-TYPE  234  280
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              55               234
  MALE                45               280
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    76   4
  XP GAIN WILD-TYPE 406  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     76    4
  XP GAIN WILD-TYPE  406   25
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               76               406
  YES               4                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XP GAIN MUTATED                     59                             9
  XP GAIN WILD-TYPE                  323                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XP GAIN MUTATED                      31                              0
  XP GAIN WILD-TYPE                   115                             13
D40V10, multiclass
                                clus
vv                               XP GAIN MUTATED XP GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        59               323
  COLON MUCINOUS ADENOCARCINOMA                9                53
  RECTAL ADENOCARCINOMA                       31               115
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  XP GAIN MUTATED    70   1   8   5
  XP GAIN WILD-TYPE 376   5  29  24
D40V11, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  R0              70               376
  R1               1                 5
  R2               8                29
  RX               5                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"
D40V12, continuous
D40V13, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     0  61
  XP GAIN WILD-TYPE   5 291
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      0   61
  XP GAIN WILD-TYPE    5  291
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              61               291
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    80  25
  XQ GAIN WILD-TYPE 386 103
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              105               489 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               25               103 
$`XQ GAIN MUTATED`
TCGA-A6-2681 TCGA-AA-3524 TCGA-AA-3562 TCGA-AA-3844 TCGA-AD-6888 TCGA-AZ-6601 
       45.60        36.03        19.99        14.93        15.52       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6310 TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A014 
        1.94         5.88        63.62        10.39        19.99        15.95 
TCGA-AG-A015 TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-6142 TCGA-A6-6650 
       36.03        12.66        44.91        37.02        25.08        20.61 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3534 TCGA-AA-3553 TCGA-AA-3558 
       24.69        23.87        56.25        29.00        24.00        20.98 
TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3696 
       78.08        54.02        14.01        47.01         5.98         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3852 TCGA-AA-3869 TCGA-AA-3994 
       10.06        35.05         0.99         0.00        27.02        27.02 
TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y TCGA-AD-A5EK 
       31.00        33.04        51.98         0.92        39.98        16.44 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6598 
        0.20        17.26        18.84         5.65        22.36        49.41 
TCGA-CA-6719 TCGA-CK-5914 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 
       14.30        21.99        22.98        32.02         5.03        15.02 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 
       21.99        14.99        13.05        19.59        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6923 TCGA-DM-A0X9 TCGA-DM-A1DA TCGA-DM-A28F 
       17.13        12.49        12.43       119.70         7.50        35.97 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6306 
       98.24        95.18         8.61         6.18        74.56        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QL-A97D TCGA-WS-AB45 
       55.04        39.42        15.65        29.46        21.90        70.03 
TCGA-AF-2692 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3592 TCGA-AG-3594 
       13.55        16.83        20.02        86.63        34.03         2.01 
TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
       19.99        19.04        35.01        28.04         1.02        46.03 
TCGA-AG-A016 TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 
        9.07        38.04        27.55        47.44        78.12        21.01 
TCGA-DC-6154 TCGA-DC-6156 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-F5-6464 
       12.00        31.00        18.28        17.69        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 
       49.51         0.39        11.87 

$`XQ GAIN WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        24.03        37.05         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       39.06        21.37        25.08        10.88        75.95       106.75 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       49.08        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 
       26.17        91.79        79.69        17.85         8.02        13.94 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       17.03        17.03        25.97        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 
       18.28        55.76        26.43        15.62         4.80         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       25.18        21.76        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3673 
       29.95        13.94        61.02         6.97         2.01        50.04 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3819 
       47.05        15.02        11.01        37.05        26.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 
        0.00        17.03        10.06         0.00        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 
       32.05         0.99        31.07        53.00        17.03        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
        2.96        39.98         2.01         5.03        22.03        41.00 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.85        19.33       109.28        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        65.00        62.79        88.21         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 
       13.02        29.06        22.03        30.08        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        12.00        14.04        29.03        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6540 TCGA-D5-6541 
       18.25        25.48        43.27        17.85        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      139.17        14.04        26.47        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
      117.07        31.96        11.11        35.74        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       67.30        65.85        53.62        85.48        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO 
       42.77        32.98         8.42        31.30        38.70        60.13 
TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       11.90        46.92        39.48        17.23        43.04        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L 
       34.49        37.74        29.98        24.36        24.59        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 
       50.04        12.03         6.05         0.99        15.95        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         3.98        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.56         2.50        43.20 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
       48.20         7.17        25.05        26.04        31.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        15.85        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       42.35        28.57        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       38.14        12.46        47.08 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                 0 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           119.70            148.01 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            20.98             22.09 
[1] "0.0 - 119.7 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D41V2, continuous
D41V3, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    77  31
  XQ GAIN WILD-TYPE 371 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     77   31
  XQ GAIN WILD-TYPE  371  131
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON               77               371
  RECTUM              31               131
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XQ GAIN MUTATED        15        0        9        22         1         0
  XQ GAIN WILD-TYPE      89        1       28       150        11         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ GAIN MUTATED           6          3         20         12        7
  XQ GAIN WILD-TYPE        18         12         64         43       56
                   vv
clus                STAGE IVA STAGE IVB
  XQ GAIN MUTATED           8         1
  XQ GAIN WILD-TYPE        16         1
D41V4, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 15                89
  STAGE IA                 0                 1
  STAGE II                 9                28
  STAGE IIA               22               150
  STAGE IIB                1                11
  STAGE IIC                0                 2
  STAGE III                6                18
  STAGE IIIA               3                12
  STAGE IIIB              20                64
  STAGE IIIC              12                43
  STAGE IV                 7                56
  STAGE IVA                8                16
  STAGE IVB                1                 1
[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     2  18  80   8
  XQ GAIN WILD-TYPE  18  87 337  61
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                18
  T2              18                87
  T3              80               337
  T4               8                61
[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
  XQ GAIN MUTATED    52  31  24
  XQ GAIN WILD-TYPE 294 119  91
D41V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              52               294
  N1              31               119
  N2              24                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    76  16
  XQ GAIN WILD-TYPE 377  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     76   16
  XQ GAIN WILD-TYPE  377   72
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              76               377
  1              16                72
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    58  51
  XQ GAIN WILD-TYPE 231 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     58   51
  XQ GAIN WILD-TYPE  231  274
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              58               231
  MALE                51               274
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    86   4
  XQ GAIN WILD-TYPE 396  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     86    4
  XQ GAIN WILD-TYPE  396   25
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               86               396
  YES               4                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                     68                             9
  XQ GAIN WILD-TYPE                  314                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XQ GAIN MUTATED                      29                              1
  XQ GAIN WILD-TYPE                   117                             12
D41V10, multiclass
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  COLON ADENOCARCINOMA                        68               314
  COLON MUCINOUS ADENOCARCINOMA                9                53
  RECTAL ADENOCARCINOMA                       29               117
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  XQ GAIN MUTATED    81   0   6   5
  XQ GAIN WILD-TYPE 365   6  31  24
D41V11, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              81               365
  R1               0                 6
  R2               6                31
  RX               5                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"
D41V12, continuous
D41V13, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  66
  XQ GAIN WILD-TYPE   5 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   66
  XQ GAIN WILD-TYPE    5  286
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              66               286
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED    97  36
  1P LOSS WILD-TYPE 369  92
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              133               461 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36                92 
$`1P LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 
       14.53        37.05        19.99        31.07        24.03        12.99 
TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 TCGA-AG-A00H TCGA-BM-6198 
        5.88        23.51        35.93        91.79        25.97        21.24 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-5660 TCGA-A6-5662 
        4.80         1.61        43.76        35.11        29.19        23.61 
TCGA-A6-6138 TCGA-A6-6651 TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3673 
       22.52        21.76         5.03        38.99         9.07        50.04 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       37.05        10.06        38.99        37.02        10.06        33.07 
TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       17.03         2.01        21.99         7.96        34.03        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02H 
       15.02        32.02        31.00        33.04        26.01         2.01 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00        24.53         5.79        22.42        26.47        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6600 
       14.50        16.31         5.65         5.13        22.36        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CK-6748 
       29.56         5.23         3.19        12.69        12.46         2.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
        8.02        13.02        22.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6533 
       15.02        11.08        10.06        56.09        17.75        25.48 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A28A 
       14.30        13.41        11.38        92.75        49.91        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 
       31.96         1.55        47.41         8.35        82.39        65.85 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 
       61.91        36.00        46.75        10.98         9.93        16.80 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-6136 TCGA-AF-A56L 
       60.13        11.90        46.92        17.23        24.36        65.98 
TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 
       11.84        36.03        24.00        34.03        29.98        37.02 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       19.04        19.99         1.02         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00Y TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       28.04        36.03        23.01        38.96        38.04        38.56 
TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 
       43.20        13.78        47.44        48.20        25.05        31.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 
       13.97        51.98        44.02       126.44       129.27         3.48 
TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
       20.55        15.85        11.97        28.57        32.19        19.66 
TCGA-G5-6572 
       47.08 

$`1P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        24.03        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       14.93        29.98        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        1.94        49.08        28.21        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       26.17        79.69        17.85        10.39         8.02        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       19.99        17.03        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H 
       51.98        18.28        55.76        26.43        15.62        12.66 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        9.53        39.45        43.76        46.65        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       42.28        44.91        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       30.44        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       27.09        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       16.24        24.92        61.84        56.25         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02         1.02        37.02        51.98         2.96        39.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       12.16        83.24        27.42         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       11.74        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        55.92        20.19        20.42        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        14.04        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       33.67        13.25         0.53        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       67.30        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       26.43        26.04        13.78        74.79        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        15.65        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 
        8.42        31.30        21.90        38.70        70.03        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 
       16.83        20.02        24.59        86.63        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       32.02         7.07        20.05         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       15.95        19.99        20.98         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       14.01        25.02        32.02        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98        13.94         6.02        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
        1.02         1.02        49.97         1.94        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       44.78        78.12         7.17        21.01        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       31.00        10.98        25.97        25.05        25.05        12.62 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.36        57.24        24.13        51.48        32.61         4.18 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46         8.45         9.96        49.51        42.35         0.39 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        37.18        38.14        11.87        12.46 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1.02              0.00 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.27            148.01 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            23.51             21.37 
[1] "1.0 - 129.3 (23.5)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.4"
D42V2, continuous
D42V3, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    94  45
  1P LOSS WILD-TYPE 354 117
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     94   45
  1P LOSS WILD-TYPE  354  117
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON               94               354
  RECTUM              45               117
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1P LOSS MUTATED        17        0        5        35         2         0
  1P LOSS WILD-TYPE      87        1       32       137        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1P LOSS MUTATED           5          4         18         18       24
  1P LOSS WILD-TYPE        19         11         66         37       39
                   vv
clus                STAGE IVA STAGE IVB
  1P LOSS MUTATED           5         0
  1P LOSS WILD-TYPE        19         2
D42V4, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 17                87
  STAGE IA                 0                 1
  STAGE II                 5                32
  STAGE IIA               35               137
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                5                19
  STAGE IIIA               4                11
  STAGE IIIB              18                66
  STAGE IIIC              18                37
  STAGE IV                24                39
  STAGE IVA                5                19
  STAGE IVB                0                 2
[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     4  21  96  17
  1P LOSS WILD-TYPE  16  84 321  52
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               4                16
  T2              21                84
  T3              96               321
  T4              17                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"
                   vv
clus                 N0  N1  N2
  1P LOSS MUTATED    65  37  36
  1P LOSS WILD-TYPE 281 113  79
D42V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              65               281
  N1              37               113
  N2              36                79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    94  30
  1P LOSS WILD-TYPE 359  58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     94   30
  1P LOSS WILD-TYPE  359   58
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              94               359
  1              30                58
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    59  80
  1P LOSS WILD-TYPE 230 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     59   80
  1P LOSS WILD-TYPE  230  245
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              59               230
  MALE                80               245
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED   111   7
  1P LOSS WILD-TYPE 371  22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED    111    7
  1P LOSS WILD-TYPE  371   22
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO              111               371
  YES               7                22
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                     85                             9
  1P LOSS WILD-TYPE                  297                            53
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1P LOSS MUTATED                      44                              0
  1P LOSS WILD-TYPE                   102                             13
D42V10, multiclass
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        85               297
  COLON MUCINOUS ADENOCARCINOMA                9                53
  RECTAL ADENOCARCINOMA                       44               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  1P LOSS MUTATED    93   2  10   5
  1P LOSS WILD-TYPE 353   4  27  24
D42V11, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              93               353
  R1               2                 4
  R2              10                27
  RX               5                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"
D42V12, continuous
D42V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     2  80
  1P LOSS WILD-TYPE   3 272
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2   80
  1P LOSS WILD-TYPE    3  272
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              80               272
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    60  19
  1Q LOSS WILD-TYPE 406 109
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               79               515 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               19               109 
$`1Q LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3867 TCGA-DM-A285 TCGA-G4-6625 TCGA-AG-A00H 
       37.05        19.99        24.03         5.88        91.79        25.97 
TCGA-BM-6198 TCGA-5M-AAT4 TCGA-A6-5660 TCGA-A6-6138 TCGA-AA-3488 TCGA-AA-3517 
       21.24         1.61        29.19        22.52         5.03        38.99 
TCGA-AA-3519 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3851 
        9.07        50.04        10.06        38.99        37.02        33.07 
TCGA-AA-3966 TCGA-AA-3989 TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6890 
        2.01         7.96        15.02        33.04        41.00        24.53 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4616 
       22.42        26.47        16.44        16.31         5.65         5.13 
TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CK-6748 
       22.36        29.56         5.23         3.19        12.46         2.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
        8.02        13.02        22.03        29.03        13.02        15.02 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 
       11.08        10.06        17.75        14.30        13.41        11.38 
TCGA-DM-A28A TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50U 
       26.47         1.55         8.35        61.91        36.00        10.98 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 
       60.13        11.90        46.92        65.98        11.84        36.03 
TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 
       24.00        37.02        19.99         1.02         1.02        48.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A00Y TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4749 
       19.99        36.03        23.01        13.78        48.20        25.05 
TCGA-DC-5869 TCGA-DC-6157 TCGA-EF-5830 TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 
       31.00        51.98         3.48        15.85        11.97        28.57 
TCGA-G5-6572 
       47.08 

$`1Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 
       75.95       106.75       100.01         1.94        49.08        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        15.95        36.03        31.00        51.98 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       18.28        55.76        26.43        15.62         4.80        12.66 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.25        37.02        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
        1.02         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        12.16        83.24         5.79        27.42 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4684 
       18.84       109.28        58.39         1.41        32.94        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 
       62.79        88.21        49.41         6.77        12.10        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       14.04        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       14.04        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        39.42        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        74.79        18.18        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 
        8.42        31.30        21.90        38.70        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
       36.03        12.00        32.02         7.07        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.04        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       25.02        32.02        28.04        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98        13.94         6.02        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46         6.05        33.17        44.78        47.44 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       78.12         7.17        21.01        26.04        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       31.00        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        42.35         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       19.66        37.18        38.14        11.87        12.46 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             1.02              0.00 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            91.79            148.01 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            19.99             22.06 
[1] "1.0 - 91.8 (20.0)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D43V2, continuous
D43V3, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    56  26
  1Q LOSS WILD-TYPE 392 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     56   26
  1Q LOSS WILD-TYPE  392  136
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON               56               392
  RECTUM              26               136
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  1Q LOSS MUTATED        12        0        2        20         2         0
  1Q LOSS WILD-TYPE      92        1       35       152        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  1Q LOSS MUTATED           3          3          8          9       15
  1Q LOSS WILD-TYPE        21         12         76         46       48
                   vv
clus                STAGE IVA STAGE IVB
  1Q LOSS MUTATED           4         0
  1Q LOSS WILD-TYPE        20         2
D43V4, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 12                92
  STAGE IA                 0                 1
  STAGE II                 2                35
  STAGE IIA               20               152
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                3                21
  STAGE IIIA               3                12
  STAGE IIIB               8                76
  STAGE IIIC               9                46
  STAGE IV                15                48
  STAGE IVA                4                20
  STAGE IVB                0                 2
[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     2  15  57   7
  1Q LOSS WILD-TYPE  18  90 360  62
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               2                18
  T2              15                90
  T3              57               360
  T4               7                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"
                   vv
clus                 N0  N1  N2
  1Q LOSS MUTATED    41  21  19
  1Q LOSS WILD-TYPE 305 129  96
D43V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              41               305
  N1              21               129
  N2              19                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    53  19
  1Q LOSS WILD-TYPE 400  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     53   19
  1Q LOSS WILD-TYPE  400   69
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              53               400
  1              19                69
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    30  52
  1Q LOSS WILD-TYPE 259 273
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     30   52
  1Q LOSS WILD-TYPE  259  273
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              30               259
  MALE                52               273
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    66   4
  1Q LOSS WILD-TYPE 416  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     66    4
  1Q LOSS WILD-TYPE  416   25
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               66               416
  YES               4                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                     50                             6
  1Q LOSS WILD-TYPE                  332                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  1Q LOSS MUTATED                      26                              0
  1Q LOSS WILD-TYPE                   120                             13
D43V10, multiclass
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        50               332
  COLON MUCINOUS ADENOCARCINOMA                6                56
  RECTAL ADENOCARCINOMA                       26               120
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  1Q LOSS MUTATED    55   2   7   3
  1Q LOSS WILD-TYPE 391   4  30  26
D43V11, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              55               391
  R1               2                 4
  R2               7                30
  RX               3                26
[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, continuous
D43V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  47
  1Q LOSS WILD-TYPE   3 305
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   47
  1Q LOSS WILD-TYPE    3  305
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              47               305
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    15   2
  2P LOSS WILD-TYPE 451 126
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17               577 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2               126 
$`2P LOSS MUTATED`
TCGA-AA-3560 TCGA-AA-3939 TCGA-AG-3611 TCGA-AG-A00H TCGA-AA-3511 TCGA-AA-3666 
       19.99        12.99        13.94        25.97         6.97         2.01 
TCGA-AA-3842 TCGA-CA-5797 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3881 
       37.02        12.59        24.36        32.02        36.03        19.04 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A02X TCGA-EF-5831 TCGA-F5-6571 
       28.04        36.03        41.00         4.18        42.35 

$`2P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
        8.02        19.99        17.03        17.03        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       31.00        51.98        21.24        18.28        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 
        1.02        37.05        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       21.90        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        16.83        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
       65.98        11.84        36.03        12.00         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       25.02        32.02        19.99        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         3.48        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.01              0.00 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            42.35            148.01 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            24.36             21.99 
[1] "2.0 - 42.4 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D44V2, continuous
D44V3, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     6  11
  2P LOSS WILD-TYPE 442 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6   11
  2P LOSS WILD-TYPE  442  151
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON                6               442
  RECTUM              11               151
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2P LOSS MUTATED         1        0        1         9         0         0
  2P LOSS WILD-TYPE     103        1       36       163        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2P LOSS MUTATED           1          1          1          2        1
  2P LOSS WILD-TYPE        23         14         83         53       62
                   vv
clus                STAGE IVA STAGE IVB
  2P LOSS MUTATED           0         0
  2P LOSS WILD-TYPE        24         2
D44V4, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 1                36
  STAGE IIA                9               163
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                1                23
  STAGE IIIA               1                14
  STAGE IIIB               1                83
  STAGE IIIC               2                53
  STAGE IV                 1                62
  STAGE IVA                0                24
  STAGE IVB                0                 2
[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     0   2  14   1
  2P LOSS WILD-TYPE  20 103 403  68
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                20
  T2               2               103
  T3              14               403
  T4               1                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"
                   vv
clus                 N0  N1  N2
  2P LOSS MUTATED    11   4   2
  2P LOSS WILD-TYPE 335 146 113
D44V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              11               335
  N1               4               146
  N2               2               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    15   1
  2P LOSS WILD-TYPE 438  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     15    1
  2P LOSS WILD-TYPE  438   87
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              15               438
  1               1                87
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     7  10
  2P LOSS WILD-TYPE 282 315
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      7   10
  2P LOSS WILD-TYPE  282  315
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               7               282
  MALE                10               315
[1] 2 2
[1] FALSE
D44V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    13   2
  2P LOSS WILD-TYPE 469  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     13    2
  2P LOSS WILD-TYPE  469   27
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               13               469
  YES               2                27
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                      6                             0
  2P LOSS WILD-TYPE                  376                            62
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2P LOSS MUTATED                       9                              1
  2P LOSS WILD-TYPE                   137                             12
D44V10, multiclass
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         6               376
  COLON MUCINOUS ADENOCARCINOMA                0                62
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  2P LOSS MUTATED    14   0   1   0
  2P LOSS WILD-TYPE 432   6  36  29
D44V11, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0              14               432
  R1               0                 6
  R2               1                36
  RX               0                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"
D44V12, continuous
D44V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     0   4
  2P LOSS WILD-TYPE   5 348
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    4
  2P LOSS WILD-TYPE    5  348
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               4               348
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    13   1
  2Q LOSS WILD-TYPE 453 127
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               14               580 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1               127 
$`2Q LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3560 TCGA-AA-3939 TCGA-AG-3611 TCGA-AG-A00H TCGA-AA-3511 
       37.05        19.99        12.99        13.94        25.97         6.97 
TCGA-AA-3666 TCGA-AA-3842 TCGA-CA-5797 TCGA-AG-3881 TCGA-AG-3999 TCGA-AG-4001 
        2.01        37.02        12.59        19.04        28.04        36.03 
TCGA-AG-A02X TCGA-F5-6571 
       41.00        42.35 

$`2Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 
       19.04        14.93        31.07        24.03        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       19.99        17.03        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       51.98        21.24        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       37.05        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       36.95         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       38.70        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98        37.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 
        1.02        48.03        25.02        32.02        19.99        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.01              0.00 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            42.35            148.01 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            22.98             22.01 
[1] "2.0 - 42.4 (23.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "2.5"
D45V2, continuous
D45V3, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     7   7
  2Q LOSS WILD-TYPE 441 155
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      7    7
  2Q LOSS WILD-TYPE  441  155
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON                7               441
  RECTUM               7               155
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  2Q LOSS MUTATED         1        0        1         8         0         0
  2Q LOSS WILD-TYPE     103        1       36       164        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  2Q LOSS MUTATED           1          1          0          2        0
  2Q LOSS WILD-TYPE        23         14         84         53       63
                   vv
clus                STAGE IVA STAGE IVB
  2Q LOSS MUTATED           0         0
  2Q LOSS WILD-TYPE        24         2
D45V4, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 1                36
  STAGE IIA                8               164
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                1                23
  STAGE IIIA               1                14
  STAGE IIIB               0                84
  STAGE IIIC               2                53
  STAGE IV                 0                63
  STAGE IVA                0                24
  STAGE IVB                0                 2
[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     0   2  11   1
  2Q LOSS WILD-TYPE  20 103 406  68
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                20
  T2               2               103
  T3              11               406
  T4               1                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"
                   vv
clus                 N0  N1  N2
  2Q LOSS MUTATED    10   2   2
  2Q LOSS WILD-TYPE 336 148 113
D45V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              10               336
  N1               2               148
  N2               2               113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    14   0
  2Q LOSS WILD-TYPE 439  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     14    0
  2Q LOSS WILD-TYPE  439   88
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              14               439
  1               0                88
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   9
  2Q LOSS WILD-TYPE 284 316
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    9
  2Q LOSS WILD-TYPE  284  316
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               5               284
  MALE                 9               316
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    11   1
  2Q LOSS WILD-TYPE 471  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     11    1
  2Q LOSS WILD-TYPE  471   28
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               11               471
  YES               1                28
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                      7                             0
  2Q LOSS WILD-TYPE                  375                            62
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  2Q LOSS MUTATED                       6                              0
  2Q LOSS WILD-TYPE                   140                             13
D45V10, multiclass
                                clus
vv                               2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         7               375
  COLON MUCINOUS ADENOCARCINOMA                0                62
  RECTAL ADENOCARCINOMA                        6               140
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  2Q LOSS MUTATED    13   0   0   0
  2Q LOSS WILD-TYPE 433   6  37  29
D45V11, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0              13               433
  R1               0                 6
  R2               0                37
  RX               0                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"
D45V12, continuous
D45V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   2
  2Q LOSS WILD-TYPE   5 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    2
  2Q LOSS WILD-TYPE    5  350
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO               2               350
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED    50  16
  3P LOSS WILD-TYPE 416 112
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               66               528 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16               112 
$`3P LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       14.53         6.05        85.05        31.07        29.98        12.99 
TCGA-AA-3979 TCGA-BM-6198 TCGA-G5-6233 TCGA-5M-AAT4 TCGA-A6-3807 TCGA-A6-4107 
       24.00        21.24        18.28         1.61        34.65        32.45 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 
       25.08        21.76         9.63         5.03        38.99         9.07 
TCGA-AA-3680 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 
       11.01        10.06        32.05        17.03         2.01        21.99 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A01F TCGA-AA-A01K TCGA-AD-A5EK TCGA-AU-3779 
        7.96        13.94        32.02        31.00        16.44        14.50 
TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 
        0.20         5.65        12.10        12.59        12.20         2.01 
TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 
        8.02         5.03        14.04        11.08        11.01        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 
       17.75        25.48        43.27        17.85        13.41        11.38 
TCGA-DM-A1DA TCGA-F4-6460 TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
        7.50        31.96         9.93        42.77        38.70        11.90 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3881 
       34.49        29.98        20.05        24.00        37.02        19.04 
TCGA-AG-3885 TCGA-AG-4021 TCGA-AH-6544 TCGA-CI-6619 TCGA-DT-5265 TCGA-F5-6810 
       17.95         3.98        38.56         6.05        12.62         0.39 

$`3P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       14.93        24.03        24.00         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        51.98        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE 
       26.43        15.62         4.80        12.66         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        56.25         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 
        0.00        36.03         0.99        31.07        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       20.98        34.03        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02        10.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        5.79        22.42        27.42        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 
       56.09        55.92        20.42        18.25        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33        19.33        15.65        12.79        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        21.90        60.13 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.97        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
        7.07        36.03         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.04         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        49.51        42.35        28.57        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              0.2               0.0 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            85.05            148.01 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           15.485            23.280 
[1] "0.2 - 85.0 (15.5)"  "0.0 - 148.0 (23.3)"
[1] "hr=" "1.8"
D46V2, continuous
D46V3, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    53  13
  3P LOSS WILD-TYPE 395 149
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     53   13
  3P LOSS WILD-TYPE  395  149
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON               53               395
  RECTUM              13               149
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3P LOSS MUTATED         5        0        2        18         0         0
  3P LOSS WILD-TYPE      99        1       35       154        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3P LOSS MUTATED           3          1          9          6       14
  3P LOSS WILD-TYPE        21         14         75         49       49
                   vv
clus                STAGE IVA STAGE IVB
  3P LOSS MUTATED           5         0
  3P LOSS WILD-TYPE        19         2
D46V4, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  5                99
  STAGE IA                 0                 1
  STAGE II                 2                35
  STAGE IIA               18               154
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                3                21
  STAGE IIIA               1                14
  STAGE IIIB               9                75
  STAGE IIIC               6                49
  STAGE IV                14                49
  STAGE IVA                5                19
  STAGE IVB                0                 2
[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     2   4  51   9
  3P LOSS WILD-TYPE  18 101 366  60
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               2                18
  T2               4               101
  T3              51               366
  T4               9                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"
                   vv
clus                 N0  N1  N2
  3P LOSS MUTATED    27  21  18
  3P LOSS WILD-TYPE 319 129  97
D46V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0              27               319
  N1              21               129
  N2              18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    39  19
  3P LOSS WILD-TYPE 414  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     39   19
  3P LOSS WILD-TYPE  414   69
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              39               414
  1              19                69
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    28  39
  3P LOSS WILD-TYPE 261 286
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     28   39
  3P LOSS WILD-TYPE  261  286
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              28               261
  MALE                39               286
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    56   3
  3P LOSS WILD-TYPE 426  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     56    3
  3P LOSS WILD-TYPE  426   26
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO               56               426
  YES               3                26
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                     49                             4
  3P LOSS WILD-TYPE                  333                            58
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3P LOSS MUTATED                       9                              3
  3P LOSS WILD-TYPE                   137                             10
D46V10, multiclass
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        49               333
  COLON MUCINOUS ADENOCARCINOMA                4                58
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  3P LOSS MUTATED    46   0   8   4
  3P LOSS WILD-TYPE 400   6  29  25
D46V11, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              46               400
  R1               0                 6
  R2               8                29
  RX               4                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"
D46V12, continuous
D46V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     1  39
  3P LOSS WILD-TYPE   4 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1   39
  3P LOSS WILD-TYPE    4  313
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO              39               313
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    34  10
  3Q LOSS WILD-TYPE 432 118
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               44               550 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               118 
$`3Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3870 TCGA-AA-3939 TCGA-BM-6198 
       14.53         6.05        85.05        29.98        12.99        21.24 
TCGA-G5-6233 TCGA-A6-4107 TCGA-AA-3517 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3966 
       18.28        32.45        38.99        10.06        32.05         2.01 
TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A01F TCGA-AD-A5EK TCGA-AY-6196 
       21.99         7.96        13.94        32.02        16.44         0.20 
TCGA-AZ-6600 TCGA-CA-6716 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 
       12.10        12.20        13.02         5.03        11.08        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 
       20.19        17.75        25.48        43.27        17.85        13.41 
TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
       11.38         7.50        31.96        42.77        38.70        11.90 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3731 TCGA-AG-4021 
       34.49        29.98        32.02        20.05        37.02         3.98 
TCGA-CI-6619 TCGA-DT-5265 
        6.05        12.62 

$`3Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        24.03        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       17.03        17.03        25.97        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       51.98        55.76        26.43        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        5.03        26.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        5.79        22.42        27.42        26.47         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       65.00        62.79        88.21        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       55.92        20.42        18.25        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        21.90        60.13 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.97        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       86.63        65.98        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
        2.50        43.20        27.55        26.43        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              0.2               0.0 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            85.05            148.01 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           17.095            22.470 
[1] "0.2 - 85.0 (17.1)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.5"
D47V2, continuous
D47V3, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    34   9
  3Q LOSS WILD-TYPE 414 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     34    9
  3Q LOSS WILD-TYPE  414  153
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON               34               414
  RECTUM               9               153
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  3Q LOSS MUTATED         3        0        2        16         0         0
  3Q LOSS WILD-TYPE     101        1       35       156        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  3Q LOSS MUTATED           1          0          5          3        9
  3Q LOSS WILD-TYPE        23         15         79         52       54
                   vv
clus                STAGE IVA STAGE IVB
  3Q LOSS MUTATED           3         0
  3Q LOSS WILD-TYPE        21         2
D47V4, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  3               101
  STAGE IA                 0                 1
  STAGE II                 2                35
  STAGE IIA               16               156
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                1                23
  STAGE IIIA               0                15
  STAGE IIIB               5                79
  STAGE IIIC               3                52
  STAGE IV                 9                54
  STAGE IVA                3                21
  STAGE IVB                0                 2
[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     0   3  35   6
  3Q LOSS WILD-TYPE  20 102 382  63
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                20
  T2               3               102
  T3              35               382
  T4               6                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"
                   vv
clus                 N0  N1  N2
  3Q LOSS MUTATED    22  11  11
  3Q LOSS WILD-TYPE 324 139 104
D47V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              22               324
  N1              11               139
  N2              11               104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    27  11
  3Q LOSS WILD-TYPE 426  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     27   11
  3Q LOSS WILD-TYPE  426   77
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              27               426
  1              11                77
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    16  28
  3Q LOSS WILD-TYPE 273 297
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     16   28
  3Q LOSS WILD-TYPE  273  297
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              16               273
  MALE                28               297
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    37   2
  3Q LOSS WILD-TYPE 445  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     37    2
  3Q LOSS WILD-TYPE  445   27
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               37               445
  YES               2                27
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  3Q LOSS MUTATED                     31                             3
  3Q LOSS WILD-TYPE                  351                            59
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  3Q LOSS MUTATED                       5                              4
  3Q LOSS WILD-TYPE                   141                              9
D47V10, multiclass
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        31               351
  COLON MUCINOUS ADENOCARCINOMA                3                59
  RECTAL ADENOCARCINOMA                        5               141
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[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                 R0  R1  R2  RX
  3Q LOSS MUTATED    32   0   5   2
  3Q LOSS WILD-TYPE 414   6  32  27
D47V11, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0              32               414
  R1               0                 6
  R2               5                32
  RX               2                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"
D47V12, continuous
D47V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     0  28
  3Q LOSS WILD-TYPE   5 324
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      0   28
  3Q LOSS WILD-TYPE    5  324
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              28               324
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED   145  42
  4P LOSS WILD-TYPE 321  86
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              187               407 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               42                86 
$`4P LOSS MUTATED`
TCGA-A6-2682 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       13.94        37.05        34.03        13.02        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       36.00        85.05        31.07        24.03        29.98        12.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 
       50.99        26.01        49.08         5.88        23.51        63.62 
TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6641 
       91.79        13.94        19.99        25.97        21.24        26.43 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        4.80         1.61        39.45        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5659 
       35.11        16.57        37.05        37.02        32.45        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 
       29.19        29.16        25.18        21.76        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3532 
       61.84         9.63         5.03         7.04        38.99        29.00 
TCGA-AA-3538 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3811 
       26.01        21.01         2.01        50.04        15.02        10.06 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02        17.03        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3966 
        0.99        31.07        17.03         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
       21.99        34.03        42.02        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W 
       33.04        26.01         2.96        39.98         2.01        41.00 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
        5.79        22.42        26.47        14.50         0.95        33.01 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 
        0.20        17.85         5.65         5.13        65.00        12.10 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 TCGA-CM-4750 TCGA-CM-5341 
       29.56         3.19        12.46        12.59         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       22.03        15.02        17.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       15.02        13.05        11.08        11.01        10.06        45.40 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6924 TCGA-D5-6926 
       56.09        20.19        17.75        25.48        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       13.41        11.38        12.59       140.38         7.50        44.32 
TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 
       14.04        26.47        43.04        33.67        47.41         8.35 
TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 TCGA-QG-A5YV 
       61.91        46.75        18.18        10.98        16.80        42.77 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 
       29.46        21.90        60.13        11.90        46.92        17.23 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
       43.04        34.49        37.74        29.98        24.36        65.98 
TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 
       36.03        34.03        34.03        34.03         6.05        20.98 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       29.98        37.02        32.98        19.04         1.02        17.95 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6643 TCGA-CI-6619 
       14.04        13.94        23.01        41.00        43.20         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       33.17        48.20        31.00        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 
       44.02       126.44       129.27        32.61         4.18        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.34        16.41        11.97        42.35        28.57         0.39 
TCGA-F5-6813 
       19.66 

$`4P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 
       13.02        24.03        36.03         8.05        19.07         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       17.95        23.01        19.99         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3979 TCGA-AA-3986 
       19.04        14.93        24.00         2.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 
       10.88        75.95       106.75       100.01         1.94        28.21 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 
       35.93        22.09        35.80        26.17        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
       10.39         8.02        17.03        17.03        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H 
       31.00        51.98        18.28        55.76        15.62        12.66 
TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2685 
        9.53        43.76        46.65        42.90        42.28        37.25 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 
       34.65        32.75        36.53        32.91        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.08        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 
       20.12        19.66        16.24        24.92        56.25         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 
        1.02         9.07        19.07         0.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 
       61.02        78.08         6.97        54.02        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        0.00         0.00         0.00        36.03        32.05        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       51.98         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK 
       40.96        12.16        83.24        24.53        27.42        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        16.31        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
        5.23        11.74        12.69        12.36        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
       25.02        26.04        27.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02         5.03        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       12.95        11.08        12.03        54.61        19.59        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       10.13        12.43         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       49.91        13.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
        6.18        47.87         1.55        34.42        41.42        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
        0.53        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V 
       36.00        26.43        26.04        13.78        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 
       19.33         9.93        15.65        12.79        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       31.30        38.70        70.03        39.48        13.55        37.97 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        24.59        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       46.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       19.99         7.99         0.99         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 
       36.95        13.02        14.01        25.02        32.02         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 
        3.98        46.03        20.98         6.02        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         2.50        27.55        26.43        19.46 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 
       25.05        26.04        12.00        13.97        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        12.62        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        3.48        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       17.46         8.45         9.96        49.51        32.19        36.49 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
              0.2               0.0 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           140.38            148.01 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            24.36             21.01 
[1] "0.2 - 140.4 (24.4)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   135  58
  4P LOSS WILD-TYPE 313 104
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    135   58
  4P LOSS WILD-TYPE  313  104
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON              135               313
  RECTUM              58               104
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4P LOSS MUTATED        26        0        6        50         3         0
  4P LOSS WILD-TYPE      78        1       31       122         9         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4P LOSS MUTATED           6          8         25         23       31
  4P LOSS WILD-TYPE        18          7         59         32       32
                   vv
clus                STAGE IVA STAGE IVB
  4P LOSS MUTATED          11         1
  4P LOSS WILD-TYPE        13         1
D48V4, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 26                78
  STAGE IA                 0                 1
  STAGE II                 6                31
  STAGE IIA               50               122
  STAGE IIB                3                 9
  STAGE IIC                0                 2
  STAGE III                6                18
  STAGE IIIA               8                 7
  STAGE IIIB              25                59
  STAGE IIIC              23                32
  STAGE IV                31                32
  STAGE IVA               11                13
  STAGE IVB                1                 1
[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     6  30 133  25
  4P LOSS WILD-TYPE  14  75 284  44
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               6                14
  T2              30                75
  T3             133               284
  T4              25                44
[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
  4P LOSS MUTATED    90  56  48
  4P LOSS WILD-TYPE 256  94  67
D48V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              90               256
  N1              56                94
  N2              48                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   128  42
  4P LOSS WILD-TYPE 325  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    128   42
  4P LOSS WILD-TYPE  325   46
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0             128               325
  1              42                46
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    89 106
  4P LOSS WILD-TYPE 200 219
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     89  106
  4P LOSS WILD-TYPE  200  219
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              89               200
  MALE               106               219
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED   149  14
  4P LOSS WILD-TYPE 333  15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED    149   14
  4P LOSS WILD-TYPE  333   15
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO              149               333
  YES              14                15
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                    125                            10
  4P LOSS WILD-TYPE                  257                            52
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4P LOSS MUTATED                      54                              3
  4P LOSS WILD-TYPE                    92                             10
D48V10, multiclass
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       125               257
  COLON MUCINOUS ADENOCARCINOMA               10                52
  RECTAL ADENOCARCINOMA                       54                92
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  4P LOSS MUTATED   141   1  15   6
  4P LOSS WILD-TYPE 305   5  22  23
D48V11, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0             141               305
  R1               1                 5
  R2              15                22
  RX               6                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"
D48V12, continuous
D48V13, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     3 106
  4P LOSS WILD-TYPE   2 246
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3  106
  4P LOSS WILD-TYPE    2  246
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             106               246
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED   142  39
  4Q LOSS WILD-TYPE 324  89
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              181               413 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               39                89 
$`4Q LOSS MUTATED`
TCGA-A6-2682 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       13.94        37.05        34.03        13.02        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       36.00        85.05        31.07        50.99        26.01        24.00 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 
       49.08         5.88        23.51        63.62        91.79        13.94 
TCGA-AG-3612 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       19.99        25.97        21.24        26.43         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       39.45        43.76        43.43        35.11        16.57        37.05 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-6654 
       32.45        30.44        29.19        29.16        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3532 
       20.28        61.84         9.63         5.03        38.99        29.00 
TCGA-AA-3538 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       26.01        33.99        21.01         2.01        50.04        37.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       10.06        38.99        36.95        37.02        17.03        10.06 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3966 
       33.07         0.99        17.03         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01T 
       21.99        34.03        42.02        15.02        32.02        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       26.01         2.96        39.98        41.00         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D 
       26.47        14.50        16.31         0.95         0.20        17.85 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-6719 
        5.13        65.00        12.10        29.56        12.46        14.30 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        8.02        13.02        29.06        22.03         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.08        11.01        45.40        56.09        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D9 TCGA-DM-A1DA 
       25.48        43.27         9.04        13.41       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6855 
       44.32        14.04        26.47        31.96        43.04        47.41 
TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
        8.35        61.91        46.75        18.18        10.98         9.93 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       16.80        42.77        29.46        21.90        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.92        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 
       37.74        29.98        24.36        65.98        36.03        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3881 
       34.03         6.05        20.98        29.98        32.98        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 
        1.02        17.95         1.02        48.03        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6544 
       36.03        14.04        13.94        23.01        41.00        38.56 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4749 
       43.20         6.05        33.17        13.78        48.20        25.05 
TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA 
       31.00        31.00        51.98        10.98        44.02       126.44 
TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
      129.27         4.18        17.00        15.85        16.34        16.41 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       11.97        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 
       19.66 

$`4Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 
       13.02        24.03        36.03         8.05        19.07         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       17.95        23.01        19.99         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        24.03        29.98        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
        2.01        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
        1.94        28.21        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 
       79.69        17.85        10.39         8.02        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       15.62        12.66         9.53        43.76        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       42.28        44.91        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       36.53        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       19.66        16.24        24.92        56.25         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 
        1.02         9.07        19.07         0.00        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       14.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01         5.98         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 
        0.99        25.02         1.02        17.98        15.95         0.00 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
        0.00         0.00        36.03        32.05        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        51.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 
       27.42        16.44         0.46         0.92        27.09        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.65        32.94        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41         6.77         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       27.02        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       14.04        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 
       54.61        19.59        55.92        20.42        18.25        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
        7.53        12.39        10.13        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       12.59       131.51       135.65         7.76       139.17        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV 
       26.43        26.04        13.78        74.79        19.33        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       15.65        12.79        32.98         8.42        31.30        38.70 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       70.03        39.48        16.83        20.02        24.59        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       11.84        36.03        12.00        32.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 
       37.02         0.99         0.99        19.99        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4021 
       35.01        14.01        25.02        32.02         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
        1.02        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 
        2.50        27.55        26.43        19.46        44.78        47.44 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       78.12         7.17        21.01        26.04        12.00        13.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05        12.62        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              0.2               0.0 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           140.38            148.01 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            24.36             21.01 
[1] "0.2 - 140.4 (24.4)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1"  
D49V2, continuous
D49V3, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   123  62
  4Q LOSS WILD-TYPE 325 100
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    123   62
  4Q LOSS WILD-TYPE  325  100
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON              123               325
  RECTUM              62               100
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  4Q LOSS MUTATED        26        0        7        50         2         0
  4Q LOSS WILD-TYPE      78        1       30       122        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  4Q LOSS MUTATED           5          7         28         26       24
  4Q LOSS WILD-TYPE        19          8         56         29       39
                   vv
clus                STAGE IVA STAGE IVB
  4Q LOSS MUTATED           9         0
  4Q LOSS WILD-TYPE        15         2
D49V4, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 26                78
  STAGE IA                 0                 1
  STAGE II                 7                30
  STAGE IIA               50               122
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                5                19
  STAGE IIIA               7                 8
  STAGE IIIB              28                56
  STAGE IIIC              26                29
  STAGE IV                24                39
  STAGE IVA                9                15
  STAGE IVB                0                 2
[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     5  30 129  24
  4Q LOSS WILD-TYPE  15  75 288  45
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               5                15
  T2              30                75
  T3             129               288
  T4              24                45
[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
  4Q LOSS MUTATED    89  55  44
  4Q LOSS WILD-TYPE 257  95  71
D49V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              89               257
  N1              55                95
  N2              44                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   130  33
  4Q LOSS WILD-TYPE 323  55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    130   33
  4Q LOSS WILD-TYPE  323   55
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0             130               323
  1              33                55
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    85 104
  4Q LOSS WILD-TYPE 204 221
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     85  104
  4Q LOSS WILD-TYPE  204  221
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              85               204
  MALE               104               221
[1] 2 2
[1] FALSE
D49V9, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED   147  13
  4Q LOSS WILD-TYPE 335  16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED    147   13
  4Q LOSS WILD-TYPE  335   16
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO              147               335
  YES              13                16
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                    112                            11
  4Q LOSS WILD-TYPE                  270                            51
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  4Q LOSS MUTATED                      58                              3
  4Q LOSS WILD-TYPE                    88                             10
D49V10, multiclass
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       112               270
  COLON MUCINOUS ADENOCARCINOMA               11                51
  RECTAL ADENOCARCINOMA                       58                88
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  4Q LOSS MUTATED   137   2  11   7
  4Q LOSS WILD-TYPE 309   4  26  22
D49V11, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0             137               309
  R1               2                 4
  R2              11                26
  RX               7                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"
D49V12, continuous
D49V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     3 107
  4Q LOSS WILD-TYPE   2 245
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3  107
  4Q LOSS WILD-TYPE    2  245
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO             107               245
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    63  19
  5P LOSS WILD-TYPE 403 109
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               82               512 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               19               109 
$`5P LOSS MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3697 TCGA-CK-5912 TCGA-AG-3611 
       13.94        14.53        24.16        85.05        49.08        13.94 
TCGA-G5-6233 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 
       18.28         1.61        39.45        43.76        43.76        42.28 
TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6654 
       36.53        29.19        32.71        27.09        25.18        23.87 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3841 
        9.63         5.03        26.01        50.04        10.06        36.95 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00F 
       10.06        33.07        36.03        24.00         2.01        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6901 
       27.02        42.02        10.98        33.04        41.00        22.42 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 
       26.47        16.31        17.26         5.65        65.00        62.79 
TCGA-AZ-6605 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        5.23         8.02        29.06        22.03         5.03        15.02 
TCGA-CM-6164 TCGA-CM-6172 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       29.03        11.01        17.85        10.13        12.43         9.04 
TCGA-G4-6295 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-QL-A97D 
        8.35        36.00        18.18        10.98        42.77        21.90 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-6136 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3731 
       46.92        43.04        24.36         6.05        20.98        37.02 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4021 TCGA-AG-A00Y 
       19.99         1.02        48.03        28.04         3.98        23.01 
TCGA-CI-6620 TCGA-CI-6621 TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD 
       33.17        13.78        13.97        51.98       126.44        57.24 
TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7004 
       20.55        16.41        13.64         8.45 

$`5P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 
       79.69        17.85        10.39         8.02        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       21.24        55.76        26.43        15.62         4.80        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 
        9.53        46.65        43.43        42.90        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        29.16        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       15.95        38.99        37.02         0.00        17.03         0.00 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
        0.00        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       19.00        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
        1.02         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
        0.95        33.01         0.20        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       19.33        18.84       109.28        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        5.13        22.36        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       13.02        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.39        14.30         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V 
       26.43        26.04        13.78        46.75        74.79        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33         9.93        15.65        12.79        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       70.03        39.48        17.23        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        16.83        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        25.02        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       25.05        26.04        31.00        12.00        31.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05        12.62        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         3.48         4.18 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.31         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.00 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           126.44            148.01 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            23.44             21.99 
[1] "1.0 - 126.4 (23.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D50V2, continuous
D50V3, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    59  25
  5P LOSS WILD-TYPE 389 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     59   25
  5P LOSS WILD-TYPE  389  137
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON               59               389
  RECTUM              25               137
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5P LOSS MUTATED        13        0        4        15         0         1
  5P LOSS WILD-TYPE      91        1       33       157        12         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5P LOSS MUTATED           3          5         13         12        8
  5P LOSS WILD-TYPE        21         10         71         43       55
                   vv
clus                STAGE IVA STAGE IVB
  5P LOSS MUTATED           7         0
  5P LOSS WILD-TYPE        17         2
D50V4, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 13                91
  STAGE IA                 0                 1
  STAGE II                 4                33
  STAGE IIA               15               157
  STAGE IIB                0                12
  STAGE IIC                1                 1
  STAGE III                3                21
  STAGE IIIA               5                10
  STAGE IIIB              13                71
  STAGE IIIC              12                43
  STAGE IV                 8                55
  STAGE IVA                7                17
  STAGE IVB                0                 2
[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     2  14  57  11
  5P LOSS WILD-TYPE  18  91 360  58
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               2                18
  T2              14                91
  T3              57               360
  T4              11                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"
                   vv
clus                 N0  N1  N2
  5P LOSS MUTATED    37  27  20
  5P LOSS WILD-TYPE 309 123  95
D50V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              37               309
  N1              27               123
  N2              20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    59  15
  5P LOSS WILD-TYPE 394  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     59   15
  5P LOSS WILD-TYPE  394   73
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              59               394
  1              15                73
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    42  42
  5P LOSS WILD-TYPE 247 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     42   42
  5P LOSS WILD-TYPE  247  283
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              42               247
  MALE                42               283
[1] 2 2
[1] FALSE
D50V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    72   4
  5P LOSS WILD-TYPE 410  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     72    4
  5P LOSS WILD-TYPE  410   25
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               72               410
  YES               4                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                     54                             5
  5P LOSS WILD-TYPE                  328                            57
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5P LOSS MUTATED                      24                              1
  5P LOSS WILD-TYPE                   122                             12
D50V10, multiclass
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        54               328
  COLON MUCINOUS ADENOCARCINOMA                5                57
  RECTAL ADENOCARCINOMA                       24               122
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  5P LOSS MUTATED    57   2   3   3
  5P LOSS WILD-TYPE 389   4  34  26
D50V11, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              57               389
  R1               2                 4
  R2               3                34
  RX               3                26
[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, continuous
D50V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  50
  5P LOSS WILD-TYPE   2 302
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   50
  5P LOSS WILD-TYPE    2  302
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              50               302
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    82  33
  5Q LOSS WILD-TYPE 384  95
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              115               479 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               33                95 
$`5Q LOSS MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3697 
       13.94        14.53        24.16        13.02        19.99        85.05 
TCGA-AA-3867 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6625 TCGA-AG-3611 
       24.03         1.94        49.08         5.88        91.79        13.94 
TCGA-AG-4008 TCGA-BM-6198 TCGA-G5-6233 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       17.03        21.24        18.28         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 
       43.76        37.02        36.53        30.44        29.19        27.09 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3538 
       25.18        21.76        23.87         9.63         5.03        26.01 
TCGA-AA-3542 TCGA-AA-3673 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3851 
       12.99        50.04        10.06        36.95        10.06        33.07 
TCGA-AA-3858 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O 
       31.07        24.00         2.01        21.99        34.03        27.02 
TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 
       42.02        10.98        33.04         2.01        41.00        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 
       27.42        26.47        16.31         0.20        17.26         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6605 TCGA-CA-5797 TCGA-CA-6719 TCGA-CM-4750 
       65.00        62.79         5.23        12.59        14.30         8.02 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6536 
       22.03         5.03        15.02        29.03        13.02        17.85 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1DB TCGA-F4-6459 
       10.13        12.43         9.04        13.41        44.32         8.61 
TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U 
        1.55         8.35        82.39        36.00        18.18        10.98 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 
       42.77         8.42        21.90        38.70        46.92        17.23 
TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-A56K TCGA-AG-3578 TCGA-AG-3725 
       43.04        37.74        24.36        86.63        32.02        20.98 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 
       29.98        37.02        32.98        19.04        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A026 
       48.03        28.04        36.03         3.98        23.01         1.94 
TCGA-AG-A02G TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       38.96        33.17        13.97        31.00        51.98        10.98 
TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 
       25.05       126.44        57.24        51.48        20.55        16.41 
TCGA-F5-6702 
       28.57 

$`5Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       36.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 
       25.08        10.88        75.95       106.75       100.01        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 
       79.69        17.85        10.39         8.02        19.99        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        51.98        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       26.43        15.62         4.80        12.66         9.53        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        34.65        32.75        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       29.16        22.52        24.13         8.38        25.08        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       37.05         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        20.98        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       35.01         1.02         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       16.44         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 
       88.21        49.41         6.77        12.10        29.56        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       26.04        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       14.04        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58         7.53        12.39        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
      133.18        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        39.42        61.91        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        46.75        74.79        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       15.65        12.79        16.80        29.46        32.98        31.30 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       60.13        11.90        70.03        39.48        13.55        37.97 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       34.49        29.98        16.83        20.02        24.59        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03        12.00         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
       19.99         7.99         0.99         0.99         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 
       17.95        36.95        13.02        35.01        14.01        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         1.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97        61.97        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 
       43.20        27.55        26.43        19.46         6.05        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
       25.05        26.04        31.00        12.00        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
       25.05        12.62        41.36       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        3.48         4.18        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              0.2               0.0 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           126.44            148.01 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            23.01             21.99 
[1] "0.2 - 126.4 (23.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D51V2, continuous
D51V3, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    80  40
  5Q LOSS WILD-TYPE 368 122
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     80   40
  5Q LOSS WILD-TYPE  368  122
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON               80               368
  RECTUM              40               122
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  5Q LOSS MUTATED        17        0        7        27         0         0
  5Q LOSS WILD-TYPE      87        1       30       145        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  5Q LOSS MUTATED           3          5         16         18       14
  5Q LOSS WILD-TYPE        21         10         68         37       49
                   vv
clus                STAGE IVA STAGE IVB
  5Q LOSS MUTATED          10         0
  5Q LOSS WILD-TYPE        14         2
D51V4, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 17                87
  STAGE IA                 0                 1
  STAGE II                 7                30
  STAGE IIA               27               145
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                3                21
  STAGE IIIA               5                10
  STAGE IIIB              16                68
  STAGE IIIC              18                37
  STAGE IV                14                49
  STAGE IVA               10                14
  STAGE IVB                0                 2
[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     2  19  87  12
  5Q LOSS WILD-TYPE  18  86 330  57
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               2                18
  T2              19                86
  T3              87               330
  T4              12                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"
                   vv
clus                 N0  N1  N2
  5Q LOSS MUTATED    56  31  33
  5Q LOSS WILD-TYPE 290 119  82
D51V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              56               290
  N1              31               119
  N2              33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    79  24
  5Q LOSS WILD-TYPE 374  64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     79   24
  5Q LOSS WILD-TYPE  374   64
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              79               374
  1              24                64
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    53  67
  5Q LOSS WILD-TYPE 236 258
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     53   67
  5Q LOSS WILD-TYPE  236  258
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              53               236
  MALE                67               258
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    99   4
  5Q LOSS WILD-TYPE 383  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     99    4
  5Q LOSS WILD-TYPE  383   25
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               99               383
  YES               4                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                     73                             7
  5Q LOSS WILD-TYPE                  309                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  5Q LOSS MUTATED                      38                              1
  5Q LOSS WILD-TYPE                   108                             12
D51V10, multiclass
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        73               309
  COLON MUCINOUS ADENOCARCINOMA                7                55
  RECTAL ADENOCARCINOMA                       38               108
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  5Q LOSS MUTATED    81   3   7   4
  5Q LOSS WILD-TYPE 365   3  30  25
D51V11, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              81               365
  R1               3                 3
  R2               7                30
  RX               4                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"
D51V12, continuous
D51V13, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3  69
  5Q LOSS WILD-TYPE   2 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   69
  5Q LOSS WILD-TYPE    2  283
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              69               283
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED    32  13
  6P LOSS WILD-TYPE 434 115
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               45               549 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13               115 
$`6P LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3939 TCGA-AG-3611 TCGA-A6-2671 
       24.16        36.00        19.04        12.99        13.94        43.76 
TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-6782 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3837 
       42.28        37.02        20.28        13.94         2.01        38.99 
TCGA-AA-3841 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00J TCGA-AA-A01X 
       36.95        18.05        24.00         2.01        18.05        26.01 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        5.79        16.44         5.65         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 
       12.46        11.08        11.01        45.40        20.19        17.75 
TCGA-D5-6898 TCGA-DM-A1D7 TCGA-F4-6808 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 
        7.53        13.32        33.67        17.23        13.55        34.49 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 TCGA-DC-6682 
       34.03        34.03         3.98        13.94        37.02        25.05 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6883 
       12.62        24.13        11.51 

$`6P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 
       19.99         6.05         0.92        19.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
      106.75       100.01         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 
       91.79        79.69        17.85        10.39         8.02        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       17.03        17.03        25.97        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       51.98        21.24        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.90        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.05        37.25        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 
       21.01        24.00        29.95        20.98        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        17.03        27.02        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       40.96        12.16        83.24        24.53        22.42        27.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       26.47         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       12.95        13.05        11.08        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       38.70        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       20.98         6.02        23.01         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.97        25.05       126.44        41.36        57.24       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             2.01              0.00 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            45.40            148.01 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            17.75             22.36 
[1] "2.0 - 45.4 (17.8)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "2"  
D52V2, continuous
D52V3, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    33  12
  6P LOSS WILD-TYPE 415 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     33   12
  6P LOSS WILD-TYPE  415  150
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON               33               415
  RECTUM              12               150
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6P LOSS MUTATED         7        0        2        20         1         1
  6P LOSS WILD-TYPE      97        1       35       152        11         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6P LOSS MUTATED           2          0          3          3        4
  6P LOSS WILD-TYPE        22         15         81         52       59
                   vv
clus                STAGE IVA STAGE IVB
  6P LOSS MUTATED           3         0
  6P LOSS WILD-TYPE        21         2
D52V4, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  7                97
  STAGE IA                 0                 1
  STAGE II                 2                35
  STAGE IIA               20               152
  STAGE IIB                1                11
  STAGE IIC                1                 1
  STAGE III                2                22
  STAGE IIIA               0                15
  STAGE IIIB               3                81
  STAGE IIIC               3                52
  STAGE IV                 4                59
  STAGE IVA                3                21
  STAGE IVB                0                 2
[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     2   6  31   7
  6P LOSS WILD-TYPE  18  99 386  62
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               2                18
  T2               6                99
  T3              31               386
  T4               7                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"
                   vv
clus                 N0  N1  N2
  6P LOSS MUTATED    30   8   8
  6P LOSS WILD-TYPE 316 142 107
D52V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              30               316
  N1               8               142
  N2               8               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    34   7
  6P LOSS WILD-TYPE 419  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     34    7
  6P LOSS WILD-TYPE  419   81
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              34               419
  1               7                81
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    20  26
  6P LOSS WILD-TYPE 269 299
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     20   26
  6P LOSS WILD-TYPE  269  299
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              20               269
  MALE                26               299
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    35   6
  6P LOSS WILD-TYPE 447  23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     35    6
  6P LOSS WILD-TYPE  447   23
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               35               447
  YES               6                23
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                     27                             5
  6P LOSS WILD-TYPE                  355                            57
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6P LOSS MUTATED                       9                              3
  6P LOSS WILD-TYPE                   137                             10
D52V10, multiclass
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        27               355
  COLON MUCINOUS ADENOCARCINOMA                5                57
  RECTAL ADENOCARCINOMA                        9               137
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  6P LOSS MUTATED    31   0   2   6
  6P LOSS WILD-TYPE 415   6  35  23
D52V11, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              31               415
  R1               0                 6
  R2               2                35
  RX               6                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"
D52V12, continuous
D52V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     0  26
  6P LOSS WILD-TYPE   5 326
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0   26
  6P LOSS WILD-TYPE    5  326
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              26               326
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED    50  16
  6Q LOSS WILD-TYPE 416 112
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               66               528 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               16               112 
$`6Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 
       24.16        13.02        36.00        19.04        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AG-3611 TCGA-G5-6233 TCGA-G5-6641 TCGA-A6-2671 
       12.99         2.01        13.94        18.28        26.43        43.76 
TCGA-A6-2678 TCGA-A6-4107 TCGA-A6-6782 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 
       42.28        32.45        20.28        13.94        61.02         2.01 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A00J 
       38.99        36.95        18.05        24.00         2.01        18.05 
TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02H TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 
       10.98        26.01         2.01         5.79        16.44         0.46 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 
        3.19        12.69        12.36        12.46        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 
       11.08        11.01        45.40        20.19        17.75        15.12 
TCGA-D5-6898 TCGA-DM-A1D7 TCGA-F4-6704 TCGA-F4-6808 TCGA-NH-A6GA TCGA-AF-2690 
        7.53        13.32         1.55        33.67         9.93        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 
       43.04        13.55        37.97        34.49        12.00        32.02 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-4005 
       24.00        46.03        34.03        34.03         6.05        14.04 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6883 
       13.94        37.02        38.56        25.05        12.62        11.51 

$`6Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       34.03         0.99        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3844 
        6.05         0.92        19.00        85.05        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.03        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-3L-AA1B 
       36.03        31.00        51.98        21.24        55.76        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.90        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 
       21.01        24.00        29.95        20.98        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       17.03        27.02        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 
       24.53        22.42        27.42        26.47         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       29.56         5.23        11.74        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.20        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       15.02        14.04        12.95        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        47.87        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98         8.42        31.30        21.90        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-4110 
       11.90        70.03        46.92        39.48        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        24.36        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       11.84        36.03         7.07        36.03        20.05         1.02 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02         3.98        46.03        20.98         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.04         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        44.02        25.97        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.46              0.00 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            61.02            148.01 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            17.49             22.47 
[1] "0.5 - 61.0 (17.5)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.6"
D53V2, continuous
D53V3, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    45  21
  6Q LOSS WILD-TYPE 403 141
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     45   21
  6Q LOSS WILD-TYPE  403  141
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON               45               403
  RECTUM              21               141
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  6Q LOSS MUTATED        10        0        4        20         1         1
  6Q LOSS WILD-TYPE      94        1       33       152        11         1
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  6Q LOSS MUTATED           2          1          7          9        7
  6Q LOSS WILD-TYPE        22         14         77         46       56
                   vv
clus                STAGE IVA STAGE IVB
  6Q LOSS MUTATED           3         1
  6Q LOSS WILD-TYPE        21         1
D53V4, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 10                94
  STAGE IA                 0                 1
  STAGE II                 4                33
  STAGE IIA               20               152
  STAGE IIB                1                11
  STAGE IIC                1                 1
  STAGE III                2                22
  STAGE IIIA               1                14
  STAGE IIIB               7                77
  STAGE IIIC               9                46
  STAGE IV                 7                56
  STAGE IVA                3                21
  STAGE IVB                1                 1
[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     4   8  48   8
  6Q LOSS WILD-TYPE  16  97 369  61
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               4                16
  T2               8                97
  T3              48               369
  T4               8                61
[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
  6Q LOSS MUTATED    35  13  20
  6Q LOSS WILD-TYPE 311 137  95
D53V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              35               311
  N1              13               137
  N2              20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    46  12
  6Q LOSS WILD-TYPE 407  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     46   12
  6Q LOSS WILD-TYPE  407   76
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              46               407
  1              12                76
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    27  41
  6Q LOSS WILD-TYPE 262 284
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     27   41
  6Q LOSS WILD-TYPE  262  284
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              27               262
  MALE                41               284
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    50   8
  6Q LOSS WILD-TYPE 432  21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     50    8
  6Q LOSS WILD-TYPE  432   21
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               50               432
  YES               8                21
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                     37                             7
  6Q LOSS WILD-TYPE                  345                            55
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  6Q LOSS MUTATED                      16                              5
  6Q LOSS WILD-TYPE                   130                              8
D53V10, multiclass
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        37               345
  COLON MUCINOUS ADENOCARCINOMA                7                55
  RECTAL ADENOCARCINOMA                       16               130
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[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                 R0  R1  R2  RX
  6Q LOSS MUTATED    50   0   3   7
  6Q LOSS WILD-TYPE 396   6  34  22
D53V11, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              50               396
  R1               0                 6
  R2               3                34
  RX               7                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"
D53V12, continuous
D53V13, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     0  34
  6Q LOSS WILD-TYPE   5 318
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0   34
  6Q LOSS WILD-TYPE    5  318
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              34               318
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 463 128
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3               591 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0               128 
$`7P LOSS MUTATED`
TCGA-5M-AATE TCGA-D5-6932 TCGA-AG-A008 
       39.45        11.38        13.94 

$`7P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       21.90        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            11.38              0.00 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            39.45            148.01 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            13.94             22.03 
[1] "11.4 - 39.5 (13.9)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D54V2, continuous
D54V3, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   1
  7P LOSS WILD-TYPE 446 161
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE  446  161
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  COLON                2               446
  RECTUM               1               161
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7P LOSS MUTATED         1        0        0         2         0         0
  7P LOSS WILD-TYPE     103        1       37       170        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7P LOSS MUTATED           0          0          0          0        0
  7P LOSS WILD-TYPE        24         15         84         55       63
                   vv
clus                STAGE IVA STAGE IVB
  7P LOSS MUTATED           0         0
  7P LOSS WILD-TYPE        24         2
D54V4, multiclass
            clus
vv           7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 0                37
  STAGE IIA                2               170
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                0                24
  STAGE IIIA               0                15
  STAGE IIIB               0                84
  STAGE IIIC               0                55
  STAGE IV                 0                63
  STAGE IVA                0                24
  STAGE IVB                0                 2
[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     0   1   2   0
  7P LOSS WILD-TYPE  20 104 415  69
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               0                20
  T2               1               104
  T3               2               415
  T4               0                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"
                   vv
clus                 N0  N1  N2
  7P LOSS MUTATED     3   0   0
  7P LOSS WILD-TYPE 343 150 115
D54V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               3               343
  N1               0               150
  N2               0               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 450  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE  450   88
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               3               450
  1               0                88
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1   2
  7P LOSS WILD-TYPE 288 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    2
  7P LOSS WILD-TYPE  288  323
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               1               288
  MALE                 2               323
[1] 2 2
[1] FALSE
D54V9, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 479  29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE  479   29
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                3               479
  YES               0                29
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7P LOSS MUTATED                      2                             0
  7P LOSS WILD-TYPE                  380                            62
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7P LOSS MUTATED                       0                              1
  7P LOSS WILD-TYPE                   146                             12
D54V10, multiclass
                                clus
vv                               7P LOSS MUTATED 7P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         2               380
  COLON MUCINOUS ADENOCARCINOMA                0                62
  RECTAL ADENOCARCINOMA                        0               146
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  7P LOSS MUTATED     3   0   0   0
  7P LOSS WILD-TYPE 443   6  37  29
D54V11, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               3               443
  R1               0                 6
  R2               0                37
  RX               0                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"
D54V12, continuous
D54V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     1   1
  7P LOSS WILD-TYPE   4 351
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    1
  7P LOSS WILD-TYPE    4  351
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               1               351
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     5   0
  7Q LOSS WILD-TYPE 461 128
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5               589 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0               128 
$`7Q LOSS MUTATED`
TCGA-5M-AATE TCGA-CM-5341 TCGA-D5-6932 TCGA-AG-3591 TCGA-AG-A008 
       39.45        29.06        11.38        34.03        13.94 

$`7Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.44        11.64        13.41        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       38.70        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            11.38              0.00 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            39.45            148.01 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            29.06             21.99 
[1] "11.4 - 39.5 (29.1)" "0.0 - 148.0 (22.0)"
[1] "hr="     "3300000"
D55V2, continuous
D55V3, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   2
  7Q LOSS WILD-TYPE 445 160
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    2
  7Q LOSS WILD-TYPE  445  160
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON                3               445
  RECTUM               2               160
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  7Q LOSS MUTATED         1        0        0         3         0         0
  7Q LOSS WILD-TYPE     103        1       37       169        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  7Q LOSS MUTATED           0          1          0          0        0
  7Q LOSS WILD-TYPE        24         14         84         55       63
                   vv
clus                STAGE IVA STAGE IVB
  7Q LOSS MUTATED           0         0
  7Q LOSS WILD-TYPE        24         2
D55V4, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1               103
  STAGE IA                 0                 1
  STAGE II                 0                37
  STAGE IIA                3               169
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                0                24
  STAGE IIIA               1                14
  STAGE IIIB               0                84
  STAGE IIIC               0                55
  STAGE IV                 0                63
  STAGE IVA                0                24
  STAGE IVB                0                 2
[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     0   2   3   0
  7Q LOSS WILD-TYPE  20 103 414  69
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                20
  T2               2               103
  T3               3               414
  T4               0                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"
                   vv
clus                 N0  N1  N2
  7Q LOSS MUTATED     4   1   0
  7Q LOSS WILD-TYPE 342 149 115
D55V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               4               342
  N1               1               149
  N2               0               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     5   0
  7Q LOSS WILD-TYPE 448  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    0
  7Q LOSS WILD-TYPE  448   88
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               5               448
  1               0                88
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   2
  7Q LOSS WILD-TYPE 286 323
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    2
  7Q LOSS WILD-TYPE  286  323
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3               286
  MALE                 2               323
[1] 2 2
[1] FALSE
D55V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     4   1
  7Q LOSS WILD-TYPE 478  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    1
  7Q LOSS WILD-TYPE  478   28
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                4               478
  YES               1                28
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  7Q LOSS MUTATED                      3                             0
  7Q LOSS WILD-TYPE                  379                            62
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  7Q LOSS MUTATED                       1                              1
  7Q LOSS WILD-TYPE                   145                             12
D55V10, multiclass
                                clus
vv                               7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         3               379
  COLON MUCINOUS ADENOCARCINOMA                0                62
  RECTAL ADENOCARCINOMA                        1               145
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  7Q LOSS MUTATED     5   0   0   0
  7Q LOSS WILD-TYPE 441   6  37  29
D55V11, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               5               441
  R1               0                 6
  R2               0                37
  RX               0                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"
D55V12, continuous
D55V13, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     1   2
  7Q LOSS WILD-TYPE   4 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      1    2
  7Q LOSS WILD-TYPE    4  350
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 4
  NOT HISPANIC OR LATINO               2               350
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   159  51
  8P LOSS WILD-TYPE 307  77
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              210               384 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               51                77 
$`8P LOSS MUTATED`
TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       45.60         1.02        24.03        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 
       19.99        19.99        19.00        36.00        85.05        31.07 
TCGA-AA-3867 TCGA-AA-3976 TCGA-AA-3979 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-DM-A285 
       24.03        26.01        24.00       106.75         1.94         5.88 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 
       23.51        35.93        91.79        10.39        13.94        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       17.03        25.97        15.95        51.98        21.24        18.28 
TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2674 
       26.43         4.80         1.61         9.53        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       43.43        42.28        44.91        35.11        16.57        34.65 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6137 TCGA-A6-6140 
       36.53        32.91        30.44        23.61        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3495 TCGA-AA-3517 TCGA-AA-3529 
       61.84        56.25         5.03        37.05        38.99         0.00 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3678 
       33.99        21.01        24.00        78.08         2.01        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3851 
       15.02        11.01         5.98        37.05        37.02        33.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3971 TCGA-AA-3975 
       17.03        27.02         2.01        24.00        16.08        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A017 TCGA-AA-A01G 
       27.02         7.96        19.00        34.03        15.02        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
       31.00         1.02        33.04        41.00        22.42        26.47 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 
       16.31        33.01         0.20        17.85       109.28         5.65 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5797 TCGA-CA-6719 
       62.79        12.10        29.56        11.74        12.59        14.30 
TCGA-CK-4952 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       15.62        13.02        22.03        22.98        30.08        32.02 
TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 
        5.03        14.04        21.99        13.02        15.02        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6534 TCGA-D5-6535 
       11.08        10.06        54.61        56.09        43.27        15.12 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       12.49        15.58         7.53        10.13         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
       11.38       130.65        49.91        13.32       140.38       131.51 
TCGA-DM-A28A TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 
       26.47        60.79        31.96        35.74         1.55        34.42 
TCGA-F4-6854 TCGA-G4-6299 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U 
        0.53        74.56        61.91        36.00        26.43        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2689 
       19.33         9.93        16.80        21.90        38.70        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-6136 
       17.23        43.04        13.55        37.97        37.74        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       20.02        24.59        36.03        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
       34.03        34.03         2.01         6.05         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3893 
        0.99        29.98        32.98         0.99         1.02        35.01 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00Y TCGA-AG-A011 
       19.99        28.04        36.03        14.04        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 
        1.02         1.02         1.94        38.96        41.00         2.50 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       48.20        78.12        21.01        25.05        31.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       51.98        10.98        25.05        12.62       126.44       129.27 
TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6884 TCGA-EI-7002 
       51.48         4.18        15.85        16.34        10.78        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
        8.45         9.96        42.35        28.57        19.66        12.46 

$`8P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53        24.16        58.03        13.02 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 
       37.05        36.03         8.05        19.07         0.99        17.95 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 
        6.05         0.92        19.04        19.04        14.93        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L 
       12.99        24.00         2.01        50.99        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 
       75.95       100.01        49.08        28.21        63.62        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3612 
       35.80        26.17        79.69        17.85         8.02        19.99 
TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE 
       36.03        31.00        55.76        15.62        12.66        39.45 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       46.65        42.90        37.05        37.25        37.02        32.75 
TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.45        31.63        29.19        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 
       32.71        29.16        22.52         8.38        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3489 
       20.12        19.66        16.24        24.92         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02         1.02        35.01        63.98         6.97         1.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02         9.07        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       12.99        14.01        29.95        20.98        13.94        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3696 
        6.97        54.02        14.01        50.04        47.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       10.06         0.00         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00        18.05        31.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 
       20.98        34.03         2.01        21.99        13.05        25.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        5.79        27.42        16.44         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       27.09         0.95        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       18.84        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        88.21        49.41         6.77         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.46        12.39        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       27.02        29.06        15.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        29.03        16.04        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        19.59        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       18.25        25.48        17.85         4.80        17.13        16.14 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        12.43        14.30         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K 
       14.04        81.37       119.93        35.97       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18         8.61        11.11        35.74         6.18        47.87 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        33.67        13.25        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18         8.35        82.39        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6322 TCGA-G4-6323 
       44.68        55.04        85.48        39.42        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        74.79        18.18        19.33        15.65        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO 
       42.77        29.46        32.98         8.42        31.30        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       11.90        70.03        46.92        34.49        29.98        16.83 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3591 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
        7.07        20.05        34.03        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       19.99        20.98        37.02         0.99        19.04        19.99 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       25.02        32.02         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 
       13.94         6.02         9.07        49.97        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       38.56        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 
       33.17        13.78        44.78        47.44         7.17        26.04 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC 
       12.00        31.00        44.02        25.97        25.05        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        24.13        32.61         3.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        18.28        17.69        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6810 
        8.61        11.51        13.64        17.46        49.51         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       32.19        36.49        37.18        38.14        11.87        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                 0 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           140.38            148.01 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           23.560            21.255 
[1] "0.0 - 140.4 (23.6)" "0.0 - 148.0 (21.3)"
[1] "hr=" "1.3"
D56V2, continuous
D56V3, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   140  73
  8P LOSS WILD-TYPE 308  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    140   73
  8P LOSS WILD-TYPE  308   89
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON              140               308
  RECTUM              73                89
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8P LOSS MUTATED        30        0        9        49         2         0
  8P LOSS WILD-TYPE      74        1       28       123        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8P LOSS MUTATED          10          8         30         25       33
  8P LOSS WILD-TYPE        14          7         54         30       30
                   vv
clus                STAGE IVA STAGE IVB
  8P LOSS MUTATED          11         1
  8P LOSS WILD-TYPE        13         1
D56V4, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 30                74
  STAGE IA                 0                 1
  STAGE II                 9                28
  STAGE IIA               49               123
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III               10                14
  STAGE IIIA               8                 7
  STAGE IIIB              30                54
  STAGE IIIC              25                30
  STAGE IV                33                30
  STAGE IVA               11                13
  STAGE IVB                1                 1
[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     4  35 151  25
  8P LOSS WILD-TYPE  16  70 266  44
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               4                16
  T2              35                70
  T3             151               266
  T4              25                44
[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
  8P LOSS MUTATED    98  62  55
  8P LOSS WILD-TYPE 248  88  60
D56V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              98               248
  N1              62                88
  N2              55                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   148  44
  8P LOSS WILD-TYPE 305  44
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    148   44
  8P LOSS WILD-TYPE  305   44
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             148               305
  1              44                44
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    92 123
  8P LOSS WILD-TYPE 197 202
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     92  123
  8P LOSS WILD-TYPE  197  202
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              92               197
  MALE               123               202
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   169  12
  8P LOSS WILD-TYPE 313  17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    169   12
  8P LOSS WILD-TYPE  313   17
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO              169               313
  YES              12                17
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                    126                            12
  8P LOSS WILD-TYPE                  256                            50
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8P LOSS MUTATED                      67                              5
  8P LOSS WILD-TYPE                    79                              8
D56V10, multiclass
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                       126               256
  COLON MUCINOUS ADENOCARCINOMA               12                50
  RECTAL ADENOCARCINOMA                       67                79
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[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                 R0  R1  R2  RX
  8P LOSS MUTATED   153   3  17   5
  8P LOSS WILD-TYPE 293   3  20  24
D56V11, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0             153               293
  R1               3                 3
  R2              17                20
  RX               5                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"
D56V12, continuous
D56V13, binary
                   cls
clus                  0   1
  8P LOSS MUTATED     4 124
  8P LOSS WILD-TYPE   1 228
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4  124
  8P LOSS WILD-TYPE    1  228
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   4                 1
  NOT HISPANIC OR LATINO             124               228
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    26   8
  8Q LOSS WILD-TYPE 440 120
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               34               560 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8               120 
$`8Q LOSS MUTATED`
TCGA-AA-3531 TCGA-AZ-6608 TCGA-G4-6314 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3890 
       34.03         1.94        35.93        91.79        13.94        17.03 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-3807 TCGA-A6-6782 TCGA-AA-3517 
       43.76        43.76        44.91        34.65        20.28        38.99 
TCGA-AA-3851 TCGA-AA-3941 TCGA-AA-3989 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 
       33.07        24.00         7.96        22.42        26.47         0.20 
TCGA-AY-A69D TCGA-AZ-5403 TCGA-CM-5860 TCGA-CM-6679 TCGA-D5-6539 TCGA-DM-A1D6 
       17.85        62.79        32.02        10.06        12.49        49.91 
TCGA-F4-6704 TCGA-QL-A97D TCGA-AG-3605 TCGA-AG-3883 TCGA-AG-A00Y TCGA-AG-A02X 
        1.55        21.90         0.99         1.02        23.01        41.00 
TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6511 TCGA-F5-6813 
       51.98        51.48        15.85        19.66 

$`8Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 
       25.08        10.88        75.95       106.75       100.01        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 
       26.17        79.69        17.85        10.39         8.02        19.99 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2675 
       12.66         1.61         9.53        39.45        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       16.08        13.05        34.06        25.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       24.53         5.79        27.42        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       17.13        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       13.97        31.00        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19        36.49        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              0.2               0.0 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            91.79            148.01 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           23.505            21.990 
[1] "0.2 - 91.8 (23.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    24  11
  8Q LOSS WILD-TYPE 424 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     24   11
  8Q LOSS WILD-TYPE  424  151
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON               24               424
  RECTUM              11               151
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  8Q LOSS MUTATED         5        0        1        10         2         0
  8Q LOSS WILD-TYPE      99        1       36       162        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  8Q LOSS MUTATED           0          1          2          5        5
  8Q LOSS WILD-TYPE        24         14         82         50       58
                   vv
clus                STAGE IVA STAGE IVB
  8Q LOSS MUTATED           2         0
  8Q LOSS WILD-TYPE        22         2
D57V4, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  5                99
  STAGE IA                 0                 1
  STAGE II                 1                36
  STAGE IIA               10               162
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                0                24
  STAGE IIIA               1                14
  STAGE IIIB               2                82
  STAGE IIIC               5                50
  STAGE IV                 5                58
  STAGE IVA                2                22
  STAGE IVB                0                 2
[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     0   6  25   4
  8Q LOSS WILD-TYPE  20  99 392  65
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                20
  T2               6                99
  T3              25               392
  T4               4                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"
                   vv
clus                 N0  N1  N2
  8Q LOSS MUTATED    20   6   9
  8Q LOSS WILD-TYPE 326 144 106
D57V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              20               326
  N1               6               144
  N2               9               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    21   7
  8Q LOSS WILD-TYPE 432  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     21    7
  8Q LOSS WILD-TYPE  432   81
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              21               432
  1               7                81
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    11  24
  8Q LOSS WILD-TYPE 278 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     11   24
  8Q LOSS WILD-TYPE  278  301
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              11               278
  MALE                24               301
[1] 2 2
[1] FALSE
D57V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    26   1
  8Q LOSS WILD-TYPE 456  28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     26    1
  8Q LOSS WILD-TYPE  456   28
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               26               456
  YES               1                28
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                     20                             4
  8Q LOSS WILD-TYPE                  362                            58
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  8Q LOSS MUTATED                      11                              0
  8Q LOSS WILD-TYPE                   135                             13
D57V10, multiclass
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        20               362
  COLON MUCINOUS ADENOCARCINOMA                4                58
  RECTAL ADENOCARCINOMA                       11               135
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[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                 R0  R1  R2  RX
  8Q LOSS MUTATED    25   1   2   0
  8Q LOSS WILD-TYPE 421   5  35  29
D57V11, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0              25               421
  R1               1                 5
  R2               2                35
  RX               0                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"
D57V12, continuous
D57V13, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  21
  8Q LOSS WILD-TYPE   5 331
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   21
  8Q LOSS WILD-TYPE    5  331
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              21               331
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    53  17
  9P LOSS WILD-TYPE 413 111
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               70               524 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               17               111 
$`9P LOSS MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 
       14.53        24.16        19.99        85.05        24.03        12.99 
TCGA-AA-3972 TCGA-AD-6888 TCGA-AZ-6608 TCGA-AG-A014 TCGA-AG-A01N TCGA-5M-AATE 
       50.99        15.52         1.94        15.95        31.00        39.45 
TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 
       43.43        36.53        29.16        21.76        61.84         6.97 
TCGA-AA-3517 TCGA-AA-3553 TCGA-AA-3685 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-A01F 
       38.99        24.00        37.05        24.00        20.98        32.02 
TCGA-AA-A01K TCGA-AA-A03J TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 
       31.00        40.96        26.47        14.50        16.31         5.65 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-6169 
        5.23         3.19        12.59        12.20         8.02        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6533 
       15.02        11.08        11.01        10.06        20.19        25.48 
TCGA-D5-6534 TCGA-D5-6898 TCGA-DM-A0XF TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 
       43.27         7.53        38.20        33.67         8.35        82.39 
TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-A56L 
        9.93        16.80        11.90        46.92        13.55        65.98 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-4021 
       20.05        34.03         6.05        37.02        19.99         3.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6158 
        1.94        38.96         6.05        48.20        25.05        10.98 
TCGA-DC-6160 TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 
       44.02        51.48         3.48        16.31 

$`9P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        45.60        13.94         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 
        0.99        13.02        17.95        23.01        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 
       31.07        29.98        24.00         2.01        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       19.07        38.04        21.99        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       10.88        75.95       106.75       100.01        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 
       13.94        19.99        17.03        17.03        25.97        36.03 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       51.98        21.24        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
        4.80        12.66         1.61         9.53        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       37.05        37.25        37.02        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 
       37.05        35.01        63.98         1.02         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
       83.24        24.53         5.79        22.42        27.42        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        27.09         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       29.56        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       12.95        13.05        11.08        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
        0.53        47.41        35.31       133.18        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       74.79        18.18        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
       21.90        38.70        60.13        70.03        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       43.04        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       24.36        20.02        24.59        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02         7.07        36.03        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       29.98        32.98         0.99         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       27.55        26.43        19.46        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       47.44        78.12         7.17        21.01        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.00        13.97        31.00        51.98        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1.94              0.00 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            85.05            148.01 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           20.120            22.075 
[1] "1.9 - 85.0 (20.1)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D58V2, continuous
D58V3, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    52  22
  9P LOSS WILD-TYPE 396 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     52   22
  9P LOSS WILD-TYPE  396  140
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON               52               396
  RECTUM              22               140
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9P LOSS MUTATED        13        0        5        17         1         0
  9P LOSS WILD-TYPE      91        1       32       155        11         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9P LOSS MUTATED           1          2          8          9       13
  9P LOSS WILD-TYPE        23         13         76         46       50
                   vv
clus                STAGE IVA STAGE IVB
  9P LOSS MUTATED           4         0
  9P LOSS WILD-TYPE        20         2
D58V4, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 13                91
  STAGE IA                 0                 1
  STAGE II                 5                32
  STAGE IIA               17               155
  STAGE IIB                1                11
  STAGE IIC                0                 2
  STAGE III                1                23
  STAGE IIIA               2                13
  STAGE IIIB               8                76
  STAGE IIIC               9                46
  STAGE IV                13                50
  STAGE IVA                4                20
  STAGE IVB                0                 2
[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     2  16  44  13
  9P LOSS WILD-TYPE  18  89 373  56
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               2                18
  T2              16                89
  T3              44               373
  T4              13                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"
                   vv
clus                 N0  N1  N2
  9P LOSS MUTATED    38  19  18
  9P LOSS WILD-TYPE 308 131  97
D58V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              38               308
  N1              19               131
  N2              18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    53  17
  9P LOSS WILD-TYPE 400  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     53   17
  9P LOSS WILD-TYPE  400   71
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              53               400
  1              17                71
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    29  46
  9P LOSS WILD-TYPE 260 279
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     29   46
  9P LOSS WILD-TYPE  260  279
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              29               260
  MALE                46               279
[1] 2 2
[1] FALSE
D58V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    62   3
  9P LOSS WILD-TYPE 420  26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     62    3
  9P LOSS WILD-TYPE  420   26
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               62               420
  YES               3                26
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                     50                             1
  9P LOSS WILD-TYPE                  332                            61
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9P LOSS MUTATED                      21                              1
  9P LOSS WILD-TYPE                   125                             12
D58V10, multiclass
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        50               332
  COLON MUCINOUS ADENOCARCINOMA                1                61
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  9P LOSS MUTATED    48   3   8   3
  9P LOSS WILD-TYPE 398   3  29  26
D58V11, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              48               398
  R1               3                 3
  R2               8                29
  RX               3                26
[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, continuous
D58V13, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     2  44
  9P LOSS WILD-TYPE   3 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2   44
  9P LOSS WILD-TYPE    3  308
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 3
  NOT HISPANIC OR LATINO              44               308
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    54  17
  9Q LOSS WILD-TYPE 412 111
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               71               523 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               17               111 
$`9Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 
       24.16        19.99        85.05        24.03        12.99        50.99 
TCGA-AZ-6608 TCGA-AG-A014 TCGA-AG-A01N TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 
        1.94        15.95        31.00        39.45        43.76        43.43 
TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 
       36.53        29.16        25.08        21.76        61.84         6.97 
TCGA-AA-3517 TCGA-AA-3553 TCGA-AA-3685 TCGA-AA-3955 TCGA-AA-A01F TCGA-AA-A01K 
       38.99        24.00        37.05        20.98        32.02        31.00 
TCGA-AA-A03J TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AZ-4614 TCGA-AZ-6603 
       40.96        14.50        16.31         0.95         5.65        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-5344 
        5.23         3.19        12.59        12.20         8.02        22.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 
       13.02        15.02        11.08        11.01        10.06        20.19 
TCGA-D5-6533 TCGA-D5-6898 TCGA-DM-A0XF TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 
       25.48         7.53        38.20        33.67         8.35        82.39 
TCGA-G4-6303 TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 
       65.85         9.93        16.80        60.13        11.90        46.92 
TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3731 TCGA-AG-3882 
       13.55        65.98        20.05        34.03        37.02        19.99 
TCGA-AG-4001 TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-4749 
       36.03         1.94        38.96         6.05        48.20        25.05 
TCGA-DC-6158 TCGA-DC-6160 TCGA-EF-5830 TCGA-EI-6514 TCGA-F5-6702 
       10.98        44.02         3.48        16.31        28.57 

$`9Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 
       14.93        31.07        29.98        24.00         2.01        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       25.97        36.03        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        46.65        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 
       37.05        35.01        63.98         1.02         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 
       26.47        16.44         0.46         0.92        27.09        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       12.10        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       25.02        26.04        27.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       13.05        11.08        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       56.09        55.92        20.42        17.75        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
        0.53        47.41        35.31       133.18        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33        15.65        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       38.70        70.03        39.48        17.23        43.04        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.59        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.04         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
       37.02         9.07         1.02         1.02        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46        33.17        13.78        44.78        47.44 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       13.97        31.00        51.98        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        42.35         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.95              0.00 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            85.05            148.01 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            22.03             21.99 
[1] "0.9 - 85.0 (22.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D59V2, continuous
D59V3, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    53  22
  9Q LOSS WILD-TYPE 395 140
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     53   22
  9Q LOSS WILD-TYPE  395  140
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON               53               395
  RECTUM              22               140
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  9Q LOSS MUTATED        14        0        5        16         2         0
  9Q LOSS WILD-TYPE      90        1       32       156        10         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  9Q LOSS MUTATED           1          2          9          7       14
  9Q LOSS WILD-TYPE        23         13         75         48       49
                   vv
clus                STAGE IVA STAGE IVB
  9Q LOSS MUTATED           4         0
  9Q LOSS WILD-TYPE        20         2
D59V4, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 14                90
  STAGE IA                 0                 1
  STAGE II                 5                32
  STAGE IIA               16               156
  STAGE IIB                2                10
  STAGE IIC                0                 2
  STAGE III                1                23
  STAGE IIIA               2                13
  STAGE IIIB               9                75
  STAGE IIIC               7                48
  STAGE IV                14                49
  STAGE IVA                4                20
  STAGE IVB                0                 2
[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     3  17  44  13
  9Q LOSS WILD-TYPE  17  88 373  56
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               3                17
  T2              17                88
  T3              44               373
  T4              13                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"
                   vv
clus                 N0  N1  N2
  9Q LOSS MUTATED    39  22  16
  9Q LOSS WILD-TYPE 307 128  99
D59V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              39               307
  N1              22               128
  N2              16                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    52  18
  9Q LOSS WILD-TYPE 401  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     52   18
  9Q LOSS WILD-TYPE  401   70
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              52               401
  1              18                70
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    33  44
  9Q LOSS WILD-TYPE 256 281
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     33   44
  9Q LOSS WILD-TYPE  256  281
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              33               256
  MALE                44               281
[1] 2 2
[1] FALSE
D59V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    65   2
  9Q LOSS WILD-TYPE 417  27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     65    2
  9Q LOSS WILD-TYPE  417   27
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               65               417
  YES               2                27
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                     51                             1
  9Q LOSS WILD-TYPE                  331                            61
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  9Q LOSS MUTATED                      21                              1
  9Q LOSS WILD-TYPE                   125                             12
D59V10, multiclass
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        51               331
  COLON MUCINOUS ADENOCARCINOMA                1                61
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[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                 R0  R1  R2  RX
  9Q LOSS MUTATED    51   2   8   3
  9Q LOSS WILD-TYPE 395   4  29  26
D59V11, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              51               395
  R1               2                 4
  R2               8                29
  RX               3                26
[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, continuous
D59V13, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     3  46
  9Q LOSS WILD-TYPE   2 306
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3   46
  9Q LOSS WILD-TYPE    2  306
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                 2
  NOT HISPANIC OR LATINO              46               306
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    84  15
  10P LOSS WILD-TYPE 382 113
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                99                495 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                15                113 
$`10P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3697 
       24.33        45.60        13.02        19.99        36.00        85.05 
TCGA-AA-3867 TCGA-AA-3972 TCGA-NH-A8F7 TCGA-AG-A00H TCGA-G5-6641 TCGA-A6-2680 
       24.03        50.99        17.85        25.97        26.43        35.11 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 
       30.44        32.71        29.16        22.52        25.18        23.87 
TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3848 
        9.63         1.02         6.97        50.04        37.05        10.06 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D 
       31.07        17.03         7.96        34.03        42.02        10.98 
TCGA-AA-A01X TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 
       26.01        41.00        22.42        16.44        14.50         0.20 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 
        5.65         5.13        65.00        62.79        29.56         3.19 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
       12.59        12.20        14.30         8.02        29.06        22.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-G4-6297 
       11.08        17.75         7.53         9.04        13.41        82.39 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC 
       65.85        55.04        61.91        26.04        46.75        12.79 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 
       38.70        60.13        46.92        13.55        34.49        24.59 
TCGA-AF-A56L TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3887 
       65.98        46.03        34.03        34.03        29.98        36.95 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 
        1.02        19.99        13.94         1.02        41.00        38.56 
TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       48.20        13.97        31.00        51.98        25.05        25.05 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
      129.27         3.48        17.00        16.34        16.31        16.41 
TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6864 
        8.45        28.57        12.46 

$`10P LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
        0.99        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       19.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00         2.01        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 
       35.80        26.17        91.79        79.69        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
       13.94        19.99        17.03        17.03        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B 
       31.00        51.98        21.24        18.28        55.76        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.45        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        5.03         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       16.08        13.05        34.06        25.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       83.24        24.53         5.79        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       58.39         1.41        32.94        22.36        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
        6.77        12.10         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.46        12.39        12.59        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       30.08        32.02        15.02         5.03        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 
       47.41        35.31       133.18         8.35        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       53.62        44.68        85.48        39.42        36.00        26.43 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 
        8.42        31.30        21.90        11.90        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       17.23        43.04        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.36        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        20.98         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       17.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
        1.02        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6158 
       21.01        25.05        26.04        31.00        12.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.97        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46        11.97         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       42.35         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       38.14        11.87        47.08 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               0.2                0.0 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            129.27             148.01 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             24.33              21.76 
[1] "0.2 - 129.3 (24.3)" "0.0 - 148.0 (21.8)"
[1] "hr=" "1.5"
D60V2, continuous
D60V3, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    67  33
  10P LOSS WILD-TYPE 381 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     67   33
  10P LOSS WILD-TYPE  381  129
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON                67                381
  RECTUM               33                129
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10P LOSS MUTATED        16        0        6        20         2         1
  10P LOSS WILD-TYPE      88        1       31       152        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10P LOSS MUTATED           2          5         16         10       13
  10P LOSS WILD-TYPE        22         10         68         45       50
                    vv
clus                 STAGE IVA STAGE IVB
  10P LOSS MUTATED           5         1
  10P LOSS WILD-TYPE        19         1
D60V4, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  16                 88
  STAGE IA                  0                  1
  STAGE II                  6                 31
  STAGE IIA                20                152
  STAGE IIB                 2                 10
  STAGE IIC                 1                  1
  STAGE III                 2                 22
  STAGE IIIA                5                 10
  STAGE IIIB               16                 68
  STAGE IIIC               10                 45
  STAGE IV                 13                 50
  STAGE IVA                 5                 19
  STAGE IVB                 1                  1
[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     2  20  67  12
  10P LOSS WILD-TYPE  18  85 350  57
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                2                 18
  T2               20                 85
  T3               67                350
  T4               12                 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"
                    vv
clus                  N0  N1  N2
  10P LOSS MUTATED    48  30  23
  10P LOSS WILD-TYPE 298 120  92
D60V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               48                298
  N1               30                120
  N2               23                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    71  19
  10P LOSS WILD-TYPE 382  69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     71   19
  10P LOSS WILD-TYPE  382   69
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               71                382
  1               19                 69
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    47  54
  10P LOSS WILD-TYPE 242 271
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     47   54
  10P LOSS WILD-TYPE  242  271
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               47                242
  MALE                 54                271
[1] 2 2
[1] FALSE
D60V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    81  11
  10P LOSS WILD-TYPE 401  18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     81   11
  10P LOSS WILD-TYPE  401   18
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                81                401
  YES               11                 18
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                     61                             6
  10P LOSS WILD-TYPE                  321                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10P LOSS MUTATED                      27                              6
  10P LOSS WILD-TYPE                   119                              7
D60V10, multiclass
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         61                321
  COLON MUCINOUS ADENOCARCINOMA                 6                 56
  RECTAL ADENOCARCINOMA                        27                119
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[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                  R0  R1  R2  RX
  10P LOSS MUTATED    76   0   6   5
  10P LOSS WILD-TYPE 370   6  31  24
D60V11, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               76                370
  R1                0                  6
  R2                6                 31
  RX                5                 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"
D60V12, continuous
D60V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     1  65
  10P LOSS WILD-TYPE   4 287
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1   65
  10P LOSS WILD-TYPE    4  287
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               65                287
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED    91  16
  10Q LOSS WILD-TYPE 375 112
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               107                487 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                16                112 
$`10Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 
       24.33        45.60        13.02        19.99         6.05        36.00 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3972 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-A00H 
       85.05        24.03        50.99        91.79        17.85        25.97 
TCGA-G5-6641 TCGA-A6-2671 TCGA-A6-2680 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 
       26.43        43.76        35.11        30.44        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       22.52        25.18        23.87         9.63         1.02         6.97 
TCGA-AA-3548 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3841 TCGA-AA-3848 TCGA-AA-3858 
       33.99        50.04        37.05        36.95        10.06        31.07 
TCGA-AA-3866 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W 
       17.03        34.03        42.02        10.98        26.01        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-4684 
       22.42        16.44        14.50        16.31         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       62.79        29.56         3.19        12.59        12.20        14.30 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
        8.02        29.06        22.03         5.03        15.02        15.02 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       29.03        13.02        15.02        11.08        11.08        10.06 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-F4-6808 
       17.75        43.27         7.53         9.04        13.41        33.67 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6322 TCGA-NH-A6GC TCGA-RU-A8FL TCGA-SS-A7HO 
       55.04        61.91        26.04        12.79        38.70        60.13 
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 
       46.92        13.55        34.49        24.59        65.98        32.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3887 
       46.03        34.03        34.03         6.05        29.98        36.95 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A020 TCGA-AG-A02X 
        1.02        19.99        13.94        37.02         1.02        41.00 
TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       48.20        13.97        51.98        25.05        25.05       129.27 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       24.13         3.48        17.00        16.34        16.31        16.41 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 
       11.97        28.57        36.49        12.46        47.08 

$`10Q LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 
        0.99        17.95        23.01        19.99         0.92        19.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       26.17        79.69        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       21.24        18.28        55.76        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        1.61         9.53        39.45        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        44.91        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        32.75        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       27.09        24.13         8.38        25.08        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84        56.25         5.03         7.04         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       37.05        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
        0.99        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04         1.02        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       26.47         0.46         0.92        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        32.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       55.92        20.19        20.42        18.25        25.48        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.43        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       70.03        39.48        17.23        43.04        37.97        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N 
       29.98        16.83        24.36        20.02        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        20.98         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       17.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        23.01         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        44.02        25.97        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       42.35         0.39        32.19        19.66        37.18        38.14 
TCGA-F5-6863 
       11.87 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1.02               0.00 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.27             148.01 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             24.59              21.37 
[1] "1.0 - 129.3 (24.6)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.5"
D61V2, continuous
D61V3, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    72  37
  10Q LOSS WILD-TYPE 376 125
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     72   37
  10Q LOSS WILD-TYPE  376  125
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON                72                376
  RECTUM               37                125
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  10Q LOSS MUTATED        17        0        6        26         2         1
  10Q LOSS WILD-TYPE      87        1       31       146        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  10Q LOSS MUTATED           2          5         16         13       13
  10Q LOSS WILD-TYPE        22         10         68         42       50
                    vv
clus                 STAGE IVA STAGE IVB
  10Q LOSS MUTATED           5         1
  10Q LOSS WILD-TYPE        19         1
D61V4, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  17                 87
  STAGE IA                  0                  1
  STAGE II                  6                 31
  STAGE IIA                26                146
  STAGE IIB                 2                 10
  STAGE IIC                 1                  1
  STAGE III                 2                 22
  STAGE IIIA                5                 10
  STAGE IIIB               16                 68
  STAGE IIIC               13                 42
  STAGE IV                 13                 50
  STAGE IVA                 5                 19
  STAGE IVB                 1                  1
[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     3  20  74  12
  10Q LOSS WILD-TYPE  17  85 343  57
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                3                 17
  T2               20                 85
  T3               74                343
  T4               12                 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"
                    vv
clus                  N0  N1  N2
  10Q LOSS MUTATED    55  29  25
  10Q LOSS WILD-TYPE 291 121  90
D61V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               55                291
  N1               29                121
  N2               25                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    81  18
  10Q LOSS WILD-TYPE 372  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     81   18
  10Q LOSS WILD-TYPE  372   70
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0               81                372
  1               18                 70
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    51  59
  10Q LOSS WILD-TYPE 238 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     51   59
  10Q LOSS WILD-TYPE  238  266
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               51                238
  MALE                 59                266
[1] 2 2
[1] FALSE
D61V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    88  12
  10Q LOSS WILD-TYPE 394  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     88   12
  10Q LOSS WILD-TYPE  394   17
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                88                394
  YES               12                 17
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                     66                             6
  10Q LOSS WILD-TYPE                  316                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  10Q LOSS MUTATED                      31                              6
  10Q LOSS WILD-TYPE                   115                              7
D61V10, multiclass
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         66                316
  COLON MUCINOUS ADENOCARCINOMA                 6                 56
  RECTAL ADENOCARCINOMA                        31                115
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[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                  R0  R1  R2  RX
  10Q LOSS MUTATED    83   1   7   5
  10Q LOSS WILD-TYPE 363   5  30  24
D61V11, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               83                363
  R1                1                  5
  R2                7                 30
  RX                5                 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"
D61V12, continuous
D61V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     1  69
  10Q LOSS WILD-TYPE   4 283
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1   69
  10Q LOSS WILD-TYPE    4  283
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               69                283
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    57  14
  11P LOSS WILD-TYPE 409 114
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                71                523 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                14                114 
$`11P LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 
       24.16         6.05        36.00        31.07        12.99         2.01 
TCGA-AA-3972 TCGA-CK-5912 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6138 
       50.99        49.08        36.53        32.45        30.44        22.52 
TCGA-A6-6651 TCGA-AA-3519 TCGA-AA-3666 TCGA-AA-3685 TCGA-AA-3855 TCGA-AA-3941 
       21.76         9.07         2.01        37.05        32.05        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
        2.01        21.99        42.02        32.02        31.00        33.04 
TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 
        2.96        40.96         5.79        16.44        14.50         0.20 
TCGA-AY-A69D TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CM-5862 TCGA-CM-5863 
       17.85         1.41        12.46        12.20         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6924 
       15.02        14.04        11.01        45.40        20.19        14.30 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A6GC 
       49.91         7.50        61.91        36.00        18.18        12.79 
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 
       43.04        29.98        24.36        24.59        32.02         7.07 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 
        6.05        32.98        19.04        17.95         1.02        13.94 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6156 
        1.02        41.00        38.56        43.20        13.97        31.00 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 TCGA-F5-6813 
       12.62        24.13        17.00        16.41        19.66 

$`11P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 
       14.93        24.03        29.98        24.00        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       55.76        26.43        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        34.65        32.75        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 
       63.98         6.97         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       83.24        24.53        22.42        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 
       22.03        22.98        30.08        32.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       13.05        11.08        11.08        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        13.32        12.59       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        46.75        74.79        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 
       70.03        46.92        39.48        17.23        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       34.49        37.74        16.83        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       11.84        36.03        12.00        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       38.96        61.97        38.04         2.50        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       31.00        12.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        25.05       126.44        41.36        57.24       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       20.91        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       32.19        36.49        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
               0.2                0.0 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             61.91             148.01 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.66              22.09 
[1] "0.2 - 61.9 (19.7)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D62V2, continuous
D62V3, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    50  23
  11P LOSS WILD-TYPE 398 139
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   23
  11P LOSS WILD-TYPE  398  139
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON                50                398
  RECTUM               23                139
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11P LOSS MUTATED        15        0        2        14         0         0
  11P LOSS WILD-TYPE      89        1       35       158        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11P LOSS MUTATED           5          2         10         11        8
  11P LOSS WILD-TYPE        19         13         74         44       55
                    vv
clus                 STAGE IVA STAGE IVB
  11P LOSS MUTATED           5         1
  11P LOSS WILD-TYPE        19         1
D62V4, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  15                 89
  STAGE IA                  0                  1
  STAGE II                  2                 35
  STAGE IIA                14                158
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 5                 19
  STAGE IIIA                2                 13
  STAGE IIIB               10                 74
  STAGE IIIC               11                 44
  STAGE IV                  8                 55
  STAGE IVA                 5                 19
  STAGE IVB                 1                  1
[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     2  14  46  12
  11P LOSS WILD-TYPE  18  91 371  57
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                 18
  T2               14                 91
  T3               46                371
  T4               12                 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"
                    vv
clus                  N0  N1  N2
  11P LOSS MUTATED    30  24  20
  11P LOSS WILD-TYPE 316 126  95
D62V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               30                316
  N1               24                126
  N2               20                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    50  13
  11P LOSS WILD-TYPE 403  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     50   13
  11P LOSS WILD-TYPE  403   75
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               50                403
  1               13                 75
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    33  41
  11P LOSS WILD-TYPE 256 284
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     33   41
  11P LOSS WILD-TYPE  256  284
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               33                256
  MALE                 41                284
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    54   6
  11P LOSS WILD-TYPE 428  23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     54    6
  11P LOSS WILD-TYPE  428   23
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                54                428
  YES                6                 23
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                     43                             7
  11P LOSS WILD-TYPE                  339                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11P LOSS MUTATED                      18                              4
  11P LOSS WILD-TYPE                   128                              9
D62V10, multiclass
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         43                339
  COLON MUCINOUS ADENOCARCINOMA                 7                 55
  RECTAL ADENOCARCINOMA                        18                128
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[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                  R0  R1  R2  RX
  11P LOSS MUTATED    52   0   5   4
  11P LOSS WILD-TYPE 394   6  32  25
D62V11, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               52                394
  R1                0                  6
  R2                5                 32
  RX                4                 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"
D62V12, continuous
D62V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  38
  11P LOSS WILD-TYPE   5 314
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   38
  11P LOSS WILD-TYPE    5  314
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               38                314
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    69  18
  11Q LOSS WILD-TYPE 397 110
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                87                507 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                18                110 
$`11Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 
       24.16         6.05        36.00        31.07        12.99         2.01 
TCGA-AA-3972 TCGA-AG-3611 TCGA-BM-6198 TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-3810 
       50.99        13.94        21.24        43.76        16.57        36.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3511 
       32.45        30.44        22.52        21.76        23.87         6.97 
TCGA-AA-3519 TCGA-AA-3666 TCGA-AA-3855 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3968 
        9.07         2.01        32.05        18.05        24.00        21.99 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F 
       42.02        32.02        31.00        33.04         2.96        39.98 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 
       40.96         5.79        22.42        16.44        14.50         0.95 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 
        0.20        17.85        19.33         1.41        12.46        12.20 
TCGA-CK-6748 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 
        2.01        30.08         5.03        15.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6924 
       11.01        11.01        45.40        20.19        17.85        14.30 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50T 
      130.65        49.91         7.50        61.91        36.00        18.18 
TCGA-NH-A6GC TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 
       12.79        43.04        13.55        37.97        29.98        24.36 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3600 
       24.59        32.02         7.07        34.03         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A020 
       32.98        19.04        17.95         1.02        13.94         1.02 
TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 
       38.56        43.20        13.97        10.98        44.02        12.62 
TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 
       24.13        17.00        16.41 

$`11Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 
       14.93        24.03        29.98        24.00        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       39.45        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        35.11        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.75        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       37.05        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
        0.00        36.03         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       27.02        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H 
        1.02         1.02        26.01        37.02        51.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       12.16        83.24        24.53        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       17.26        18.84       109.28        58.39         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.39        12.59        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       27.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       54.61        19.59        56.09        55.92        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.43         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        39.42        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        74.79        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       31.30        21.90        38.70        60.13        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       46.92        39.48        17.23        34.49        37.74        16.83 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 
        6.02        23.01        37.02         9.07         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.96        61.97        41.00        38.04         2.50 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               0.2                0.0 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            130.65             148.01 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             18.18              22.98 
[1] "0.2 - 130.7 (18.2)" "0.0 - 148.0 (23.0)"
[1] "hr=" "1.3"
D63V2, continuous
D63V3, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    60  27
  11Q LOSS WILD-TYPE 388 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     60   27
  11Q LOSS WILD-TYPE  388  135
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON                60                388
  RECTUM               27                135
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  11Q LOSS MUTATED        19        0        2        20         0         0
  11Q LOSS WILD-TYPE      85        1       35       152        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  11Q LOSS MUTATED           5          2         13         10       12
  11Q LOSS WILD-TYPE        19         13         71         45       51
                    vv
clus                 STAGE IVA STAGE IVB
  11Q LOSS MUTATED           4         1
  11Q LOSS WILD-TYPE        20         1
D63V4, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  19                 85
  STAGE IA                  0                  1
  STAGE II                  2                 35
  STAGE IIA                20                152
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 5                 19
  STAGE IIIA                2                 13
  STAGE IIIB               13                 71
  STAGE IIIC               10                 45
  STAGE IV                 12                 51
  STAGE IVA                 4                 20
  STAGE IVB                 1                  1
[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     4  16  59  12
  11Q LOSS WILD-TYPE  16  89 358  57
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                4                 16
  T2               16                 89
  T3               59                358
  T4               12                 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"
                    vv
clus                  N0  N1  N2
  11Q LOSS MUTATED    42  30  19
  11Q LOSS WILD-TYPE 304 120  96
D63V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               42                304
  N1               30                120
  N2               19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    61  16
  11Q LOSS WILD-TYPE 392  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     61   16
  11Q LOSS WILD-TYPE  392   72
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               61                392
  1               16                 72
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    45  46
  11Q LOSS WILD-TYPE 244 279
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     45   46
  11Q LOSS WILD-TYPE  244  279
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               45                244
  MALE                 46                279
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    71   7
  11Q LOSS WILD-TYPE 411  22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     71    7
  11Q LOSS WILD-TYPE  411   22
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                71                411
  YES                7                 22
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                     53                             7
  11Q LOSS WILD-TYPE                  329                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  11Q LOSS MUTATED                      21                              5
  11Q LOSS WILD-TYPE                   125                              8
D63V10, multiclass
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         53                329
  COLON MUCINOUS ADENOCARCINOMA                 7                 55
  RECTAL ADENOCARCINOMA                        21                125
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[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                  R0  R1  R2  RX
  11Q LOSS MUTATED    64   0   6   4
  11Q LOSS WILD-TYPE 382   6  31  25
D63V11, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               64                382
  R1                0                  6
  R2                6                 31
  RX                4                 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"
D63V12, continuous
D63V13, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  50
  11Q LOSS WILD-TYPE   4 302
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   50
  11Q LOSS WILD-TYPE    4  302
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               50                302
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    47  21
  12P LOSS WILD-TYPE 419 107
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                68                526 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                21                107 
$`12P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       24.33        45.60        13.02        24.03         2.01        50.99 
TCGA-CK-5912 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 
       49.08        17.85        10.39        43.76        34.65        36.53 
TCGA-A6-5659 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3548 
       30.44        20.28        61.84         9.63        26.01        33.99 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-A01F TCGA-AA-A01T 
        2.01        50.04        31.07        17.03        32.02        33.04 
TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AZ-4684 TCGA-CA-5256 
        2.96         5.79        22.42        16.44        65.00        12.46 
TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 
        8.02         5.03        14.04        29.03        15.02        11.01 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA 
       11.08        10.06        25.48        11.38        12.59         7.50 
TCGA-F4-6460 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-RU-A8FL 
       31.96        43.04        65.85        61.91        36.00        38.70 
TCGA-SS-A7HO TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3591 TCGA-AG-3593 
       60.13        43.04        29.98        24.36        34.03        34.03 
TCGA-AG-3728 TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A00Y TCGA-DC-6155 TCGA-DC-6158 
       29.98        48.03         3.98        23.01        13.97        10.98 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 
       24.13        51.48        20.91        17.00        16.31        16.41 
TCGA-F5-6702 TCGA-F5-6812 
       28.57        36.49 

$`12P LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 
       14.93        31.07        29.98        12.99        24.00        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AG-3580 
       22.09        35.80        26.17        91.79        79.69         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       13.94        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       39.45        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.45        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        56.25         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       29.00        12.99        14.01        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 
        0.00        36.03        32.05         0.99        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       12.16        83.24        24.53        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       12.00        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 
       14.04        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.41        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
        8.35        82.39        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        39.42        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.92        39.48        17.23        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        16.83        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       31.00        12.00        31.00        51.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        17.69        16.34         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       49.51        42.35         0.39        32.19        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              2.01               0.00 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             65.85             148.01 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            24.345             21.830 
[1] "2.0 - 65.8 (24.3)"  "0.0 - 148.0 (21.8)"
[1] "hr=" "1.6"
D64V2, continuous
D64V3, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    48  22
  12P LOSS WILD-TYPE 400 140
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     48   22
  12P LOSS WILD-TYPE  400  140
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON                48                400
  RECTUM               22                140
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12P LOSS MUTATED        10        0        2        15         2         0
  12P LOSS WILD-TYPE      94        1       35       157        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12P LOSS MUTATED           2          3          8         12        9
  12P LOSS WILD-TYPE        22         12         76         43       54
                    vv
clus                 STAGE IVA STAGE IVB
  12P LOSS MUTATED           5         0
  12P LOSS WILD-TYPE        19         2
D64V4, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  10                 94
  STAGE IA                  0                  1
  STAGE II                  2                 35
  STAGE IIA                15                157
  STAGE IIB                 2                 10
  STAGE IIC                 0                  2
  STAGE III                 2                 22
  STAGE IIIA                3                 12
  STAGE IIIB                8                 76
  STAGE IIIC               12                 43
  STAGE IV                  9                 54
  STAGE IVA                 5                 19
  STAGE IVB                 0                  2
[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     3   9  54   5
  12P LOSS WILD-TYPE  17  96 363  64
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                 17
  T2                9                 96
  T3               54                363
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  12P LOSS MUTATED    31  22  18
  12P LOSS WILD-TYPE 315 128  97
D64V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0               31                315
  N1               22                128
  N2               18                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    47  13
  12P LOSS WILD-TYPE 406  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     47   13
  12P LOSS WILD-TYPE  406   75
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0               47                406
  1               13                 75
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    36  35
  12P LOSS WILD-TYPE 253 290
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     36   35
  12P LOSS WILD-TYPE  253  290
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               36                253
  MALE                 35                290
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    57   4
  12P LOSS WILD-TYPE 425  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     57    4
  12P LOSS WILD-TYPE  425   25
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                57                425
  YES                4                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                     47                             1
  12P LOSS WILD-TYPE                  335                            61
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12P LOSS MUTATED                      22                              0
  12P LOSS WILD-TYPE                   124                             13
D64V10, multiclass
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         47                335
  COLON MUCINOUS ADENOCARCINOMA                 1                 61
  RECTAL ADENOCARCINOMA                        22                124
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  12P LOSS MUTATED    55   0   4   2
  12P LOSS WILD-TYPE 391   6  33  27
D64V11, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               55                391
  R1                0                  6
  R2                4                 33
  RX                2                 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"
D64V12, continuous
D64V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0  45
  12P LOSS WILD-TYPE   5 307
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0   45
  12P LOSS WILD-TYPE    5  307
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               45                307
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    50  20
  12Q LOSS WILD-TYPE 416 108
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                70                524 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                108 
$`12Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 
       24.33        45.60        13.02        24.03         2.01        50.99 
TCGA-CK-5912 TCGA-AG-A014 TCGA-G5-6233 TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 
       49.08        15.95        18.28        43.76        34.65        36.53 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 
       30.44        23.61        20.28        61.84         9.63        26.01 
TCGA-AA-3548 TCGA-AA-3673 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-A01F TCGA-AA-A01T 
       33.99        50.04        31.07        17.03        32.02        33.04 
TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 
        2.96         5.79        22.42        16.44        14.50         0.20 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6163 
       12.46        12.20         8.02        29.06         5.03        14.04 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6929 
       29.03        15.02        11.01        11.08        25.48        13.41 
TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6460 TCGA-F4-6807 TCGA-G4-6303 
       11.38        12.59         7.50        31.96        43.04        65.85 
TCGA-G4-6315 TCGA-G4-6317 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2691 TCGA-AF-4110 
       61.91        36.00        38.70        60.13        43.04        29.98 
TCGA-AF-6136 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A00Y 
       24.36        34.03        29.98        48.03         3.98        23.01 
TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 
       38.56        13.97        10.98        24.13        51.48        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       16.31        16.41        28.57        36.49 

$`12Q LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        0.92        19.00        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 
       14.93        31.07        29.98        12.99        24.00        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       25.97        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       39.45        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.45        32.91        31.63        29.19        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.69        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        56.25         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 
        0.00        36.03        32.05         0.99        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 
       12.16        83.24        24.53        27.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        25.02        26.04        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       67.30        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        37.74        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.96        61.97        41.00        38.04         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       51.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24       129.27        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        4.18        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
               0.2                0.0 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             65.85             148.01 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             24.23              21.83 
[1] "0.2 - 65.8 (24.2)"  "0.0 - 148.0 (21.8)"
[1] "hr=" "1.5"
D65V2, continuous
D65V3, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    50  20
  12Q LOSS WILD-TYPE 398 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     50   20
  12Q LOSS WILD-TYPE  398  142
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON                50                398
  RECTUM               20                142
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  12Q LOSS MUTATED        11        0        1        14         2         0
  12Q LOSS WILD-TYPE      93        1       36       158        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  12Q LOSS MUTATED           1          4          7         12        9
  12Q LOSS WILD-TYPE        23         11         77         43       54
                    vv
clus                 STAGE IVA STAGE IVB
  12Q LOSS MUTATED           5         0
  12Q LOSS WILD-TYPE        19         2
D65V4, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  11                 93
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                14                158
  STAGE IIB                 2                 10
  STAGE IIC                 0                  2
  STAGE III                 1                 23
  STAGE IIIA                4                 11
  STAGE IIIB                7                 77
  STAGE IIIC               12                 43
  STAGE IV                  9                 54
  STAGE IVA                 5                 19
  STAGE IVB                 0                  2
[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     3  11  52   5
  12Q LOSS WILD-TYPE  17  94 365  64
D65V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                3                 17
  T2               11                 94
  T3               52                365
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  12Q LOSS MUTATED    30  22  19
  12Q LOSS WILD-TYPE 316 128  96
D65V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0               30                316
  N1               22                128
  N2               19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    46  14
  12Q LOSS WILD-TYPE 407  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     46   14
  12Q LOSS WILD-TYPE  407   74
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0               46                407
  1               14                 74
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    34  37
  12Q LOSS WILD-TYPE 255 288
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     34   37
  12Q LOSS WILD-TYPE  255  288
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               34                255
  MALE                 37                288
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    60   2
  12Q LOSS WILD-TYPE 422  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     60    2
  12Q LOSS WILD-TYPE  422   27
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                60                422
  YES                2                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                     48                             2
  12Q LOSS WILD-TYPE                  334                            60
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  12Q LOSS MUTATED                      20                              0
  12Q LOSS WILD-TYPE                   126                             13
D65V10, multiclass
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         48                334
  COLON MUCINOUS ADENOCARCINOMA                 2                 60
  RECTAL ADENOCARCINOMA                        20                126
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  12Q LOSS MUTATED    53   0   4   3
  12Q LOSS WILD-TYPE 393   6  33  26
D65V11, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               53                393
  R1                0                  6
  R2                4                 33
  RX                3                 26
[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, continuous
D65V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0  47
  12Q LOSS WILD-TYPE   5 305
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0   47
  12Q LOSS WILD-TYPE    5  305
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               47                305
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    12   5
  13Q LOSS WILD-TYPE 454 123
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                577 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                123 
$`13Q LOSS MUTATED`
TCGA-AA-3556 TCGA-AZ-4681 TCGA-G4-6314 TCGA-AA-3875 TCGA-AA-A01D TCGA-AU-3779 
       23.01       106.75        35.93        18.05        10.98        14.50 
TCGA-AY-6196 TCGA-AZ-6607 TCGA-CA-5797 TCGA-F4-6704 TCGA-QG-A5Z1 TCGA-AG-3591 
        0.20         3.19        12.59         1.55         8.42        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-4021 TCGA-AG-A020 TCGA-DY-A0XA 
        2.01         6.05         3.98         1.02       126.44 

$`13Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 
       19.07        34.03         0.99        13.02        17.95        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       12.99        24.00         2.01        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       25.08        10.88        75.95       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       13.94        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.02        34.65        32.75        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
        8.38        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       20.98        34.03         2.01        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       29.46        32.98        31.30        21.90        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 
       24.00         1.02        46.03        34.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05        12.62        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               0.2                0.0 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            126.44             148.01 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             10.98              22.09 
[1] "0.2 - 126.4 (11.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.7"
D66V2, continuous
D66V3, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    12   6
  13Q LOSS WILD-TYPE 436 156
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12    6
  13Q LOSS WILD-TYPE  436  156
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON                12                436
  RECTUM                6                156
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  13Q LOSS MUTATED         3        0        0         6         0         0
  13Q LOSS WILD-TYPE     101        1       37       166        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  13Q LOSS MUTATED           1          0          1          4        3
  13Q LOSS WILD-TYPE        23         15         83         51       60
                    vv
clus                 STAGE IVA STAGE IVB
  13Q LOSS MUTATED           0         0
  13Q LOSS WILD-TYPE        24         2
D66V4, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  0                 37
  STAGE IIA                 6                166
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 1                 23
  STAGE IIIA                0                 15
  STAGE IIIB                1                 83
  STAGE IIIC                4                 51
  STAGE IV                  3                 60
  STAGE IVA                 0                 24
  STAGE IVB                 0                  2
[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     1   2  14   1
  13Q LOSS WILD-TYPE  19 103 403  68
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                1                 19
  T2                2                103
  T3               14                403
  T4                1                 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"
                    vv
clus                  N0  N1  N2
  13Q LOSS MUTATED     9   2   7
  13Q LOSS WILD-TYPE 337 148 108
D66V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                9                337
  N1                2                148
  N2                7                108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11   3
  13Q LOSS WILD-TYPE 442  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11    3
  13Q LOSS WILD-TYPE  442   85
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               11                442
  1                3                 85
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     9   9
  13Q LOSS WILD-TYPE 280 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    9
  13Q LOSS WILD-TYPE  280  316
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                280
  MALE                  9                316
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    11   2
  13Q LOSS WILD-TYPE 471  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     11    2
  13Q LOSS WILD-TYPE  471   27
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                11                471
  YES                2                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                      8                             3
  13Q LOSS WILD-TYPE                  374                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  13Q LOSS MUTATED                       4                              2
  13Q LOSS WILD-TYPE                   142                             11
D66V10, multiclass
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          8                374
  COLON MUCINOUS ADENOCARCINOMA                 3                 59
  RECTAL ADENOCARCINOMA                         4                142
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[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                  R0  R1  R2  RX
  13Q LOSS MUTATED    14   0   1   1
  13Q LOSS WILD-TYPE 432   6  36  28
D66V11, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               14                432
  R1                0                  6
  R2                1                 36
  RX                1                 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"
D66V12, continuous
D66V13, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0  10
  13Q LOSS WILD-TYPE   5 342
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0   10
  13Q LOSS WILD-TYPE    5  342
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               10                342
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   158  39
  14Q LOSS WILD-TYPE 308  89
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               197                397 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                39                 89 
$`14Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       14.53        24.03        19.07        34.03        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 
       19.99        19.00        85.05        31.07        24.03        12.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AZ-6608 
       50.99        26.01        24.00        38.04        21.99         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3890 TCGA-AG-4008 
       49.08        28.21        91.79        17.85        17.03        17.03 
TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T 
       25.97        21.24        18.28        55.76        26.43         4.80 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       39.45        43.76        42.28        35.11        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6138 
       36.53        32.45        32.91        30.44        23.61        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        20.61        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       20.28        61.84         5.03         6.97        38.99         9.07 
TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       13.94         2.01        14.01        50.04        47.01        37.05 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3866 
       10.06        25.02        36.95        37.02        17.03        17.03 
TCGA-AA-3875 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3989 
       18.05        34.03        21.99        16.08        34.06         7.96 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K 
       27.02        42.02        14.99        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 
       33.04        26.01         2.96         2.01        40.96         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
       22.42        27.42        16.44        14.50         0.95        33.01 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 
       17.85        18.84       109.28         1.41         5.65        22.36 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
       29.56         5.23        12.36        12.46        12.59        12.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
        2.01        25.02         8.02        17.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       13.02        15.02        11.08        10.06        45.40        54.61 
TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 
       56.09        18.25        25.48        15.12        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A288 TCGA-DM-A28E 
       11.38        38.20        13.32       140.38        14.04       119.93 
TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 
       31.96        41.42        33.67        13.25         0.53         8.35 
TCGA-G4-6297 TCGA-G4-6315 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 
       82.39        61.91        18.18        19.33        15.65        16.80 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       38.70        60.13        11.90        39.48        17.23        13.55 
TCGA-AF-3911 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3587 
       37.74        24.59        65.98        11.84        36.03        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 
       34.03        34.03        34.03        50.04         6.05         0.99 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 
        0.99        19.04         1.02        17.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 
       48.03        36.03        14.04         6.02        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
       38.96        38.04        38.56         6.05        33.17        47.44 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       48.20         7.17        25.05        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
       10.98        25.05        25.05       129.27        51.48        20.55 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 
       17.00        16.34        16.31        16.41        10.78        11.97 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 
       42.35         0.39        32.19        36.49        11.87 

$`14Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        37.05        36.03         8.05         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         6.05         0.92        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 
       14.93        29.98        24.00         2.01        19.07        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
      100.01         5.88        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       35.80        26.17        79.69        10.39         8.02        13.94 
TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-3L-AA1B 
       19.99        15.95        36.03        31.00        51.98        15.62 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       12.66         1.61         9.53        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       42.90        44.91        37.05        37.25        37.02        32.75 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       29.16        27.09         8.38        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       19.66        16.24        24.92        56.25         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        3.02         1.02        37.05        35.01        63.98         1.02 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        1.02        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 
       20.98        61.02        78.08         6.97        54.02        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01         5.98         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
        0.99         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
        0.99        31.07        53.00        27.02        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3973 
       24.00        33.01        26.01        20.98         2.01        13.05 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       17.03        34.98        15.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98        39.98         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 
       39.98        18.05        12.16        83.24        24.53        26.47 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
        0.46         0.92        27.09        16.31         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 
       17.82        17.26        19.33        58.39        32.94         5.13 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
       11.74         3.19        12.69        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       23.05        20.02        37.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        11.01        12.03        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        17.75        43.27        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        12.59         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
        7.76       139.17        26.47        81.37        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       35.74         6.18        47.87         1.55        34.42        43.04 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       47.41        35.31       133.18        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50U 
       26.43        26.04        13.78        46.75        74.79        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33         9.93        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 
        8.42        31.30        21.90        70.03        46.92        43.04 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        29.98        16.83        24.36        20.02 
TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       86.63        36.03        12.00        32.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       24.00         1.02         2.01        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99        20.98         7.99        29.98        37.02        32.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 
        0.99        19.99        36.95        13.02        14.01        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        28.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       20.98        13.94        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       49.97        61.97        41.00         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 
       26.43        19.46        13.78        44.78        78.12        21.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       26.04        12.00        31.00        44.02        25.97        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        4.18        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       49.51        28.57        19.66        37.18        38.14        12.46 
TCGA-G5-6572 
       47.08 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.39               0.00 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            140.38             148.01 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             22.42              21.99 
[1] "0.4 - 140.4 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   137  66
  14Q LOSS WILD-TYPE 311  96
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    137   66
  14Q LOSS WILD-TYPE  311   96
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON               137                311
  RECTUM               66                 96
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  14Q LOSS MUTATED        30        0        9        59         2         0
  14Q LOSS WILD-TYPE      74        1       28       113        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  14Q LOSS MUTATED           9          8         27         15       26
  14Q LOSS WILD-TYPE        15          7         57         40       37
                    vv
clus                 STAGE IVA STAGE IVB
  14Q LOSS MUTATED          12         0
  14Q LOSS WILD-TYPE        12         2
D67V4, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  30                 74
  STAGE IA                  0                  1
  STAGE II                  9                 28
  STAGE IIA                59                113
  STAGE IIB                 2                 10
  STAGE IIC                 0                  2
  STAGE III                 9                 15
  STAGE IIIA                8                  7
  STAGE IIIB               27                 57
  STAGE IIIC               15                 40
  STAGE IV                 26                 37
  STAGE IVA                12                 12
  STAGE IVB                 0                  2
[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     9  31 144  20
  14Q LOSS WILD-TYPE  11  74 273  49
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                9                 11
  T2               31                 74
  T3              144                273
  T4               20                 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"
                    vv
clus                  N0  N1  N2
  14Q LOSS MUTATED   105  63  36
  14Q LOSS WILD-TYPE 241  87  79
D67V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              105                241
  N1               63                 87
  N2               36                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   145  38
  14Q LOSS WILD-TYPE 308  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    145   38
  14Q LOSS WILD-TYPE  308   50
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              145                308
  1               38                 50
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    92 113
  14Q LOSS WILD-TYPE 197 212
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     92  113
  14Q LOSS WILD-TYPE  197  212
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               92                197
  MALE                113                212
[1] 2 2
[1] FALSE
D67V9, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   165  13
  14Q LOSS WILD-TYPE 317  16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    165   13
  14Q LOSS WILD-TYPE  317   16
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO               165                317
  YES               13                 16
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                    131                             3
  14Q LOSS WILD-TYPE                  251                            59
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  14Q LOSS MUTATED                      64                              1
  14Q LOSS WILD-TYPE                    82                             12
D67V10, multiclass
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        131                251
  COLON MUCINOUS ADENOCARCINOMA                 3                 59
  RECTAL ADENOCARCINOMA                        64                 82
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[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                  R0  R1  R2  RX
  14Q LOSS MUTATED   144   2  12  10
  14Q LOSS WILD-TYPE 302   4  25  19
D67V11, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0              144                302
  R1                2                  4
  R2               12                 25
  RX               10                 19
[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, continuous
D67V13, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED     2 115
  14Q LOSS WILD-TYPE   3 237
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2  115
  14Q LOSS WILD-TYPE    3  237
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              115                237
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED   180  43
  15Q LOSS WILD-TYPE 286  85
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               223                371 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                43                 85 
$`15Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       63.62        91.79        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       25.97        21.24        18.28        26.43         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2683 
       39.45        43.76        43.76        43.43        44.91        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 
       29.16        22.52        25.08        20.61        21.76        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 
       61.84         5.03         7.04         1.02         6.97         9.07 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 
       29.00        12.99        33.99        21.01         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       37.05        38.99        36.95        37.02        17.03        10.06 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 
       36.03         0.99        31.07        17.03         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       13.05        34.06        27.02        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T 
       17.03        14.99        15.02        15.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       26.01         2.96        41.00         5.79        22.42        27.42 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        16.31         0.95        33.01        17.85        18.84 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        62.79        88.21        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 
       12.46        12.20        14.30       148.01         2.01        25.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       27.02        13.02        29.06         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 
       14.04        29.03        16.04        15.02        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       11.01        10.06        12.03        20.19        25.48        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.13        12.49         7.53        10.13         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.38       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
      131.51        95.18        31.96        47.87         1.55        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 
       33.67        13.25         0.53        47.41         8.35        65.85 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       55.04        61.91        36.00        46.75        10.98        19.33 
TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 
       12.79        29.46        21.90        38.70        11.90        46.92 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L 
       43.04        13.55        37.74        29.98        24.59        65.98 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       32.02        36.03        20.05        24.00        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 
       34.03         6.05        20.98        29.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 
       19.99        35.01         1.02        25.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 
       14.04        13.94        23.01        37.02         1.02         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 
       38.96        41.00        38.04        38.56        43.20         6.05 
TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 
       13.78        47.44         7.17        21.01        31.00        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 
       51.98        25.05        41.36        57.24        24.13         3.48 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        4.18        15.85        16.31        16.41        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       13.64        11.97        42.35        28.57        32.19        36.49 
TCGA-F5-6813 
       19.66 

$`15Q LOSS WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       100.01         1.94        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       22.09        35.80        26.17        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
        8.02        15.95        36.03        31.00        51.98        55.76 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
       15.62        12.66         9.53        46.65        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 
       35.11        37.05        37.25        37.02        32.75        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.13         8.38        25.18        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.12        19.66        16.24        24.92        56.25         9.63 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 
        3.02        37.05        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 
        1.02        19.07         0.00        29.00        26.01        14.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 
        0.99        25.02         1.02        17.98        15.95         0.00 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 
        0.00        33.07         0.00        32.05        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       20.98        34.03        16.08        25.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       27.02         0.99        34.98        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       24.53        26.47        16.44         0.46         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
        0.20        21.44        17.82        17.26        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       49.41         6.77        12.10        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.39        12.59        12.59        12.76        10.06        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
       82.95       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        12.00        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-D5-5537 
       13.02        14.04        11.01        12.95        13.05        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       54.61        19.59        56.09        55.92        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27        17.85         4.80        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        12.43        14.30         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 
       12.00        10.26       119.70        24.43        38.20        49.91 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 
       34.42        41.42        35.31       133.18        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 
       67.30        53.62        44.68        85.48        39.42        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA 
       26.04        13.78        74.79        18.18        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        16.80        42.77        32.98         8.42        31.30 
TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 
       60.13        70.03        39.48        17.23        37.97        34.49 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        24.36        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       12.00         7.07         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       37.02        32.98         0.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       13.02        14.01        48.03        32.02        36.03         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A016 TCGA-AG-A020 
        3.98        46.03        20.98         6.02         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97         2.50        27.55        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 
       33.17        44.78        48.20        78.12        25.05        26.04 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       12.00        31.00        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       12.62       126.44       129.27        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
        8.61        17.46         8.45         9.96        49.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.53               0.00 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            148.01             139.17 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             22.42              21.99 
[1] "0.5 - 148.0 (22.4)" "0.0 - 139.2 (22.0)"
[1] "hr=" "1.2"
D68V2, continuous
D68V3, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   156  70
  15Q LOSS WILD-TYPE 292  92
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    156   70
  15Q LOSS WILD-TYPE  292   92
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON               156                292
  RECTUM               70                 92
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  15Q LOSS MUTATED        34        0        8        59         3         1
  15Q LOSS WILD-TYPE      70        1       29       113         9         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  15Q LOSS MUTATED           6          8         31         26       32
  15Q LOSS WILD-TYPE        18          7         53         29       31
                    vv
clus                 STAGE IVA STAGE IVB
  15Q LOSS MUTATED          12         1
  15Q LOSS WILD-TYPE        12         1
D68V4, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  34                 70
  STAGE IA                  0                  1
  STAGE II                  8                 29
  STAGE IIA                59                113
  STAGE IIB                 3                  9
  STAGE IIC                 1                  1
  STAGE III                 6                 18
  STAGE IIIA                8                  7
  STAGE IIIB               31                 53
  STAGE IIIC               26                 29
  STAGE IV                 32                 31
  STAGE IVA                12                 12
  STAGE IVB                 1                  1
[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     9  33 164  23
  15Q LOSS WILD-TYPE  11  72 253  46
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                9                 11
  T2               33                 72
  T3              164                253
  T4               23                 46
[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
  15Q LOSS MUTATED   113  66  50
  15Q LOSS WILD-TYPE 233  84  65
D68V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0              113                233
  N1               66                 84
  N2               50                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   158  44
  15Q LOSS WILD-TYPE 295  44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    158   44
  15Q LOSS WILD-TYPE  295   44
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0              158                295
  1               44                 44
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   101 128
  15Q LOSS WILD-TYPE 188 197
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    101  128
  15Q LOSS WILD-TYPE  188  197
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE              101                188
  MALE                128                197
[1] 2 2
[1] FALSE
D68V9, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED   182  14
  15Q LOSS WILD-TYPE 300  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED    182   14
  15Q LOSS WILD-TYPE  300   15
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO               182                300
  YES               14                 15
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                    142                            12
  15Q LOSS WILD-TYPE                  240                            50
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  15Q LOSS MUTATED                      64                              5
  15Q LOSS WILD-TYPE                    82                              8
D68V10, multiclass
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        142                240
  COLON MUCINOUS ADENOCARCINOMA                12                 50
  RECTAL ADENOCARCINOMA                        64                 82
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[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                  R0  R1  R2  RX
  15Q LOSS MUTATED   163   2  15   9
  15Q LOSS WILD-TYPE 283   4  22  20
D68V11, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0              163                283
  R1                2                  4
  R2               15                 22
  RX                9                 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"
D68V12, continuous
D68V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     2 130
  15Q LOSS WILD-TYPE   3 222
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2  130
  15Q LOSS WILD-TYPE    3  222
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  3
  NOT HISPANIC OR LATINO              130                222
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED    30   9
  16P LOSS WILD-TYPE 436 119
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                39                555 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                119 
$`16P LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3860 TCGA-G5-6233 TCGA-A6-3807 TCGA-A6-6651 TCGA-A6-A567 
       14.53        31.07        18.28        34.65        21.76        61.84 
TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3966 TCGA-AA-A02W TCGA-AD-A5EK TCGA-AM-5820 
       37.05        38.99         2.01        41.00        16.44         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 
       14.50        16.31         0.20        17.85         5.65         3.19 
TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 
       22.03        15.02        13.02        11.01        11.01        20.19 
TCGA-D5-6531 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-NH-A50T TCGA-NH-A50U TCGA-RU-A8FL 
       17.75        49.91         7.50        18.18        10.98        38.70 
TCGA-T9-A92H TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-4005 
       11.90        32.02        34.03        19.99        19.04        14.04 
TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 
       25.05        32.19        37.18 

$`16P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        5.79        22.42        27.42        26.47         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23        11.74        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02         5.03        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        15.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        20.42        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV 
       26.04        13.78        46.75        74.79        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        60.13        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       42.35        28.57         0.39        36.49        19.66        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               0.2                0.0 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             61.84             148.01 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             18.18              22.42 
[1] "0.2 - 61.8 (18.2)"  "0.0 - 148.0 (22.4)"
[1] "hr=" "1.4"
D69V2, continuous
D69V3, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    31   9
  16P LOSS WILD-TYPE 417 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     31    9
  16P LOSS WILD-TYPE  417  153
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON                31                417
  RECTUM                9                153
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16P LOSS MUTATED         3        0        1        17         0         0
  16P LOSS WILD-TYPE     101        1       36       155        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16P LOSS MUTATED           0          0          6          5        3
  16P LOSS WILD-TYPE        24         15         78         50       60
                    vv
clus                 STAGE IVA STAGE IVB
  16P LOSS MUTATED           4         0
  16P LOSS WILD-TYPE        20         2
D69V4, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   3                101
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                17                155
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 0                 24
  STAGE IIIA                0                 15
  STAGE IIIB                6                 78
  STAGE IIIC                5                 50
  STAGE IV                  3                 60
  STAGE IVA                 4                 20
  STAGE IVB                 0                  2
[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     0   3  32   5
  16P LOSS WILD-TYPE  20 102 385  64
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                 20
  T2                3                102
  T3               32                385
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  16P LOSS MUTATED    22   8  10
  16P LOSS WILD-TYPE 324 142 105
D69V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               22                324
  N1                8                142
  N2               10                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    27   7
  16P LOSS WILD-TYPE 426  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     27    7
  16P LOSS WILD-TYPE  426   81
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               27                426
  1                7                 81
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    21  19
  16P LOSS WILD-TYPE 268 306
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     21   19
  16P LOSS WILD-TYPE  268  306
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               21                268
  MALE                 19                306
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    33   1
  16P LOSS WILD-TYPE 449  28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     33    1
  16P LOSS WILD-TYPE  449   28
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                33                449
  YES                1                 28
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16P LOSS MUTATED                     25                             6
  16P LOSS WILD-TYPE                  357                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16P LOSS MUTATED                       7                              1
  16P LOSS WILD-TYPE                   139                             12
D69V10, multiclass
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         25                357
  COLON MUCINOUS ADENOCARCINOMA                 6                 56
  RECTAL ADENOCARCINOMA                         7                139
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[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                  R0  R1  R2  RX
  16P LOSS MUTATED    29   1   0   1
  16P LOSS WILD-TYPE 417   5  37  28
D69V11, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0               29                417
  R1                1                  5
  R2                0                 37
  RX                1                 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"
D69V12, continuous
D69V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     1  28
  16P LOSS WILD-TYPE   4 324
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1   28
  16P LOSS WILD-TYPE    4  324
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               28                324
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    35   7
  16Q LOSS WILD-TYPE 431 121
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                42                552 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                121 
$`16Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3860 TCGA-G5-6233 TCGA-A6-3807 TCGA-A6-5660 TCGA-A6-6651 
       14.53        31.07        18.28        34.65        29.19        21.76 
TCGA-AA-3494 TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3966 TCGA-AA-A02W TCGA-AD-A5EK 
        1.02        37.05        38.99         2.01        41.00        16.44 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-5344 
       16.31         0.20        17.85         5.65         3.19        22.03 
TCGA-CM-5863 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       15.02        13.02        11.01        11.01        20.19        17.75 
TCGA-DM-A1DA TCGA-NH-A50T TCGA-NH-A50U TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-6672 
        7.50        18.18        10.98        38.70        11.90        24.59 
TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3732 
       32.02        34.03         6.05        19.99         7.99        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-4005 TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 
       19.04         1.02        14.04        25.05        32.19        37.18 

$`16Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
        9.63         5.03         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       33.04         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       19.33        18.84       109.28        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
        6.77        12.10        29.56         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02        25.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       30.08        32.02        15.02         5.03        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       60.13        70.03        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       24.36        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        20.98         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       19.99        28.04        36.03         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        38.14        11.87        12.46        47.08 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
               0.2                0.0 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             41.00             148.01 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            18.015             22.470 
[1] "0.2 - 41.0 (18.0)"  "0.0 - 148.0 (22.5)"
[1] "hr=" "1.2"
D70V2, continuous
D70V3, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    29  14
  16Q LOSS WILD-TYPE 419 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     29   14
  16Q LOSS WILD-TYPE  419  148
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON                29                419
  RECTUM               14                148
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  16Q LOSS MUTATED         6        0        1        15         0         0
  16Q LOSS WILD-TYPE      98        1       36       157        12         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  16Q LOSS MUTATED           0          0          6          7        4
  16Q LOSS WILD-TYPE        24         15         78         48       59
                    vv
clus                 STAGE IVA STAGE IVB
  16Q LOSS MUTATED           3         0
  16Q LOSS WILD-TYPE        21         2
D70V4, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   6                 98
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                15                157
  STAGE IIB                 0                 12
  STAGE IIC                 0                  2
  STAGE III                 0                 24
  STAGE IIIA                0                 15
  STAGE IIIB                6                 78
  STAGE IIIC                7                 48
  STAGE IV                  4                 59
  STAGE IVA                 3                 21
  STAGE IVB                 0                  2
[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     0   6  32   5
  16Q LOSS WILD-TYPE  20  99 385  64
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                 20
  T2                6                 99
  T3               32                385
  T4                5                 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"
                    vv
clus                  N0  N1  N2
  16Q LOSS MUTATED    24   7  12
  16Q LOSS WILD-TYPE 322 143 103
D70V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               24                322
  N1                7                143
  N2               12                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    30   6
  16Q LOSS WILD-TYPE 423  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     30    6
  16Q LOSS WILD-TYPE  423   82
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               30                423
  1                6                 82
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    21  22
  16Q LOSS WILD-TYPE 268 303
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     21   22
  16Q LOSS WILD-TYPE  268  303
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               21                268
  MALE                 22                303
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    34   3
  16Q LOSS WILD-TYPE 448  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     34    3
  16Q LOSS WILD-TYPE  448   26
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                34                448
  YES                3                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  16Q LOSS MUTATED                     24                             5
  16Q LOSS WILD-TYPE                  358                            57
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  16Q LOSS MUTATED                      12                              1
  16Q LOSS WILD-TYPE                   134                             12
D70V10, multiclass
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         24                358
  COLON MUCINOUS ADENOCARCINOMA                 5                 57
  RECTAL ADENOCARCINOMA                        12                134
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[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                  R0  R1  R2  RX
  16Q LOSS MUTATED    31   1   1   1
  16Q LOSS WILD-TYPE 415   5  36  28
D70V11, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               31                415
  R1                1                  5
  R2                1                 36
  RX                1                 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"
D70V12, continuous
D70V13, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  27
  16Q LOSS WILD-TYPE   4 325
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   27
  16Q LOSS WILD-TYPE    4  325
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               27                325
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED   248  77
  17P LOSS WILD-TYPE 218  51
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               325                269 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                77                 51 
$`17P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3522 
       24.33        14.53        24.16         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       36.03        13.02        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3952 
       19.00        36.00        85.05        24.03        29.98         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 
       50.99        26.01        24.00        38.04        21.99        21.37 
TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 
       15.52       106.75         1.94        49.08         5.88        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3611 TCGA-AG-4008 
       63.62        35.93        91.79        17.85        13.94        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       25.97        15.95        31.00        51.98        21.24        55.76 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        1.61        39.45        43.76        43.76        43.43        42.28 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
       35.11        16.57        37.05        37.25        34.65        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       32.91        31.63        30.44        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-6782 
       22.52        24.13        25.18        20.61        23.87        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 
       61.84         5.03         7.04         1.02        37.05         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       38.99         9.07        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 
       21.01        24.00        13.94        61.02        78.08         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 
       14.01        50.04        47.01         5.98        37.05        10.06 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       25.02        38.99        36.95        37.02        10.06        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       32.05         0.99        31.07        17.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3982 
        2.01        24.00        20.98        34.03        16.08        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        19.00        34.03        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S 
       14.99        15.02        10.98        32.02        12.00         1.02 
TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       33.04        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       41.00        40.96        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       26.47        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
       33.01         0.20        17.85       109.28         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        65.00        88.21        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 
        5.23         3.19        12.69        12.46        12.59        12.20 
TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       14.30        21.99         2.01        25.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6164 
       13.02        29.06         5.03        15.02        17.03        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
       21.99        14.99        13.02        15.02        11.01        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        10.06        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6538 
       55.92        17.75        18.25        25.48        43.27        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
        9.04        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59       140.38        44.32       131.51       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 
       14.04        26.47       119.93        35.97       117.07        31.96 
TCGA-F4-6461 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 
       11.11        34.42        43.04        33.67        13.25         8.35 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       65.85        44.68        55.04        39.42        61.91        26.43 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        10.98        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       16.80        42.77        32.98         8.42        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       60.13        11.90        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        24.36        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 
       86.63        65.98        11.84        12.00        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
       24.00        34.03        34.03         2.01        50.04         0.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       19.04         1.02        17.95        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 
       32.02        19.99        28.04        36.03        14.04         3.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 
       13.94         6.02        23.01        37.02         1.02         1.94 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6620 
       41.00        38.56        43.20        27.55         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6158 
       13.78        44.78         7.17        25.05        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
      129.27        24.13        51.48         3.48         4.18        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 
       42.35        28.57         0.39        19.66        37.18        11.87 
TCGA-F5-6864 
       12.46 

$`17P LOSS WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3530 
       45.60        13.94        58.03        13.02         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
       34.03         0.99        17.95         0.92        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A024 
       14.93        31.07        12.99        24.00        19.07        39.06 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6321 
       25.08        10.88        75.95       100.01        28.21        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 
       35.80        26.17        79.69        10.39         8.02        19.99 
TCGA-AG-3890 TCGA-AG-A015 TCGA-G5-6233 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       17.03        36.03        18.28        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2686 
       12.66         9.53        46.65        42.90        44.91        37.02 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.75        36.53        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       22.06         8.38        25.08        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.12        19.66        16.24        24.92        56.25         9.63 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
        3.02        35.01        63.98         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 
        0.00        29.00        26.01        29.95        20.98         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 
       54.02        47.05        15.02        11.01         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 
       35.05         0.99         1.02        17.98        15.95         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 
       17.03         0.00         0.00        36.03        53.00        31.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       33.01        26.01         2.01        21.99        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       25.02        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I 
       18.05         4.01         0.99        34.98        15.02        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       51.98         0.92        22.03        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       83.24         0.92        27.09        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-6598 
       19.33        18.84        58.39        32.94        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        6.77        11.74        12.36        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       37.02        26.04        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        14.04        16.04 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       12.99        14.04        12.95        11.08        11.01        12.03 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       20.19        20.42        15.12        17.85         4.80        16.14 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
       12.39         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       10.26       119.70        49.91         7.50       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 
       81.37        60.79        98.24        95.18         8.61        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6854 
       35.74         6.18        47.87         1.55        41.42         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       47.41        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       53.62        85.48        36.00        26.04        13.78        74.79 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       18.18        19.33        29.46        31.30        70.03        46.92 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 
       16.83        24.59        36.03         7.07        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
       46.03        34.03        12.03         6.05        15.95        19.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       29.98         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-3901 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A016 TCGA-AG-A020 
       25.02         1.02        46.03        20.98         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 
       49.97        38.96        61.97        38.04         2.50        26.43 
TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 
       19.46        47.44        48.20        78.12        21.01        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       31.00        12.00        31.00        51.98        25.97        25.05 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6885 
       32.61        20.55        19.96        15.85         8.61        13.64 
TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6572 
       17.46        32.19        36.49        38.14        47.08 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               0.2                0.0 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            140.38             148.01 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             22.52              21.44 
[1] "0.2 - 140.4 (22.5)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.3"
D71V2, continuous
D71V3, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   233 101
  17P LOSS WILD-TYPE 215  61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    233  101
  17P LOSS WILD-TYPE  215   61
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON               233                215
  RECTUM              101                 61
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17P LOSS MUTATED        45        0       19        84         4         2
  17P LOSS WILD-TYPE      59        1       18        88         8         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17P LOSS MUTATED          12         12         47         37       44
  17P LOSS WILD-TYPE        12          3         37         18       19
                    vv
clus                 STAGE IVA STAGE IVB
  17P LOSS MUTATED          16         2
  17P LOSS WILD-TYPE         8         0
D71V4, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  45                 59
  STAGE IA                  0                  1
  STAGE II                 19                 18
  STAGE IIA                84                 88
  STAGE IIB                 4                  8
  STAGE IIC                 2                  0
  STAGE III                12                 12
  STAGE IIIA               12                  3
  STAGE IIIB               47                 37
  STAGE IIIC               37                 18
  STAGE IV                 44                 19
  STAGE IVA                16                  8
  STAGE IVB                 2                  0
[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     9  51 237  40
  17P LOSS WILD-TYPE  11  54 180  29
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                9                 11
  T2               51                 54
  T3              237                180
  T4               40                 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
  17P LOSS MUTATED   168  94  74
  17P LOSS WILD-TYPE 178  56  41
D71V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0              168                178
  N1               94                 56
  N2               74                 41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   238  62
  17P LOSS WILD-TYPE 215  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    238   62
  17P LOSS WILD-TYPE  215   26
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0              238                215
  1               62                 26
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   151 187
  17P LOSS WILD-TYPE 138 138
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    151  187
  17P LOSS WILD-TYPE  138  138
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE              151                138
  MALE                187                138
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED   262  16
  17P LOSS WILD-TYPE 220  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED    262   16
  17P LOSS WILD-TYPE  220   13
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO               262                220
  YES               16                 13
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                    216                            14
  17P LOSS WILD-TYPE                  166                            48
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17P LOSS MUTATED                      94                              6
  17P LOSS WILD-TYPE                    52                              7
D71V10, multiclass
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        216                166
  COLON MUCINOUS ADENOCARCINOMA                14                 48
  RECTAL ADENOCARCINOMA                        94                 52
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[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                  R0  R1  R2  RX
  17P LOSS MUTATED   237   4  25  11
  17P LOSS WILD-TYPE 209   2  12  18
D71V11, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0              237                209
  R1                4                  2
  R2               25                 12
  RX               11                 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"
D71V12, continuous
D71V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     3 192
  17P LOSS WILD-TYPE   2 160
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      3  192
  17P LOSS WILD-TYPE    2  160
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO              192                160
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    66  24
  17Q LOSS WILD-TYPE 400 104
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                90                504 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                104 
$`17Q LOSS MUTATED`
TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3976 TCGA-CK-5912 
       24.16        24.03        19.99         6.05        26.01        49.08 
TCGA-G4-6314 TCGA-AG-3611 TCGA-AG-A00H TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       35.93        13.94        25.97        51.98        21.24        55.76 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-AA-3495 TCGA-AA-3542 
       43.76        43.76        37.05        32.45        37.05        12.99 
TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3842 
       21.01         2.01        50.04        37.05        10.06        37.02 
TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D 
       27.02        24.00         7.96        34.03        42.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
       32.02        12.00        33.04        37.02         2.96        39.98 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D 
        5.79        22.42        26.47        14.50         0.20        17.85 
TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5862 
       12.10        12.59        12.20        27.02        13.02         5.03 
TCGA-CM-5864 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6924 TCGA-D5-6932 
       15.02        45.40        43.27        12.49        14.30        11.38 
TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6809 
       38.20        12.59       140.38        31.96         1.55        13.25 
TCGA-G4-6295 TCGA-G4-6303 TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV 
        8.35        65.85        10.98        15.65        12.79        42.77 
TCGA-QG-A5YX TCGA-QL-A97D TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L 
       32.98        21.90        29.98        24.36        86.63        65.98 
TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3725 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 
       36.03        34.03        20.98         1.02        32.02        28.04 
TCGA-AG-A008 TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-EF-5830 
       13.94        41.00        13.97        10.98        24.13         3.48 
TCGA-EF-5831 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6814 
        4.18        17.69        16.41        11.51        28.57        37.18 

$`17Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3672 
        0.99        13.02        17.95        23.01        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       31.07        24.03        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       50.99        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
      100.01         1.94         5.88        28.21        23.51        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       36.03        31.00        18.28        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2675 
       12.66         1.61         9.53        39.45        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
       42.90        42.28        44.91        35.11        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        32.75        36.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
        1.02        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       26.01        14.01        33.99        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       16.08        13.05        34.06        25.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        15.02        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02H 
       35.01         1.02         1.02        26.01        51.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK 
       40.96        12.16        83.24        24.53        27.42        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        27.09        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 
       65.00        62.79        88.21        49.41         6.77        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
       37.02        25.02        26.04         8.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        32.02        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       13.35        12.00        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       92.75        49.91        13.32         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        33.67         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       35.31       133.18        82.39        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5Z1 
       19.33        19.33         9.93        16.80        29.46         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 
       37.74        16.83        20.02        24.59        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00        32.02         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       14.01        48.03        25.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02         3.98        46.03        20.98         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       41.36        57.24       129.27        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.31         8.61        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        42.35         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        38.14        11.87        12.46        47.08 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               0.2                0.0 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            140.38             148.01 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            24.015             21.990 
[1] "0.2 - 140.4 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D72V2, continuous
D72V3, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    65  27
  17Q LOSS WILD-TYPE 383 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     65   27
  17Q LOSS WILD-TYPE  383  135
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON                65                383
  RECTUM               27                135
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  17Q LOSS MUTATED        11        0        5        20         1         1
  17Q LOSS WILD-TYPE      93        1       32       152        11         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  17Q LOSS MUTATED           4          4         11         14       12
  17Q LOSS WILD-TYPE        20         11         73         41       51
                    vv
clus                 STAGE IVA STAGE IVB
  17Q LOSS MUTATED           6         1
  17Q LOSS WILD-TYPE        18         1
D72V4, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  11                 93
  STAGE IA                  0                  1
  STAGE II                  5                 32
  STAGE IIA                20                152
  STAGE IIB                 1                 11
  STAGE IIC                 1                  1
  STAGE III                 4                 20
  STAGE IIIA                4                 11
  STAGE IIIB               11                 73
  STAGE IIIC               14                 41
  STAGE IV                 12                 51
  STAGE IVA                 6                 18
  STAGE IVB                 1                  1
[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     0  14  66  13
  17Q LOSS WILD-TYPE  20  91 351  56
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                 20
  T2               14                 91
  T3               66                351
  T4               13                 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"
                    vv
clus                  N0  N1  N2
  17Q LOSS MUTATED    40  29  24
  17Q LOSS WILD-TYPE 306 121  91
D72V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               40                306
  N1               29                121
  N2               24                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    59  18
  17Q LOSS WILD-TYPE 394  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     59   18
  17Q LOSS WILD-TYPE  394   70
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               59                394
  1               18                 70
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    42  51
  17Q LOSS WILD-TYPE 247 274
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     42   51
  17Q LOSS WILD-TYPE  247  274
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               42                247
  MALE                 51                274
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    76   4
  17Q LOSS WILD-TYPE 406  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     76    4
  17Q LOSS WILD-TYPE  406   25
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                76                406
  YES                4                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                     55                             9
  17Q LOSS WILD-TYPE                  327                            53
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  17Q LOSS MUTATED                      26                              1
  17Q LOSS WILD-TYPE                   120                             12
D72V10, multiclass
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         55                327
  COLON MUCINOUS ADENOCARCINOMA                 9                 53
  RECTAL ADENOCARCINOMA                        26                120
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[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                  R0  R1  R2  RX
  17Q LOSS MUTATED    68   2   7   5
  17Q LOSS WILD-TYPE 378   4  30  24
D72V11, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               68                378
  R1                2                  4
  R2                7                 30
  RX                5                 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"
D72V12, continuous
D72V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     0  52
  17Q LOSS WILD-TYPE   5 300
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      0   52
  17Q LOSS WILD-TYPE    5  300
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               52                300
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   293  75
  18P LOSS WILD-TYPE 173  53
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               368                226 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                75                 53 
$`18P LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3522 
       24.33        45.60        13.94        14.53         1.02        37.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       19.07        34.03        13.02        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        6.05        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       24.03        29.98        12.99        50.99        26.01        24.00 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       38.04        21.99        15.52       106.75         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-NH-A8F7 TCGA-AF-3913 
       28.21        23.51        63.62        35.93        17.85        10.39 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       13.94        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       31.00        51.98        21.24        18.28        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       15.62         4.80        12.66         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        23.61        22.09        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       27.09        24.13        25.18        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.39        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 
        5.03         7.04         1.02        37.05         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        9.07        19.07        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 
       33.99        24.00        13.94        61.02        78.08         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3819 
       14.01        50.04        47.01        15.02        37.05        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02        17.03        10.06        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 
        0.99        31.07        17.03        27.02        18.05        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        21.99        16.08        13.05        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       27.02         7.96        19.00        34.03        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S 
       14.99        15.02        15.02        32.02        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       33.04        26.01         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       41.00        40.96        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L 
       26.47        16.44        14.50         0.95        33.01        17.26 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 
       17.85        18.84       109.28         5.65         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 
       65.00        62.79        12.10        29.56         5.23        12.69 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 
       12.46        12.59        12.59        12.20        14.30        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        2.01        25.02         8.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
       16.04        21.99        13.02        15.02        11.01        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 
       55.92        20.19        18.25        25.48        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       12.49         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 
       13.41        11.38        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59       140.38        44.32       131.51       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
       14.04        26.47       119.93        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        11.11        35.74         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
        8.35        82.39        65.85        55.04        61.91        36.00 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-NH-A8F8 
       46.75        74.79        18.18        10.98        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       42.77        32.98         8.42        21.90        38.70        60.13 
TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       11.90        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       34.49        37.74        29.98        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        36.03        12.00         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00        46.03        34.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 
       50.04         0.99        15.95        20.98         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       37.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       35.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 
       28.04        36.03         1.02         3.98        46.03        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43         6.05        33.17        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         3.48         4.18        20.55 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 
       16.41        11.51        10.78        13.64        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6863 TCGA-F5-6864 
       11.87        12.46 

$`18P LOSS WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       24.16        58.03        13.02        24.03        36.03         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 
        0.99        17.95         0.92        19.04        19.04        24.00 
TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
        2.01        19.07        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       75.95       100.01         5.88        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A015 TCGA-5M-AAT6 TCGA-A6-2672 
       91.79        79.69         8.02        36.03         9.53        46.65 
TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 
       42.90        37.02        32.75        31.63        33.53        22.06 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.52         8.38        25.08        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
       24.92         3.02        35.01        63.98         1.02         1.02 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 
        0.00        29.00        21.01        29.95        20.98         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       54.02        47.05        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        0.00         0.00         0.00        36.03        32.05        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 
       31.00         2.01        33.01        26.01         2.01        25.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G 
        4.01         0.99        17.03        34.98        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z 
       31.00        38.07         1.02        35.01         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       51.98         0.92        22.03        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 
       83.24         0.46         0.92        27.09        16.31         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       21.44        17.82        19.33        58.39         1.41        32.94 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       88.21        49.41         6.77        11.74         3.19        12.36 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.39        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       23.05        20.02        37.02        26.04        27.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 
       32.02        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 
       12.99        14.04        12.95        13.05        11.08        19.59 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        43.27        15.12         4.80        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       15.58        12.39         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       10.26       119.70        92.75         7.50       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       81.37        60.79        98.24        35.74         6.18        47.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50V 
       85.48        39.42        26.43        26.04        13.78        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 
       19.33         9.93        15.65        29.46        31.30        70.03 
TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3594 
       37.97        16.83        24.59        32.02         1.02         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3881 
       12.03         6.05        19.99         0.99         0.99        19.04 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A025 
       17.95        13.02        14.01        14.04        20.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6621 TCGA-DT-5265 
       38.96        61.97         2.50        19.46        13.78        12.62 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       32.61        19.96        20.91         8.61        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 
        9.96        37.18        38.14        47.08 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.39               0.00 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            140.38             148.01 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             24.00              19.81 
[1] "0.4 - 140.4 (24.0)" "0.0 - 148.0 (19.8)"
[1] "hr=" "1.2"
D73V2, continuous
D73V3, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   251 126
  18P LOSS WILD-TYPE 197  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    251  126
  18P LOSS WILD-TYPE  197   36
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON               251                197
  RECTUM              126                 36
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18P LOSS MUTATED        58        0       17        98         5         2
  18P LOSS WILD-TYPE      46        1       20        74         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18P LOSS MUTATED          10         12         55         37       50
  18P LOSS WILD-TYPE        14          3         29         18       13
                    vv
clus                 STAGE IVA STAGE IVB
  18P LOSS MUTATED          22         1
  18P LOSS WILD-TYPE         2         1
D73V4, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  58                 46
  STAGE IA                  0                  1
  STAGE II                 17                 20
  STAGE IIA                98                 74
  STAGE IIB                 5                  7
  STAGE IIC                 2                  0
  STAGE III                10                 14
  STAGE IIIA               12                  3
  STAGE IIIB               55                 29
  STAGE IIIC               37                 18
  STAGE IV                 50                 13
  STAGE IVA                22                  2
  STAGE IVB                 1                  1
[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    12  62 263  42
  18P LOSS WILD-TYPE   8  43 154  27
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               12                  8
  T2               62                 43
  T3              263                154
  T4               42                 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
  18P LOSS MUTATED   194 106  78
  18P LOSS WILD-TYPE 152  44  37
D73V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0              194                152
  N1              106                 44
  N2               78                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   266  73
  18P LOSS WILD-TYPE 187  15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    266   73
  18P LOSS WILD-TYPE  187   15
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0              266                187
  1               73                 15
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   173 207
  18P LOSS WILD-TYPE 116 118
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    173  207
  18P LOSS WILD-TYPE  116  118
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE              173                116
  MALE                207                118
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   301  20
  18P LOSS WILD-TYPE 181   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    301   20
  18P LOSS WILD-TYPE  181    9
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO               301                181
  YES               20                  9
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                    237                            11
  18P LOSS WILD-TYPE                  145                            51
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18P LOSS MUTATED                     119                              7
  18P LOSS WILD-TYPE                    27                              6
D73V10, multiclass
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        237                145
  COLON MUCINOUS ADENOCARCINOMA                11                 51
  RECTAL ADENOCARCINOMA                       119                 27
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[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                  R0  R1  R2  RX
  18P LOSS MUTATED   271   3  29  14
  18P LOSS WILD-TYPE 175   3   8  15
D73V11, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0              271                175
  R1                3                  3
  R2               29                  8
  RX               14                 15
[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, continuous
D73V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     4 219
  18P LOSS WILD-TYPE   1 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4  219
  18P LOSS WILD-TYPE    1  133
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              219                133
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   311  83
  18Q LOSS WILD-TYPE 155  45
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               394                200 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                83                 45 
$`18Q LOSS MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 
       50.99        26.01        24.00        21.99        15.52       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 
       35.93        91.79        17.85        10.39        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        25.97        15.95        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       12.66         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       24.13        25.18        20.61        21.76        24.39        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
        1.02        37.05         6.97        38.99         9.07        19.07 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        33.99        24.00 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        61.02        78.08         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       47.01        15.02        37.05        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       37.02        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       17.03        27.02        18.05        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        27.02         7.96 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02        10.98        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       41.00        40.96        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 
       26.47        16.44         0.46        14.50        16.31        33.01 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 
       17.26        17.85        18.84       109.28         5.65         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        88.21        12.10        29.56 
TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        5.23        12.69        12.46        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
       14.30       148.01        21.99         2.01        25.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
       27.02        13.02        29.06        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        14.04        29.03        16.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 
       55.92        20.19        18.25        25.48        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
       44.32       131.51       139.17        14.04        26.47       119.93 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        34.42        41.42        43.04        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       47.41         8.35        82.39        65.85        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       39.42        61.91        36.00        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       10.98        19.33         9.93        12.79        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        21.90        38.70        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       34.49        37.74        29.98        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05        24.00        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 
       34.03         2.01        50.04         0.99        15.95        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 
       19.04        19.99         1.02        36.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 
       23.01        37.02         9.07         1.02         1.02         1.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04        38.56        43.20        27.55        26.43 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        25.05       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         3.48         4.18        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.41        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        11.87        12.46        47.08 

$`18Q LOSS WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88        75.95       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A015 
       22.09        35.80        26.17        79.69         8.02        36.03 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 
        9.53        46.65        42.90        32.75        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6780 
       22.06        22.52         8.38        25.08        24.69        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3549 TCGA-AA-3555 
        1.02         1.02         0.00        29.00        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 
       20.98         6.97        54.02        47.05        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
        5.03        26.99        10.06        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       17.98        15.95         0.00         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       32.05        53.00        31.00         2.01        33.01        26.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
        2.01        25.02        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        18.05         4.01        27.02         0.99        34.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       51.98         0.92        22.03        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 
       83.24         0.92        27.09         0.95         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 
       17.82        19.33        58.39         1.41        32.94        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
        6.77        11.74         3.19        12.36        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       26.04        22.98        32.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       12.00        14.99        12.99        14.04        12.95        13.05 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75        43.27        15.12         4.80        16.14 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.39         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G 
      119.70       135.65         7.76        81.37        35.97        60.79 
TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 TCGA-F4-6856 
       98.24        35.74         6.18        47.87        33.67        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6320 
      133.18        74.56        67.30        53.62        85.48        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 
       26.04        13.78        19.33        15.65        29.46        31.30 
TCGA-WS-AB45 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3600 
       70.03        16.83        24.59         1.02        12.03         6.05 
TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
       19.99         0.99        17.95        13.02        14.01        20.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6621 
       49.97        38.96        61.97         2.50        19.46        13.78 
TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 
       12.62        32.61        19.96         8.61        17.46         9.96 
TCGA-F5-6814 TCGA-F5-6861 
       37.18        38.14 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.39               0.00 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            148.01             135.65 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            23.935             20.070 
[1] "0.4 - 148.0 (23.9)" "0.0 - 135.7 (20.1)"
[1] "hr=" "1.1"
D74V2, continuous
D74V3, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   269 135
  18Q LOSS WILD-TYPE 179  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    269  135
  18Q LOSS WILD-TYPE  179   27
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON               269                179
  RECTUM              135                 27
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  18Q LOSS MUTATED        59        0       21       104         5         2
  18Q LOSS WILD-TYPE      45        1       16        68         7         0
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  18Q LOSS MUTATED          13         13         59         40       52
  18Q LOSS WILD-TYPE        11          2         25         15       11
                    vv
clus                 STAGE IVA STAGE IVB
  18Q LOSS MUTATED          22         1
  18Q LOSS WILD-TYPE         2         1
D74V4, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  59                 45
  STAGE IA                  0                  1
  STAGE II                 21                 16
  STAGE IIA               104                 68
  STAGE IIB                 5                  7
  STAGE IIC                 2                  0
  STAGE III                13                 11
  STAGE IIIA               13                  2
  STAGE IIIB               59                 25
  STAGE IIIC               40                 15
  STAGE IV                 52                 11
  STAGE IVA                22                  2
  STAGE IVB                 1                  1
[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    11  65 285  44
  18Q LOSS WILD-TYPE   9  40 132  25
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               11                  9
  T2               65                 40
  T3              285                132
  T4               44                 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
  18Q LOSS MUTATED   205 113  86
  18Q LOSS WILD-TYPE 141  37  29
D74V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0              205                141
  N1              113                 37
  N2               86                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   289  75
  18Q LOSS WILD-TYPE 164  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    289   75
  18Q LOSS WILD-TYPE  164   13
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0              289                164
  1               75                 13
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   186 221
  18Q LOSS WILD-TYPE 103 104
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    186  221
  18Q LOSS WILD-TYPE  103  104
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE              186                103
  MALE                221                104
[1] 2 2
[1] FALSE
D74V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   322  20
  18Q LOSS WILD-TYPE 160   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    322   20
  18Q LOSS WILD-TYPE  160    9
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO               322                160
  YES               20                  9
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                    252                            14
  18Q LOSS WILD-TYPE                  130                            48
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  18Q LOSS MUTATED                     124                             10
  18Q LOSS WILD-TYPE                    22                              3
D74V10, multiclass
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        252                130
  COLON MUCINOUS ADENOCARCINOMA                14                 48
  RECTAL ADENOCARCINOMA                       124                 22
  RECTAL MUCINOUS ADENOCARCINOMA               10                  3
[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                  R0  R1  R2  RX
  18Q LOSS MUTATED   293   4  29  14
  18Q LOSS WILD-TYPE 153   2   8  15
D74V11, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              293                153
  R1                4                  2
  R2               29                  8
  RX               14                 15
[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, continuous
D74V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     4 236
  18Q LOSS WILD-TYPE   1 116
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4  236
  18Q LOSS WILD-TYPE    1  116
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              236                116
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    42  17
  19P LOSS WILD-TYPE 424 111
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                59                535 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                17                111 
$`19P LOSS MUTATED`
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3867 TCGA-AA-3952 
       13.02        23.01        19.99        36.00        24.03         2.01 
TCGA-CK-5912 TCGA-DM-A285 TCGA-AG-4008 TCGA-G5-6233 TCGA-A6-3807 TCGA-A6-5667 
       49.08         5.88        17.03        18.28        34.65        29.16 
TCGA-A6-6142 TCGA-A6-A567 TCGA-AA-3538 TCGA-AA-3666 TCGA-AA-3866 TCGA-AA-3941 
       25.08        61.84        26.01         2.01        17.03        24.00 
TCGA-AA-3966 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F 
        2.01        10.98        12.00        33.04        26.01        39.98 
TCGA-AA-A02W TCGA-AD-6965 TCGA-AY-6196 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CA-5797 
       41.00        26.47         0.20         5.13        65.00        12.59 
TCGA-CK-4948 TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-6533 TCGA-D5-6537 TCGA-DM-A1DB 
      148.01        13.05        45.40        25.48         4.80        44.32 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL TCGA-SS-A7HO 
       33.67         8.35        36.00        10.98        38.70        60.13 
TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3881 TCGA-AG-A016 
       46.92        29.98        15.95        20.98        19.04         9.07 
TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       48.20        31.00        13.97        24.13        51.48         3.48 
TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       16.34        11.51        11.97        42.35        28.57 

$`19P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3662 
       19.07        34.03         0.99        17.95        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        19.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 
       31.07        29.98        12.99        24.00        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        1.94        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 
       36.03        31.00        51.98        21.24        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       43.76        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 
       27.09        22.52        24.13         8.38        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       78.08         6.97        54.02        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       32.05         0.99        31.07        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
        1.02         1.02        37.02        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        22.36        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       26.04        13.78        46.75        74.79        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        23.01        37.02         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       21.01        25.05        26.04        12.00        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        57.24       129.27        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
       17.46         8.45         9.96        49.51         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               0.2                0.0 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            148.01             140.38 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             24.03              21.99 
[1] "0.2 - 148.0 (24.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.5"
D75V2, continuous
D75V3, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    41  20
  19P LOSS WILD-TYPE 407 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     41   20
  19P LOSS WILD-TYPE  407  142
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON                41                407
  RECTUM               20                142
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19P LOSS MUTATED         7        0        2        10         2         1
  19P LOSS WILD-TYPE      97        1       35       162        10         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19P LOSS MUTATED           5          1          5         10        9
  19P LOSS WILD-TYPE        19         14         79         45       54
                    vv
clus                 STAGE IVA STAGE IVB
  19P LOSS MUTATED           7         1
  19P LOSS WILD-TYPE        17         1
D75V4, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   7                 97
  STAGE IA                  0                  1
  STAGE II                  2                 35
  STAGE IIA                10                162
  STAGE IIB                 2                 10
  STAGE IIC                 1                  1
  STAGE III                 5                 19
  STAGE IIIA                1                 14
  STAGE IIIB                5                 79
  STAGE IIIC               10                 45
  STAGE IV                  9                 54
  STAGE IVA                 7                 17
  STAGE IVB                 1                  1
[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     1   8  45   8
  19P LOSS WILD-TYPE  19  97 372  61
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                1                 19
  T2                8                 97
  T3               45                372
  T4                8                 61
[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
  19P LOSS MUTATED    23  15  24
  19P LOSS WILD-TYPE 323 135  91
D75V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               23                323
  N1               15                135
  N2               24                 91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    38  16
  19P LOSS WILD-TYPE 415  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     38   16
  19P LOSS WILD-TYPE  415   72
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               38                415
  1               16                 72
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    31  31
  19P LOSS WILD-TYPE 258 294
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     31   31
  19P LOSS WILD-TYPE  258  294
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               31                258
  MALE                 31                294
[1] 2 2
[1] FALSE
D75V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    48   2
  19P LOSS WILD-TYPE 434  27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     48    2
  19P LOSS WILD-TYPE  434   27
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                48                434
  YES                2                 27
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                     33                             7
  19P LOSS WILD-TYPE                  349                            55
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19P LOSS MUTATED                      19                              0
  19P LOSS WILD-TYPE                   127                             13
D75V10, multiclass
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         33                349
  COLON MUCINOUS ADENOCARCINOMA                 7                 55
  RECTAL ADENOCARCINOMA                        19                127
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  19P LOSS MUTATED    41   1   5   3
  19P LOSS WILD-TYPE 405   5  32  26
D75V11, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               41                405
  R1                1                  5
  R2                5                 32
  RX                3                 26
[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, continuous
D75V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     0  36
  19P LOSS WILD-TYPE   5 316
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0   36
  19P LOSS WILD-TYPE    5  316
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               36                316
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    40  14
  19Q LOSS WILD-TYPE 426 114
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                54                540 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                14                114 
$`19Q LOSS MUTATED`
TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-A00Z 
       23.01        19.99        36.00        24.03         2.01        21.99 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G5-6233 TCGA-A6-3807 TCGA-A6-5667 TCGA-AA-3538 
       49.08         5.88        18.28        34.65        29.16        26.01 
TCGA-AA-3666 TCGA-AA-3866 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 TCGA-AA-A01D 
        2.01        17.03        24.00         2.01        13.94        10.98 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AZ-4616 TCGA-AZ-4684 
       33.04        26.01        39.98        41.00         5.13        65.00 
TCGA-CK-4948 TCGA-CM-5862 TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-6533 TCGA-DM-A1DB 
      148.01         5.03        13.05        45.40        25.48        44.32 
TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL 
        1.55        33.67         8.35        36.00        10.98        38.70 
TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3591 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3881 
       46.92        29.98        34.03        15.95        20.98        19.04 
TCGA-AG-4001 TCGA-AG-A011 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-5869 TCGA-DY-A1DF 
       36.03        37.02        48.20        21.01        31.00        24.13 
TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
        3.48        16.34        11.51        11.97        42.35        28.57 

$`19Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3560 
       19.07        34.03         0.99        13.02        17.95        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 
       14.93        31.07        29.98        12.99        24.00        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 
       26.01        24.00        19.07        38.04        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        1.94        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        27.02        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        25.02        27.02         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        5.79        22.42        27.42        26.47        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.20        21.44        17.82        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        14.30        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        39.42        61.91        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        31.30        21.90        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       70.03        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        19.99         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       44.78        47.44        78.12         7.17        25.05        26.04 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        51.48        32.61         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45         9.96        49.51         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              1.55               0.00 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            148.01             140.38 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            24.080             21.945 
[1] "1.6 - 148.0 (24.1)" "0.0 - 140.4 (21.9)"
[1] "hr=" "1.3"
D76V2, continuous
D76V3, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    36  19
  19Q LOSS WILD-TYPE 412 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     36   19
  19Q LOSS WILD-TYPE  412  143
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON                36                412
  RECTUM               19                143
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  19Q LOSS MUTATED         7        0        2        11         1         1
  19Q LOSS WILD-TYPE      97        1       35       161        11         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  19Q LOSS MUTATED           5          0          5          8        7
  19Q LOSS WILD-TYPE        19         15         79         47       56
                    vv
clus                 STAGE IVA STAGE IVB
  19Q LOSS MUTATED           6         1
  19Q LOSS WILD-TYPE        18         1
D76V4, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   7                 97
  STAGE IA                  0                  1
  STAGE II                  2                 35
  STAGE IIA                11                161
  STAGE IIB                 1                 11
  STAGE IIC                 1                  1
  STAGE III                 5                 19
  STAGE IIIA                0                 15
  STAGE IIIB                5                 79
  STAGE IIIC                8                 47
  STAGE IV                  7                 56
  STAGE IVA                 6                 18
  STAGE IVB                 1                  1
[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     1   7  42   6
  19Q LOSS WILD-TYPE  19  98 375  63
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                1                 19
  T2                7                 98
  T3               42                375
  T4                6                 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"
                    vv
clus                  N0  N1  N2
  19Q LOSS MUTATED    23  12  21
  19Q LOSS WILD-TYPE 323 138  94
D76V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               23                323
  N1               12                138
  N2               21                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    36  13
  19Q LOSS WILD-TYPE 417  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     36   13
  19Q LOSS WILD-TYPE  417   75
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0               36                417
  1               13                 75
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    30  26
  19Q LOSS WILD-TYPE 259 299
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     30   26
  19Q LOSS WILD-TYPE  259  299
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               30                259
  MALE                 26                299
[1] 2 2
[1] FALSE
D76V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    43   3
  19Q LOSS WILD-TYPE 439  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     43    3
  19Q LOSS WILD-TYPE  439   26
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                43                439
  YES                3                 26
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                     29                             6
  19Q LOSS WILD-TYPE                  353                            56
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  19Q LOSS MUTATED                      18                              0
  19Q LOSS WILD-TYPE                   128                             13
D76V10, multiclass
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         29                353
  COLON MUCINOUS ADENOCARCINOMA                 6                 56
  RECTAL ADENOCARCINOMA                        18                128
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  19Q LOSS MUTATED    40   0   4   3
  19Q LOSS WILD-TYPE 406   6  33  26
D76V11, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               40                406
  R1                0                  6
  R2                4                 33
  RX                3                 26
[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, continuous
D76V13, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     0  31
  19Q LOSS WILD-TYPE   5 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0   31
  19Q LOSS WILD-TYPE    5  321
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO               31                321
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    46  12
  20P LOSS WILD-TYPE 420 116
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                58                536 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                116 
$`20P LOSS MUTATED`
TCGA-AA-3867 TCGA-AA-3952 TCGA-G4-6298 TCGA-NH-A8F7 TCGA-G5-6641 TCGA-A6-5666 
       24.03         2.01        23.51        17.85        26.43        32.71 
TCGA-A6-5667 TCGA-A6-6140 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3553 
       29.16        24.13        38.99         9.07        26.01        24.00 
TCGA-AA-3681 TCGA-AA-3841 TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F 
        5.98        36.95        32.05         2.01        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A01Z TCGA-AA-A03J TCGA-AZ-4308 TCGA-AZ-6606 TCGA-CK-5914 
       42.02        37.02        40.96       109.28        11.74        21.99 
TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-6168 TCGA-CM-6170 TCGA-D5-5540 
        2.01        22.03        30.08        12.99        15.02        56.09 
TCGA-D5-5541 TCGA-D5-6534 TCGA-D5-6923 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-F4-6809 
       55.92        43.27        12.43        92.75        49.91        13.25 
TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50V TCGA-RU-A8FL 
        0.53         8.35        36.00        26.43        19.33        38.70 
TCGA-SS-A7HO TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 
       60.13        29.98        86.63        11.84        36.03        32.02 
TCGA-AG-3600 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G 
        6.05        32.02        46.03         1.02         1.94        38.96 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-F5-6571 TCGA-F5-6702 
       41.36        57.24        42.35        28.57 

$`20P LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       85.05        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       26.17        91.79        79.69        10.39         8.02        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       19.99        17.03        17.03        25.97        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B 
       31.00        51.98        21.24        18.28        55.76        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       22.52         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        6.97         1.02         1.02        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       29.00        12.99        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01        37.05         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
        0.00        36.03         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       22.03        41.00        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33        18.84        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10        29.56         5.23         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02        25.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        29.06        22.98        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 
       14.04        29.03        16.04        21.99        14.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        45.40        54.61        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       20.19        20.42        17.75        18.25        25.48        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 
       34.42        41.42        43.04        33.67        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        61.91        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       34.49        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       65.98        12.00         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.02        49.97        61.97        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05        25.05        12.62       126.44       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       17.46        11.97         8.45         9.96        49.51         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.53               0.00 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            109.28             148.01 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            28.865             21.075 
[1] "0.5 - 109.3 (28.9)" "0.0 - 148.0 (21.1)"
[1] "hr=" "1.1"
D77V2, continuous
D77V3, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    43  20
  20P LOSS WILD-TYPE 405 142
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     43   20
  20P LOSS WILD-TYPE  405  142
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON                43                405
  RECTUM               20                142
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20P LOSS MUTATED         7        0        7        19         1         1
  20P LOSS WILD-TYPE      97        1       30       153        11         1
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20P LOSS MUTATED           3          1         12          5        5
  20P LOSS WILD-TYPE        21         14         72         50       58
                    vv
clus                 STAGE IVA STAGE IVB
  20P LOSS MUTATED           3         0
  20P LOSS WILD-TYPE        21         2
D77V4, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   7                 97
  STAGE IA                  0                  1
  STAGE II                  7                 30
  STAGE IIA                19                153
  STAGE IIB                 1                 11
  STAGE IIC                 1                  1
  STAGE III                 3                 21
  STAGE IIIA                1                 14
  STAGE IIIB               12                 72
  STAGE IIIC                5                 50
  STAGE IV                  5                 58
  STAGE IVA                 3                 21
  STAGE IVB                 0                  2
[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     1   8  46   9
  20P LOSS WILD-TYPE  19  97 371  60
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                1                 19
  T2                8                 97
  T3               46                371
  T4                9                 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"
                    vv
clus                  N0  N1  N2
  20P LOSS MUTATED    35  19  10
  20P LOSS WILD-TYPE 311 131 105
D77V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               35                311
  N1               19                131
  N2               10                105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    48   7
  20P LOSS WILD-TYPE 405  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     48    7
  20P LOSS WILD-TYPE  405   81
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0               48                405
  1                7                 81
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    32  32
  20P LOSS WILD-TYPE 257 293
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     32   32
  20P LOSS WILD-TYPE  257  293
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               32                257
  MALE                 32                293
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    45   4
  20P LOSS WILD-TYPE 437  25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     45    4
  20P LOSS WILD-TYPE  437   25
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                45                437
  YES                4                 25
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                     39                             4
  20P LOSS WILD-TYPE                  343                            58
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20P LOSS MUTATED                      18                              2
  20P LOSS WILD-TYPE                   128                             11
D77V10, multiclass
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  COLON ADENOCARCINOMA                         39                343
  COLON MUCINOUS ADENOCARCINOMA                 4                 58
  RECTAL ADENOCARCINOMA                        18                128
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[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                  R0  R1  R2  RX
  20P LOSS MUTATED    48   1   4   2
  20P LOSS WILD-TYPE 398   5  33  27
D77V11, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               48                398
  R1                1                  5
  R2                4                 33
  RX                2                 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"
D77V12, continuous
D77V13, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1  34
  20P LOSS WILD-TYPE   4 318
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1   34
  20P LOSS WILD-TYPE    4  318
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  4
  NOT HISPANIC OR LATINO               34                318
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   3
  20Q LOSS WILD-TYPE 462 125
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 7                587 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                125 
$`20Q LOSS MUTATED`
TCGA-AA-3952 TCGA-G4-6298 TCGA-AA-3681 TCGA-D5-6534 TCGA-DM-A1D4 TCGA-NH-A50V 
        2.01        23.51         5.98        43.27        92.75        19.33 
TCGA-SS-A7HO 
       60.13 

$`20Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       29.98        12.99        24.00        50.99        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
       49.08         5.88        28.21        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       55.76        26.43        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 
       37.25        37.02        34.65        32.75        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 
       50.04        47.05        47.01        15.02        11.01        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02        25.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       17.75        18.25        25.48        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       60.79       117.07        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        74.79        18.18        10.98        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        38.70        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              2.01               0.00 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             92.75             148.01 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             23.51              21.99 
[1] "2.0 - 92.8 (23.5)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D78V2, continuous
D78V3, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     7   1
  20Q LOSS WILD-TYPE 441 161
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      7    1
  20Q LOSS WILD-TYPE  441  161
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON                 7                441
  RECTUM                1                161
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  20Q LOSS MUTATED         0        0        1         2         1         0
  20Q LOSS WILD-TYPE     104        1       36       170        11         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  20Q LOSS MUTATED           1          0          2          1        0
  20Q LOSS WILD-TYPE        23         15         82         54       63
                    vv
clus                 STAGE IVA STAGE IVB
  20Q LOSS MUTATED           0         0
  20Q LOSS WILD-TYPE        24         2
D78V4, multiclass
            clus
vv           20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                   0                104
  STAGE IA                  0                  1
  STAGE II                  1                 36
  STAGE IIA                 2                170
  STAGE IIB                 1                 11
  STAGE IIC                 0                  2
  STAGE III                 1                 23
  STAGE IIIA                0                 15
  STAGE IIIB                2                 82
  STAGE IIIC                1                 54
  STAGE IV                  0                 63
  STAGE IVA                 0                 24
  STAGE IVB                 0                  2
[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     0   0   6   2
  20Q LOSS WILD-TYPE  20 105 411  67
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                 20
  T2                0                105
  T3                6                411
  T4                2                 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"
                    vv
clus                  N0  N1  N2
  20Q LOSS MUTATED     4   2   2
  20Q LOSS WILD-TYPE 342 148 113
D78V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                4                342
  N1                2                148
  N2                2                113
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     7   0
  20Q LOSS WILD-TYPE 446  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      7    0
  20Q LOSS WILD-TYPE  446   88
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                7                446
  1                0                 88
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     4   4
  20Q LOSS WILD-TYPE 285 321
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      4    4
  20Q LOSS WILD-TYPE  285  321
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                4                285
  MALE                  4                321
[1] 2 2
[1] FALSE
D78V9, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   0
  20Q LOSS WILD-TYPE 477  29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    0
  20Q LOSS WILD-TYPE  477   29
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 5                477
  YES                0                 29
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                      6                             1
  20Q LOSS WILD-TYPE                  376                            61
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  20Q LOSS MUTATED                       1                              0
  20Q LOSS WILD-TYPE                   145                             13
D78V10, multiclass
                                clus
vv                               20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                          6                376
  COLON MUCINOUS ADENOCARCINOMA                 1                 61
  RECTAL ADENOCARCINOMA                         1                145
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[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                  R0  R1  R2  RX
  20Q LOSS MUTATED     7   0   0   0
  20Q LOSS WILD-TYPE 439   6  37  29
D78V11, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                7                439
  R1                0                  6
  R2                0                 37
  RX                0                 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"
D78V12, continuous
D78V13, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     0   5
  20Q LOSS WILD-TYPE   5 347
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      0    5
  20Q LOSS WILD-TYPE    5  347
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                347
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED   141  39
  21Q LOSS WILD-TYPE 325  89
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               180                414 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                39                 89 
$`21Q LOSS MUTATED`
TCGA-A6-4105 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3688 TCGA-AA-3692 
       14.53        19.07        34.03        19.99        19.00        36.00 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-A00L TCGA-AA-A00Z TCGA-CK-5912 TCGA-G4-6314 
       14.93        24.03        38.04        21.99        49.08        35.93 
TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A01N TCGA-G5-6233 
       91.79        17.85        17.03        17.03        31.00        18.28 
TCGA-G5-6641 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 
       26.43         1.61        39.45        43.76        43.76        37.05 
TCGA-A6-5659 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       30.44        22.06        29.16        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       23.87        20.28        61.84         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3660 TCGA-AA-3685 TCGA-AA-3811 
       38.99         9.07        26.01        78.08        37.05        10.06 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3875 
       38.99        37.02        10.06         0.99        17.03        18.05 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 
       24.00        20.98         2.01        21.99         7.96        13.94 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K 
       27.02        42.02        15.02        10.98        32.02        31.00 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 
       51.98        39.98        41.00        24.53        22.42        26.47 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4616 
       16.44        14.50        16.31         0.20        17.85         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       65.00        12.10        29.56         5.23         3.19        12.69 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 
       12.46        12.59        12.20        21.99        20.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       27.02        13.02        22.03        22.98        32.02         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        29.03        15.02        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A1D9 
       45.40        17.75        25.48        13.41        49.91       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6703 
        7.50       131.51        26.47         8.61        31.96        47.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 
        1.55        41.42        43.04        33.67         0.53        47.41 
TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50T 
        8.35        61.91        36.00        26.43        46.75        18.18 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        9.93        42.77        60.13        46.92        39.48        17.23 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       29.98        24.36        20.02        24.59        86.63        11.84 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       12.00         7.07        36.03        24.00        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 
       34.03        12.03         6.05        19.99        20.98        29.98 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       19.04        19.99         1.02        48.03        19.99        36.03 
TCGA-AG-A020 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6643 TCGA-CI-6621 
        1.02        38.96        61.97        41.00        43.20        13.78 
TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       48.20        21.01        13.97        10.98        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
      126.44        57.24       129.27        51.48        32.61        20.55 
TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
       20.91        15.85        17.69        16.34        16.41        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
        8.45        42.35         0.39        36.49        37.18        11.87 

$`21Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 
       13.02        24.03        37.05        36.03         8.05         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       85.05        19.04        19.04        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 
       63.62        22.09        35.80        26.17        79.69        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
        8.02        13.94        19.99        25.97        15.95        36.03 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       51.98        21.24        55.76        15.62         4.80        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
        9.53        46.65        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       35.11        16.57        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.45        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
        8.38        25.08        25.18        24.69        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       16.24        24.92        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
       37.05        35.01        63.98         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       36.95         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 
       36.03        32.05        31.07        53.00        27.02        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
        2.01        33.01        26.01        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       34.06        25.02        27.02        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I 
       17.03        14.99        34.98        15.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        37.02         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
        5.79        27.42         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
       33.01        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
      109.28        58.39         1.41         5.65        32.94        22.36 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 
       62.79        88.21        49.41         6.77        11.74        12.36 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
      148.01        85.45        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       82.95         2.01       124.27        23.05        37.02        25.02 
TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       26.04        29.06        30.08        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 
       11.11        35.74        35.74         6.18        34.42        13.25 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6322 
       53.62        44.68        55.04        85.48        39.42        26.04 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       13.78        74.79        10.98        19.33        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       12.79        16.80        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 
       21.90        38.70        11.90        70.03        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-A56L TCGA-AG-3574 
       37.97        34.49        37.74        16.83        65.98        36.03 
TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       32.02        20.05         1.02        34.03         2.01        50.04 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        0.99        15.95         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       35.01        14.01        25.02        32.02        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         2.50        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17        44.78        47.44        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EF-5830 
       44.02        25.97        12.62        41.36        24.13         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 
        4.18        19.96        17.00        18.28        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        17.46         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       28.57        32.19        19.66        38.14        12.46        47.08 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               0.2                0.0 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            140.38             148.01 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             22.01              22.01 
[1] "0.2 - 140.4 (22.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D79V2, continuous
D79V3, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   124  67
  21Q LOSS WILD-TYPE 324  95
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    124   67
  21Q LOSS WILD-TYPE  324   95
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON               124                324
  RECTUM               67                 95
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  21Q LOSS MUTATED        26        0       11        50         2         0
  21Q LOSS WILD-TYPE      78        1       26       122        10         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  21Q LOSS MUTATED           6          8         27         23       25
  21Q LOSS WILD-TYPE        18          7         57         32       38
                    vv
clus                 STAGE IVA STAGE IVB
  21Q LOSS MUTATED           6         0
  21Q LOSS WILD-TYPE        18         2
D79V4, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  26                 78
  STAGE IA                  0                  1
  STAGE II                 11                 26
  STAGE IIA                50                122
  STAGE IIB                 2                 10
  STAGE IIC                 0                  2
  STAGE III                 6                 18
  STAGE IIIA                8                  7
  STAGE IIIB               27                 57
  STAGE IIIC               23                 32
  STAGE IV                 25                 38
  STAGE IVA                 6                 18
  STAGE IVB                 0                  2
[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     6  32 134  19
  21Q LOSS WILD-TYPE  14  73 283  50
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                6                 14
  T2               32                 73
  T3              134                283
  T4               19                 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"
                    vv
clus                  N0  N1  N2
  21Q LOSS MUTATED    93  51  47
  21Q LOSS WILD-TYPE 253  99  68
D79V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               93                253
  N1               51                 99
  N2               47                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   138  29
  21Q LOSS WILD-TYPE 315  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    138   29
  21Q LOSS WILD-TYPE  315   59
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0              138                315
  1               29                 59
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    93  99
  21Q LOSS WILD-TYPE 196 226
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     93   99
  21Q LOSS WILD-TYPE  196  226
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               93                196
  MALE                 99                226
[1] 2 2
[1] FALSE
D79V9, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED   146  12
  21Q LOSS WILD-TYPE 336  17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED    146   12
  21Q LOSS WILD-TYPE  336   17
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO               146                336
  YES               12                 17
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                    116                             8
  21Q LOSS WILD-TYPE                  266                            54
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  21Q LOSS MUTATED                      62                              3
  21Q LOSS WILD-TYPE                    84                             10
D79V10, multiclass
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        116                266
  COLON MUCINOUS ADENOCARCINOMA                 8                 54
  RECTAL ADENOCARCINOMA                        62                 84
  RECTAL MUCINOUS ADENOCARCINOMA                3                 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                  R0  R1  R2  RX
  21Q LOSS MUTATED   139   2  12   6
  21Q LOSS WILD-TYPE 307   4  25  23
D79V11, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0              139                307
  R1                2                  4
  R2               12                 25
  RX                6                 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"
D79V12, continuous
D79V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4 110
  21Q LOSS WILD-TYPE   1 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4  110
  21Q LOSS WILD-TYPE    1  242
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                  1
  NOT HISPANIC OR LATINO              110                242
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED   146  47
  22Q LOSS WILD-TYPE 320  81
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               193                401 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                 81 
$`22Q LOSS MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3552 
       45.60        13.94        14.53        24.03        37.05        13.02 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 
       19.99         6.05        85.05        31.07        24.03        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
        2.01        50.99        26.01         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 
       63.62        91.79        13.94        25.97        21.24        18.28 
TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 
       26.43         4.80         1.61        39.45        43.76        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5657 
       44.91        35.11        16.57        34.65        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 
       30.44        29.19        23.61        22.52        20.61        21.76 
TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 
       23.87        61.84        56.25         9.63         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 
        9.07        29.00        26.01        12.99        33.99        21.01 
TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 
       13.94         2.01        50.04        37.05        10.06        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03        10.06        33.07        32.05 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 
       17.03        27.02        18.05         2.01         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       13.05         7.96        13.94        34.03        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       17.03        14.99        15.02        33.04        26.01        37.02 
TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       39.98        41.00        40.96         5.79        22.42        26.47 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A69D TCGA-AZ-4323 
       16.44        14.50        16.31        33.01        17.85         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        5.65         5.13        12.10        29.56         5.23         3.19 
TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
       12.36        12.20        14.30         2.01        25.02         8.02 
TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6170 TCGA-CM-6677 
       29.06        30.08         5.03        15.02        15.02        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       11.01        45.40        56.09        20.19        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6929 TCGA-D5-6932 
       15.12        17.85        12.49         7.53        13.41        11.38 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 
       12.59       140.38       131.51        26.47        31.96         1.55 
TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6317 
       43.04        13.25         8.35        82.39        61.91        36.00 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75        18.18        10.98        19.33         9.93        42.77 
TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       29.46        21.90        13.55        29.98        24.36        24.59 
TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3591 
       65.98        12.00        32.02         7.07        20.05        34.03 
TCGA-AG-3593 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 
       34.03        20.98        29.98        37.02        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 
       17.95         1.02        19.99        36.03        14.04         3.98 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6619 
        1.02         1.94        38.96        38.56        27.55         6.05 
TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
       13.78        48.20        21.01        31.00        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5831 
       44.02        25.05        25.05        41.36        51.48         4.18 
TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
       20.55        17.69        16.41        28.57         0.39        36.49 
TCGA-F5-6863 
       11.87 

$`22Q LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3524 
       24.33        24.16         1.02        58.03        13.02        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 
        8.05        19.07        34.03         0.99        17.95        23.01 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       14.93        29.98        24.00        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       106.75       100.01        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       22.09        35.80        26.17        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
        8.02        19.99        17.03        17.03        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 
       31.00        51.98        55.76        15.62        12.66         9.53 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 
       46.65        43.76        43.43        42.90        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5664 
       37.02        32.75        32.45        32.91        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        25.18        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       20.28        16.24        24.92         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
        1.02        37.05        35.01        63.98         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 
       19.07         0.00        29.00        14.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       20.98        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       15.95         0.00         0.00         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00        31.00        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       20.98        34.03        16.08        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
        4.01         0.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
        1.02         1.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        0.92        22.03        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       24.53        27.42         0.46         0.92        27.09         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.20        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
      109.28        58.39        32.94        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5256 
       88.21        49.41         6.77        11.74        12.69        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.39        12.59        12.59        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       26.04        27.02        13.02        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       12.03        54.61        19.59        55.92        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       18.25         4.80        17.13        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       41.42        33.67         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       85.48        39.42        26.43        26.04        13.78        74.79 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 
       19.33        15.65        12.79        16.80        32.98         8.42 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       31.30        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        17.23        43.04        37.97        34.49        37.74 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3582 
       16.83        20.02        86.63        11.84        36.03        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3887 
        0.99        32.98         0.99         0.99        19.04        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       28.04         1.02        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A02N 
       23.01        37.02         9.07         1.02        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         2.50        43.20        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
       33.17        44.78        47.44        78.12         7.17        25.05 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 
       26.04        12.00        31.00        51.98        25.97        12.62 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24       129.27        24.13        32.61         3.48 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       11.97         8.45         9.96        49.51        42.35        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        12.46        47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.39               0.00 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            140.38             148.01 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             21.24              22.09 
[1] "0.4 - 140.4 (21.2)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.4"
D80V2, continuous
D80V3, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   144  55
  22Q LOSS WILD-TYPE 304 107
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    144   55
  22Q LOSS WILD-TYPE  304  107
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON               144                304
  RECTUM               55                107
[1] 2 2
[1] FALSE
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  22Q LOSS MUTATED        24        0       10        46         1         0
  22Q LOSS WILD-TYPE      80        1       27       126        11         2
                    vv
clus                 STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  22Q LOSS MUTATED           7          9         29         23       31
  22Q LOSS WILD-TYPE        17          6         55         32       32
                    vv
clus                 STAGE IVA STAGE IVB
  22Q LOSS MUTATED          11         0
  22Q LOSS WILD-TYPE        13         2
D80V4, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  24                 80
  STAGE IA                  0                  1
  STAGE II                 10                 27
  STAGE IIA                46                126
  STAGE IIB                 1                 11
  STAGE IIC                 0                  2
  STAGE III                 7                 17
  STAGE IIIA                9                  6
  STAGE IIIB               29                 55
  STAGE IIIC               23                 32
  STAGE IV                 31                 32
  STAGE IVA                11                 13
  STAGE IVB                 0                  2
[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     4  31 138  27
  22Q LOSS WILD-TYPE  16  74 279  42
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                4                 16
  T2               31                 74
  T3              138                279
  T4               27                 42
[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
  22Q LOSS MUTATED    86  67  46
  22Q LOSS WILD-TYPE 260  83  69
D80V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               86                260
  N1               67                 83
  N2               46                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   134  41
  22Q LOSS WILD-TYPE 319  47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    134   41
  22Q LOSS WILD-TYPE  319   47
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0              134                319
  1               41                 47
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    92 109
  22Q LOSS WILD-TYPE 197 216
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     92  109
  22Q LOSS WILD-TYPE  197  216
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               92                197
  MALE                109                216
[1] 2 2
[1] FALSE
D80V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED   166   9
  22Q LOSS WILD-TYPE 316  20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED    166    9
  22Q LOSS WILD-TYPE  316   20
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO               166                316
  YES                9                 20
[1] 2 2
[1] FALSE
                    vv
clus                 COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                    134                            10
  22Q LOSS WILD-TYPE                  248                            52
                    vv
clus                 RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  22Q LOSS MUTATED                      51                              4
  22Q LOSS WILD-TYPE                    95                              9
D80V10, multiclass
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        134                248
  COLON MUCINOUS ADENOCARCINOMA                10                 52
  RECTAL ADENOCARCINOMA                        51                 95
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[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                  R0  R1  R2  RX
  22Q LOSS MUTATED   137   3  15  11
  22Q LOSS WILD-TYPE 309   3  22  18
D80V11, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0              137                309
  R1                3                  3
  R2               15                 22
  RX               11                 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"
D80V12, continuous
D80V13, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3 110
  22Q LOSS WILD-TYPE   2 242
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3  110
  22Q LOSS WILD-TYPE    2  242
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  2
  NOT HISPANIC OR LATINO              110                242
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    60  25
  XP LOSS WILD-TYPE 406 103
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               85               509 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               25               103 
$`XP LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3952 TCGA-AA-3979 
       37.05        19.99        85.05        31.07         2.01        24.00 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-BM-6198 TCGA-4N-A93T TCGA-A6-2678 
      100.01        49.08         5.88        21.24         4.80        42.28 
TCGA-A6-2686 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3548 
       37.02        61.84        56.25        38.99         9.07        33.99 
TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3941 TCGA-AA-3968 TCGA-AA-3989 
       15.02        10.06        38.99        24.00        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       13.94        19.00         0.99        32.02        31.00        33.04 
TCGA-AA-A02F TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6606 
       39.98        26.47        14.50        17.85         5.65        11.74 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CM-5348 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 
        3.19        12.59        22.98        15.02        11.01        13.05 
TCGA-D5-5537 TCGA-D5-6923 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1D9 
       45.40        12.43        12.00        24.43        49.91       140.38 
TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6303 
      131.51        26.47        31.96        33.67         8.35        65.85 
TCGA-G4-6315 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       61.91        26.04        10.98         9.93        15.65        16.80 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       11.90        70.03        37.97        11.84        12.00        32.02 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 
       24.00        34.03        34.03         2.01         6.05        32.98 
TCGA-AG-3881 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6544 
       19.04         3.98        13.94        23.01        41.00        38.56 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-7002 
       13.97        44.02        12.62        57.24       129.27        11.97 
TCGA-F5-6571 
       42.35 

$`XP LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 
       14.93        24.03        29.98        12.99        24.00        50.99 
TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       26.01        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6608 
       15.52        25.08        10.88        75.95       106.75         1.94 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       13.94        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       36.03        31.00        51.98        18.28        55.76        26.43 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.76        43.43        42.90        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.05        37.25        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        16.24        24.92         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       26.01        12.99        14.01        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        2.01        14.01        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        36.95        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
       25.02        27.02        27.02        38.04        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        18.05         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       33.01         0.20        21.44        17.82        17.26        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         5.23        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       13.02        14.04        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.41        13.35        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
      119.70        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
       47.87         1.55        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 
        0.53        47.41        35.31       133.18        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       67.30        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       36.00        26.43        13.78        46.75        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        19.33        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 
        8.42        31.30        21.90        38.70        60.13        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 
       39.48        17.23        43.04        13.55        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       65.98        36.03         7.07        36.03        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       46.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
        1.02        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       31.00        51.98        10.98        25.97        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.99              0.00 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           140.38            148.01 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            24.00             21.99 
[1] "1.0 - 140.4 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D81V2, continuous
D81V3, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    63  26
  XP LOSS WILD-TYPE 385 136
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     63   26
  XP LOSS WILD-TYPE  385  136
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  COLON               63               385
  RECTUM              26               136
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XP LOSS MUTATED        12        0        6        25         0         0
  XP LOSS WILD-TYPE      92        1       31       147        12         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XP LOSS MUTATED           4          1         11         12       14
  XP LOSS WILD-TYPE        20         14         73         43       49
                   vv
clus                STAGE IVA STAGE IVB
  XP LOSS MUTATED           3         1
  XP LOSS WILD-TYPE        21         1
D81V4, multiclass
            clus
vv           XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 12                92
  STAGE IA                 0                 1
  STAGE II                 6                31
  STAGE IIA               25               147
  STAGE IIB                0                12
  STAGE IIC                0                 2
  STAGE III                4                20
  STAGE IIIA               1                14
  STAGE IIIB              11                73
  STAGE IIIC              12                43
  STAGE IV                14                49
  STAGE IVA                3                21
  STAGE IVB                1                 1
[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     1  12  66  11
  XP LOSS WILD-TYPE  19  93 351  58
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               1                19
  T2              12                93
  T3              66               351
  T4              11                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"
                   vv
clus                 N0  N1  N2
  XP LOSS MUTATED    43  21  26
  XP LOSS WILD-TYPE 303 129  89
D81V6, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              43               303
  N1              21               129
  N2              26                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    63  19
  XP LOSS WILD-TYPE 390  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     63   19
  XP LOSS WILD-TYPE  390   69
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              63               390
  1              19                69
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    39  51
  XP LOSS WILD-TYPE 250 274
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     39   51
  XP LOSS WILD-TYPE  250  274
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              39               250
  MALE                51               274
[1] 2 2
[1] FALSE
D81V9, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    69   5
  XP LOSS WILD-TYPE 413  24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     69    5
  XP LOSS WILD-TYPE  413   24
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               69               413
  YES               5                24
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XP LOSS MUTATED                     57                             6
  XP LOSS WILD-TYPE                  325                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XP LOSS MUTATED                      21                              4
  XP LOSS WILD-TYPE                   125                              9
D81V10, multiclass
                                clus
vv                               XP LOSS MUTATED XP LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        57               325
  COLON MUCINOUS ADENOCARCINOMA                6                56
  RECTAL ADENOCARCINOMA                       21               125
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[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                 R0  R1  R2  RX
  XP LOSS MUTATED    63   1   6   4
  XP LOSS WILD-TYPE 383   5  31  25
D81V11, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              63               383
  R1               1                 5
  R2               6                31
  RX               4                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"
D81V12, continuous
D81V13, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     0  48
  XP LOSS WILD-TYPE   5 304
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      0   48
  XP LOSS WILD-TYPE    5  304
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              48               304
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    56  18
  XQ LOSS WILD-TYPE 410 110
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               74               520 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               18               110 
$`XQ LOSS MUTATED`
TCGA-AA-3522 TCGA-AA-3860 TCGA-AA-3952 TCGA-AA-3979 TCGA-CK-5912 TCGA-AG-A01N 
       37.05        31.07         2.01        24.00        49.08        31.00 
TCGA-BM-6198 TCGA-4N-A93T TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-A567 TCGA-AA-3517 
       21.24         4.80        42.28        35.11        61.84        38.99 
TCGA-AA-3519 TCGA-AA-3548 TCGA-AA-3679 TCGA-AA-3837 TCGA-AA-3941 TCGA-AA-3966 
        9.07        33.99        15.02        38.99        24.00         2.01 
TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00R TCGA-AA-A01F 
       21.99         7.96        13.94        19.00         0.99        32.02 
TCGA-AA-A01K TCGA-AA-A02F TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-5543 TCGA-AY-A69D 
       31.00        39.98        26.47        14.50        33.01        17.85 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CK-6748 TCGA-CM-6170 TCGA-CM-6172 
       11.74         3.19        12.59         2.01        15.02        11.01 
TCGA-D5-5537 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1HA 
       45.40        12.00        24.43        49.91       140.38       131.51 
TCGA-DM-A28A TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6322 
       26.47        33.67         8.35        65.85        61.91        26.04 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2693 
       10.98         9.93        16.80        60.13        11.90        37.97 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3600 
       11.84        12.00        32.02        24.00        34.03         6.05 
TCGA-AG-3732 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6544 
       32.98         3.98        13.94        23.01        41.00        38.56 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
       13.97        44.02        12.62        57.24       129.27        32.61 
TCGA-EI-7002 TCGA-F5-6571 
       11.97        42.35 

$`XQ LOSS WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       24.00        50.99        26.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75       100.01         1.94         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 
       17.03        17.03        25.97        15.95        36.03        51.98 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 
       18.28        55.76        26.43        15.62        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       42.90        44.91        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 
        1.02        17.98        15.95        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       34.03        16.08        13.05        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        30.02        34.03        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
       83.24        24.53         5.79        22.42        27.42        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 
        0.46         0.92        27.09        16.31         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       29.56         5.23        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 
        9.04         9.44        11.64        13.41        13.35        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
       10.26       119.70        38.20       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       14.04        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        74.56        67.30        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 
       85.48        39.42        36.00        26.43        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       74.79        18.18        19.33        19.33        15.65        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       42.77        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       38.70        70.03        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3581 
       20.02        24.59        86.63        65.98        36.03         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       36.03        20.05         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
        1.02        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       31.00        51.98        10.98        25.97        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        24.13        51.48         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.99              0.00 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           140.38            148.01 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           24.215            21.830 
[1] "1.0 - 140.4 (24.2)" "0.0 - 148.0 (21.8)"
[1] "hr=" "1.1"
D82V2, continuous
D82V3, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    52  25
  XQ LOSS WILD-TYPE 396 137
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     52   25
  XQ LOSS WILD-TYPE  396  137
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON               52               396
  RECTUM              25               137
[1] 2 2
[1] FALSE
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB STAGE IIC
  XQ LOSS MUTATED        11        0        5        21         1         0
  XQ LOSS WILD-TYPE      93        1       32       151        11         2
                   vv
clus                STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  XQ LOSS MUTATED           1          2          8         10       15
  XQ LOSS WILD-TYPE        23         13         76         45       48
                   vv
clus                STAGE IVA STAGE IVB
  XQ LOSS MUTATED           3         0
  XQ LOSS WILD-TYPE        21         2
D82V4, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 11                93
  STAGE IA                 0                 1
  STAGE II                 5                32
  STAGE IIA               21               151
  STAGE IIB                1                11
  STAGE IIC                0                 2
  STAGE III                1                23
  STAGE IIIA               2                13
  STAGE IIIB               8                76
  STAGE IIIC              10                45
  STAGE IV                15                48
  STAGE IVA                3                21
  STAGE IVB                0                 2
[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     1  13  53  11
  XQ LOSS WILD-TYPE  19  92 364  58
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               1                19
  T2              13                92
  T3              53               364
  T4              11                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"
                   vv
clus                 N0  N1  N2
  XQ LOSS MUTATED    39  19  20
  XQ LOSS WILD-TYPE 307 131  95
D82V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              39               307
  N1              19               131
  N2              20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    53  19
  XQ LOSS WILD-TYPE 400  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     53   19
  XQ LOSS WILD-TYPE  400   69
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              53               400
  1              19                69
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    36  42
  XQ LOSS WILD-TYPE 253 283
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     36   42
  XQ LOSS WILD-TYPE  253  283
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              36               253
  MALE                42               283
[1] 2 2
[1] FALSE
D82V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    58   4
  XQ LOSS WILD-TYPE 424  25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     58    4
  XQ LOSS WILD-TYPE  424   25
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               58               424
  YES               4                25
[1] 2 2
[1] FALSE
                   vv
clus                COLON ADENOCARCINOMA COLON MUCINOUS ADENOCARCINOMA
  XQ LOSS MUTATED                     46                             6
  XQ LOSS WILD-TYPE                  336                            56
                   vv
clus                RECTAL ADENOCARCINOMA RECTAL MUCINOUS ADENOCARCINOMA
  XQ LOSS MUTATED                      22                              3
  XQ LOSS WILD-TYPE                   124                             10
D82V10, multiclass
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  COLON ADENOCARCINOMA                        46               336
  COLON MUCINOUS ADENOCARCINOMA                6                56
  RECTAL ADENOCARCINOMA                       22               124
  RECTAL MUCINOUS ADENOCARCINOMA               3                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                 R0  R1  R2  RX
  XQ LOSS MUTATED    51   1   7   4
  XQ LOSS WILD-TYPE 395   5  30  25
D82V11, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              51               395
  R1               1                 5
  R2               7                30
  RX               4                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"
D82V12, continuous
D82V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     0  42
  XQ LOSS WILD-TYPE   5 310
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0   42
  XQ LOSS WILD-TYPE    5  310
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 5
  NOT HISPANIC OR LATINO              42               310
[1] 2 2
[1] FALSE
