[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"       "-oTACC-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/ACC-TP/10005775/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/10013669/transformed.cor.cli.txt"

nPatients in clinical file=82, in cluster file=90, common to both=80
[1] "Reduce the number of clustering variables from 80 to 75."
[1] 75 80
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                74 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                74 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11                69 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               11                69 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9                71 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                9                71 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                70 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                70 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                68 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                68 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               32                48 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               32                48 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               29                51 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               29                51 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               51                29 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               51                29 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               49                31 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               49                31 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               16                64 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               16                64 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               14                66 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               14                66 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               42                38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               42                38 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               42                38 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               42                38 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               30                50 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               30                50 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34                46 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34                46 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16                64 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16                64 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24                56 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24                56 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                 58 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                 58 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                23                 57 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                23                 57 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 77 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 77 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 76 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 76 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                56                 24 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                56                 24 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                57                 23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                57                 23 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 75 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 75 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                18                 62 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                18                 62 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 70 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 70 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                43                 37 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                43                 37 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                43                 37 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                43                 37 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 76 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 75 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 75 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                49                 31 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                49                 31 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                45                 35 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                45                 35 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                41                 39 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                41                 39 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                44                 36 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                44                 36 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                 54 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                 54 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               35                45 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               35                45 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27                53 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27                53 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18                62 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18                62 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17                63 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17                63 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                65 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                65 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               18                62 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               18                62 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               18                62 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               18                62 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                71 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                71 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                70 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                70 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                73 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                73 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                74 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                74 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17                63 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17                63 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20                60 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20                60 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                76 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                76 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5                75 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5                75 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                67 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                67 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10                70 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10                70 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19                61 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19                61 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               10                70 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               10                70 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                 69 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                 69 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 71 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 71 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                23                 57 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                23                 57 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 58 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 58 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 75 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 75 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 76 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 76 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                33                 47 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                33                 47 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                 63 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                 63 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                20                 60 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                20                 60 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 74 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 74 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 75 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 75 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                29                 51 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                29                 51 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                 56 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                 56 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                36                 44 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                36                 44 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                34                 46 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                34                 46 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 77 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 77 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 77 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 77 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 73 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 73 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 65 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 65 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                 35 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                 35 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                65 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                65 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "RADIATIONTHERAPY"                      
[12] "RADIATIONS.RADIATION.REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCHNUMBER"                           

Input Data has 15 rows and 80 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
          NA           NA         1942           NA           NA         2428 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
          NA           NA         1183           NA           NA           NA 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
        2782           NA         1259           NA         1227         1424 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
         309         1255          670           NA          889          149 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
         674         3688          383          488           NA         1541 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
        1924          950           NA          211         1029         2723 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
          NA         2842          528          253         1130           NA 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
        1414         2673         4673         3659         1525         1091 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
          NA           NA         3897          724          840          628 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
         555          645          487           NA           NA           NA 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
          NA           NA         1589           NA           NA         2222 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
          NA         1858         1916         1949         1583          639 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-P6-A5OH TCGA-PK-A5H9 
         882          365          709           NA           NA          307 
TCGA-PK-A5HA TCGA-PK-A5HB 
         830         1293 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 80 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=46, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 8 39 11 18 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 8 39 11 18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 8 39 11 18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 8 39 11 18 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1Q GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    2  4
  1Q GAIN WILD-TYPE 50 23
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                23 
$`1Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JE TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5LS TCGA-P6-A5OG 
       55.13        69.21         8.32        11.31        29.00        12.59 

$`1Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       22.03        18.48        29.23         4.90        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36        37.15        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14        35.87        12.85         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
        5.23        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        73.05        53.03        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA 
       52.04        21.01        12.00        23.31        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             8.32              4.11 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            69.21            153.63 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           20.795            32.680 
[1] "8.3 - 69.2 (20.8)"  "4.1 - 153.6 (32.7)"
[1] "hr=" "2.8"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1        2         1        2
  1Q GAIN WILD-TYPE       7       32        16       15
D1V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1                 7
  STAGE II                2                32
  STAGE III               1                16
  STAGE IV                2                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"
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    1  2  2  1
  1Q GAIN WILD-TYPE  7 37  9 17
D1V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               1                 7
  T2               2                37
  T3               2                 9
  T4               1                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"
D1V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6  0
  1Q GAIN WILD-TYPE 61 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    0
  1Q GAIN WILD-TYPE   61   10
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               6                61
  1               0                10
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    6  0
  1Q GAIN WILD-TYPE 46 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      6    0
  1Q GAIN WILD-TYPE   46   28
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               6                46
  MALE                 0                28
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1  1
  1Q GAIN WILD-TYPE  7 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    1
  1Q GAIN WILD-TYPE    7   26
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(2) Variable = 2P GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    3  7
  2P GAIN WILD-TYPE 49 20
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                69 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                20 
$`2P GAIN MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JU 
       79.82        16.11        69.21        18.48         4.90         9.50 
TCGA-OR-A5K5 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LL 
        8.32         5.23        39.35        53.03 

$`2P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       38.89        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV 
       29.23        22.16       121.25        12.59        16.04        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       63.25        31.23        18.15         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO 
       32.68        93.44        17.36        37.15        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       21.21        16.01        39.58        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        73.05        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       52.04        21.01        29.00        12.00        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             4.90              4.11 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            79.82            153.63 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           17.295            32.680 
[1] "4.9 - 79.8 (17.3)"  "4.1 - 153.6 (32.7)"
[1] "hr=" "3.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         1        3         4        3
  2P GAIN WILD-TYPE       7       31        13       14
D2V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 1                 7
  STAGE II                3                31
  STAGE III               4                13
  STAGE IV                3                14
[1] 4 2
[1] 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    1  3  3  4
  2P GAIN WILD-TYPE  7 36  8 14
D2V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               1                 7
  T2               3                36
  T3               3                 8
  T4               4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   11  0
  2P GAIN WILD-TYPE 56 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     11    0
  2P GAIN WILD-TYPE   56   10
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              11                56
  1               0                10
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    9  2
  2P GAIN WILD-TYPE 43 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      9    2
  2P GAIN WILD-TYPE   43   26
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               9                43
  MALE                 2                26
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  3
  2P GAIN WILD-TYPE  6 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    3
  2P GAIN WILD-TYPE    6   24
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               3                24
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2Q GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    3  5
  2Q GAIN WILD-TYPE 49 22
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                71 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                5                22 
$`2Q GAIN MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JU TCGA-OR-A5K5 TCGA-OR-A5KX 
       79.82        16.11        69.21         9.50         8.32        35.87 
TCGA-OR-A5LC TCGA-OR-A5LD 
        5.23        39.35 

$`2Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       38.89        30.31        18.12        57.53        91.46        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       18.48        29.23         4.90        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       16.04        50.66        63.25        31.23        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 
       33.83        89.52        32.68        93.44        17.36        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LF 
       18.25        21.21        16.01        39.58        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        12.59        10.09        27.29        42.51 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             5.23              4.11 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            79.82            153.63 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            25.99             31.23 
[1] "5.2 - 79.8 (26.0)"  "4.1 - 153.6 (31.2)"
[1] "hr=" "2.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         1        1         5        2
  2Q GAIN WILD-TYPE       7       33        12       15
D3V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 1                 7
  STAGE II                1                33
  STAGE III               5                12
  STAGE IV                2                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"
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    1  2  3  3
  2Q GAIN WILD-TYPE  7 37  8 15
D3V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               1                 7
  T2               2                37
  T3               3                 8
  T4               3                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"
D3V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    8  1
  2Q GAIN WILD-TYPE 59  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      8    1
  2Q GAIN WILD-TYPE   59    9
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               8                59
  1               1                 9
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    8  1
  2Q GAIN WILD-TYPE 44 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      8    1
  2Q GAIN WILD-TYPE   44   27
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               8                44
  MALE                 1                27
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  4
  2Q GAIN WILD-TYPE  6 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    4
  2Q GAIN WILD-TYPE    6   23
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(4) Variable = 3P GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    8  2
  3P GAIN WILD-TYPE 44 25
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               10                69 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                25 
$`3P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5KO TCGA-OR-A5L8 
       55.13        22.16       121.25        50.66        46.49        18.25 
TCGA-OR-A5LK TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       73.05        12.00        23.31        12.59 

$`3P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       41.26        22.03        18.48        29.23         4.90        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       16.04         9.50        63.25        31.23        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       37.15        11.31        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       35.87        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LL 
       21.76        14.63        52.24        78.41        36.33        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        64.08        52.04        21.01        29.00 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            12.00              4.11 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           121.25            153.63 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            34.90             31.23 
[1] "12.0 - 121.2 (34.9)" "4.1 - 153.6 (31.2)" 
[1] "hr=" "2"  
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         1        4         1        4
  3P GAIN WILD-TYPE       7       30        16       13
D4V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1                 7
  STAGE II                4                30
  STAGE III               1                16
  STAGE IV                4                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                T1 T2 T3 T4
  3P GAIN MUTATED    1  5  2  2
  3P GAIN WILD-TYPE  7 34  9 16
D4V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1                 7
  T2               5                34
  T3               2                 9
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    9  1
  3P GAIN WILD-TYPE 58  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      9    1
  3P GAIN WILD-TYPE   58    9
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               9                58
  1               1                 9
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    6  4
  3P GAIN WILD-TYPE 46 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      6    4
  3P GAIN WILD-TYPE   46   24
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               6                46
  MALE                 4                24
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  4
  3P GAIN WILD-TYPE  7 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    4
  3P GAIN WILD-TYPE    7   23
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3Q GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    9  3
  3Q GAIN WILD-TYPE 43 24
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               12                67 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                24 
$`3Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5KO TCGA-OR-A5L8 
       55.13        22.16       121.25        50.66        46.49        18.25 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       36.33        73.05        29.00        12.00        23.31        12.59 

$`3Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       41.26        22.03        18.48        29.23         4.90        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       16.04         9.50        63.25        31.23        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       37.15        11.31        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       35.87        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LL TCGA-OR-A5LM 
       21.76        14.63        52.24        78.41        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5H9 TCGA-PK-A5HA 
       62.99        64.08        52.04        21.01        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.00              4.11 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           121.25            153.63 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           32.665            31.230 
[1] "12.0 - 121.2 (32.7)" "4.1 - 153.6 (31.2)" 
[1] "hr=" "1.5"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         1        5         1        5
  3Q GAIN WILD-TYPE       7       29        16       12
D5V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 1                 7
  STAGE II                5                29
  STAGE III               1                16
  STAGE IV                5                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                T1 T2 T3 T4
  3Q GAIN MUTATED    1  7  2  2
  3Q GAIN WILD-TYPE  7 32  9 16
D5V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               1                 7
  T2               7                32
  T3               2                 9
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   10  2
  3Q GAIN WILD-TYPE 57  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     10    2
  3Q GAIN WILD-TYPE   57    8
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              10                57
  1               2                 8
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    8  4
  3Q GAIN WILD-TYPE 44 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      8    4
  3Q GAIN WILD-TYPE   44   24
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               8                44
  MALE                 4                24
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    1  5
  3Q GAIN WILD-TYPE  7 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    5
  3Q GAIN WILD-TYPE    7   22
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               5                22
[1] 2 2
[1] FALSE

Clustering(6) Variable = 4P GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   23  9
  4P GAIN WILD-TYPE 29 18
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               32                47 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9                18 
$`4P GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC 
       15.45        12.00        16.11        38.89        30.31        57.53 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       41.39        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K3 TCGA-OR-A5K4 
       22.16       121.25        16.04        50.66        93.44        17.36 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LH 
      153.63        50.14        16.01        39.58        14.63        78.41 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LS 
       73.05        53.03        61.08        62.99        64.08        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI 
       12.00        23.31 

$`4P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB 
       44.55        55.13        63.85        79.82        19.04        18.12 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       91.46        69.21        17.79        18.48        29.23         4.90 
TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       12.59         9.50        63.25        31.23        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       33.83        89.52        32.68         8.32        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       46.49        87.88       120.30        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LJ TCGA-OR-A5LP 
        5.23        39.35        21.76        52.24        36.33        52.04 
TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       21.01        12.59        10.09        27.29        42.51 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            10.16              4.11 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           153.63            128.12 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            39.96             27.62 
[1] "10.2 - 153.6 (40.0)" "4.1 - 128.1 (27.6)" 
[1] "hr=" "1.6"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         3       16         6        6
  4P GAIN WILD-TYPE       5       18        11       11
D6V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 3                 5
  STAGE II               16                18
  STAGE III               6                11
  STAGE IV                6                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                T1 T2 T3 T4
  4P GAIN MUTATED    3 18  4  6
  4P GAIN WILD-TYPE  5 21  7 12
D6V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               3                 5
  T2              18                21
  T3               4                 7
  T4               6                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"
D6V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   27  4
  4P GAIN WILD-TYPE 40  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     27    4
  4P GAIN WILD-TYPE   40    6
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              27                40
  1               4                 6
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   20 12
  4P GAIN WILD-TYPE 32 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     20   12
  4P GAIN WILD-TYPE   32   16
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              20                32
  MALE                12                16
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    4  6
  4P GAIN WILD-TYPE  4 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4    6
  4P GAIN WILD-TYPE    4   21
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO               6                21
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4Q GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   22  7
  4Q GAIN WILD-TYPE 30 20
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               29                50 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                7                20 
$`4Q GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JF 
       15.45        12.00        38.89        30.31        57.53        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ 
       40.34        46.82        10.16        41.26        22.03        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K4 TCGA-OR-A5KU TCGA-OR-A5KW 
      121.25        16.04        50.66        17.36       153.63        50.14 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       16.01        39.58        14.63        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       62.99        64.08        29.00        12.00        23.31 

$`4Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        55.13        63.85        79.82        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JM TCGA-OR-A5JO 
       18.12        91.46        69.21        17.79        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
        4.90        12.59         9.50        63.25        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 
        6.94        33.83        89.52        32.68        93.44         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       37.15        11.31        46.49        87.88       120.30        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       18.25        21.21         5.23        39.35        21.76        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 
       78.41        36.33        52.04        21.01        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            10.16              4.11 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           153.63            128.12 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           39.580            28.425 
[1] "10.2 - 153.6 (39.6)" "4.1 - 128.1 (28.4)" 
[1] "hr=" "1.8"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         3       14         5        6
  4Q GAIN WILD-TYPE       5       20        12       11
D7V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 3                 5
  STAGE II               14                20
  STAGE III               5                12
  STAGE IV                6                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                T1 T2 T3 T4
  4Q GAIN MUTATED    3 16  3  6
  4Q GAIN WILD-TYPE  5 23  8 12
D7V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               3                 5
  T2              16                23
  T3               3                 8
  T4               6                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"
D7V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   24  4
  4Q GAIN WILD-TYPE 43  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     24    4
  4Q GAIN WILD-TYPE   43    6
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              24                43
  1               4                 6
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   18 11
  4Q GAIN WILD-TYPE 34 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     18   11
  4Q GAIN WILD-TYPE   34   17
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              18                34
  MALE                11                17
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  5
  4Q GAIN WILD-TYPE  5 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    5
  4Q GAIN WILD-TYPE    5   22
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO               5                22
[1] 2 2
[1] FALSE

Clustering(8) Variable = 5P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   35 15
  5P GAIN WILD-TYPE 17 12
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               50                29 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               15                12 
$`5P GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       63.85        15.45        12.00        79.82        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       38.89        30.31        57.53        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ 
       40.34        46.82        10.16        41.26        22.03        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        16.04        50.66        18.15         6.94        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5L4 
       93.44        17.36         8.32        46.49       153.63        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
        5.23        14.63        78.41        36.33        73.05        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG 
       23.31        12.59 

$`5P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO 
       44.55        55.13        18.12        91.46        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5K0 
        4.90        12.59         9.50        63.25        31.23        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       32.68        37.15        11.31        87.88       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE 
       35.87        12.85         4.11       128.12        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LL TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       52.24        53.03        10.09        27.29        42.51 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             5.23              4.11 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           153.63            128.12 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            28.31             33.83 
[1] "5.2 - 153.6 (28.3)" "4.1 - 128.1 (33.8)"
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         5       23         9       13
  5P GAIN WILD-TYPE       3       11         8        4
D8V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 5                 3
  STAGE II               23                11
  STAGE III               9                 8
  STAGE IV               13                 4
[1] 4 2
[1] 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    5 25  7 13
  5P GAIN WILD-TYPE  3 14  4  5
D8V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               5                 3
  T2              25                14
  T3               7                 4
  T4              13                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   44  6
  5P GAIN WILD-TYPE 23  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     44    6
  5P GAIN WILD-TYPE   23    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              44                23
  1               6                 4
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   34 17
  5P GAIN WILD-TYPE 18 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     34   17
  5P GAIN WILD-TYPE   18   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              34                18
  MALE                17                11
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7 15
  5P GAIN WILD-TYPE  1 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   15
  5P GAIN WILD-TYPE    1   12
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              15                12
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   33 15
  5Q GAIN WILD-TYPE 19 12
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               48                31 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               15                12 
$`5Q GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       63.85        15.45        12.00        79.82        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       38.89        30.31        57.53        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JT 
       40.34        46.82        10.16        22.03        22.16        16.04 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       50.66        63.25        18.15        89.52        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5L4 TCGA-OR-A5L5 
        8.32        46.49       153.63        12.85        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       14.63        78.41        73.05        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       52.04        21.01        29.00        12.00        23.31        12.59 

$`5Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JK TCGA-OR-A5JM 
       44.55        55.13        18.12        91.46        41.26        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JX 
       29.23         4.90       121.25        12.59         9.50        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT 
        6.94        33.83        32.68        37.15        11.31        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5LD 
      120.30        50.14        35.87         4.11       128.12        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-PK-A5H9 TCGA-PK-A5HA 
       21.76        52.24        36.33        53.03        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             5.23              4.11 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           153.63            128.12 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            25.71             35.87 
[1] "5.2 - 153.6 (25.7)" "4.1 - 128.1 (35.9)"
[1] "hr=" "1.2"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         4       23         9       12
  5Q GAIN WILD-TYPE       4       11         8        5
D9V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 4                 4
  STAGE II               23                11
  STAGE III               9                 8
  STAGE IV               12                 5
[1] 4 2
[1] 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    4 24  7 13
  5Q GAIN WILD-TYPE  4 15  4  5
D9V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               4                 4
  T2              24                15
  T3               7                 4
  T4              13                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   42  6
  5Q GAIN WILD-TYPE 25  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     42    6
  5Q GAIN WILD-TYPE   25    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              42                25
  1               6                 4
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   34 15
  5Q GAIN WILD-TYPE 18 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     34   15
  5Q GAIN WILD-TYPE   18   13
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              34                18
  MALE                15                13
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7 15
  5Q GAIN WILD-TYPE  1 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   15
  5Q GAIN WILD-TYPE    1   12
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              15                12
[1] 2 2
[1] FALSE

Clustering(10) Variable = 6P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    8  8
  6P GAIN WILD-TYPE 44 19
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               16                63 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8                19 
$`6P GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC 
       15.45        79.82        16.11        19.04        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KZ 
       69.21        22.03        18.48        46.49        87.88         4.11 
TCGA-OR-A5L4 TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       23.80        73.05        61.08        62.99 

$`6P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JB 
       44.55        55.13        63.85        12.00        38.89        18.12 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       91.46        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       41.26        29.23         4.90        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       16.04         9.50        50.66        63.25        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
        8.32        37.15        11.31       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       35.87        12.85       128.12        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       21.21        16.01        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO 
       14.63        52.24        78.41        36.33        53.03        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       52.04        21.01        29.00        12.00        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             4.11              4.90 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            87.88            153.63 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            38.40             31.23 
[1] "4.1 - 87.9 (38.4)"  "4.9 - 153.6 (31.2)"
[1] "hr=" "1.3"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         3        5         3        4
  6P GAIN WILD-TYPE       5       29        14       13
D10V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 3                 5
  STAGE II                5                29
  STAGE III               3                14
  STAGE IV                4                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                T1 T2 T3 T4
  6P GAIN MUTATED    3  5  3  4
  6P GAIN WILD-TYPE  5 34  8 14
D10V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               3                 5
  T2               5                34
  T3               3                 8
  T4               4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   14  1
  6P GAIN WILD-TYPE 53  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     14    1
  6P GAIN WILD-TYPE   53    9
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              14                53
  1               1                 9
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   11  5
  6P GAIN WILD-TYPE 41 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     11    5
  6P GAIN WILD-TYPE   41   23
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              11                41
  MALE                 5                23
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    4  4
  6P GAIN WILD-TYPE  4 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    4
  6P GAIN WILD-TYPE    4   23
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6Q GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    8  6
  6Q GAIN WILD-TYPE 44 21
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               14                65 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                21 
$`6Q GAIN MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JL 
       79.82        19.04        30.31        57.53        69.21        22.03 
TCGA-OR-A5KT TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5LE TCGA-OR-A5LK TCGA-OR-A5LM 
       87.88         4.11        23.80        21.76        73.05        61.08 
TCGA-OR-A5LN TCGA-PK-A5HA 
       62.99        27.29 

$`6Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 
       44.55        55.13        63.85        15.45        12.00        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       38.89        18.12        91.46        41.39        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        10.16        41.26        18.48        29.23         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       22.16       121.25        12.59        16.04         9.50        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       63.25        31.23        18.15         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       32.68        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       46.49       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       39.58         5.23        39.35        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       36.33        53.03        64.08        52.04        21.01        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       12.00        23.31        12.59        10.09        42.51 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             4.11              4.90 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            87.88            153.63 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            43.92             31.23 
[1] "4.1 - 87.9 (43.9)"  "4.9 - 153.6 (31.2)"
[1] "hr=" "1"  
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         3        6         2        1
  6Q GAIN WILD-TYPE       5       28        15       16
D11V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 3                 5
  STAGE II                6                28
  STAGE III               2                15
  STAGE IV                1                16
[1] 4 2
[1] 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    3  6  1  2
  6Q GAIN WILD-TYPE  5 33 10 16
D11V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3                 5
  T2               6                33
  T3               1                10
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   13  0
  6Q GAIN WILD-TYPE 54 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     13    0
  6Q GAIN WILD-TYPE   54   10
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              13                54
  1               0                10
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    7  7
  6Q GAIN WILD-TYPE 45 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7    7
  6Q GAIN WILD-TYPE   45   21
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               7                45
  MALE                 7                21
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    2  4
  6Q GAIN WILD-TYPE  6 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    4
  6Q GAIN WILD-TYPE    6   23
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(12) Variable = 7P GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   28 14
  7P GAIN WILD-TYPE 24 13
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               42                37 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               14                13 
$`7P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       55.13        63.85        12.00        79.82        16.11        19.04 
TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JK 
       30.31        41.39        17.79        40.34        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       22.03        22.16       121.25        16.04        50.66        31.23 
TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KU 
       18.15        89.52        93.44         8.32        46.49       153.63 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LA 
       50.14        12.85         4.11        23.80        18.25        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.58         5.23        14.63        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OU-A5PI 
       61.08        62.99        64.08        52.04        29.00        23.31 

$`7P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       44.55        15.45        38.89        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       69.21        46.82        18.48        29.23         4.90        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K4 
        9.50        63.25         6.94        33.83        32.68        17.36 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 
       37.15        11.31        87.88       120.30        35.87       128.12 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       27.62        20.65        21.21        39.35        21.76        52.24 
TCGA-OR-A5LL TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       53.03        21.01        12.00        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             4.11              4.90 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           153.63            128.12 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            33.78             29.23 
[1] "4.1 - 153.6 (33.8)" "4.9 - 128.1 (29.2)"
[1] "hr=" "1.2"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         2       19         9       12
  7P GAIN WILD-TYPE       6       15         8        5
D12V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 2                 6
  STAGE II               19                15
  STAGE III               9                 8
  STAGE IV               12                 5
[1] 4 2
[1] 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    2 22  7 11
  7P GAIN WILD-TYPE  6 17  4  7
D12V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               2                 6
  T2              22                17
  T3               7                 4
  T4              11                 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"
D12V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   35  7
  7P GAIN WILD-TYPE 32  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     35    7
  7P GAIN WILD-TYPE   32    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              35                32
  1               7                 3
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   28 14
  7P GAIN WILD-TYPE 24 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     28   14
  7P GAIN WILD-TYPE   24   14
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              28                24
  MALE                14                14
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6 13
  7P GAIN WILD-TYPE  2 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   13
  7P GAIN WILD-TYPE    2   14
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO              13                14
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7Q GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   28 14
  7Q GAIN WILD-TYPE 24 13
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               42                37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               14                13 
$`7Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       55.13        63.85        12.00        79.82        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ 
       38.89        30.31        41.39        17.79        40.34        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       41.26        22.03        22.16       121.25        16.04        50.66 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5KO TCGA-OR-A5KU 
       31.23        18.15        89.52        93.44        46.49       153.63 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LA 
       50.14        12.85         4.11        23.80        18.25        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.58         5.23        14.63        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OU-A5PI 
       61.08        62.99        64.08        52.04        29.00        23.31 

$`7Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.55        15.45        18.12        57.53        91.46        69.21 
TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU 
       46.82        18.48        29.23         4.90        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K4 TCGA-OR-A5K5 
       63.25         6.94        33.83        32.68        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 
       37.15        11.31        87.88       120.30        35.87       128.12 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       27.62        20.65        21.21        39.35        21.76        52.24 
TCGA-OR-A5LL TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       53.03        21.01        12.00        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             4.11              4.90 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           153.63            128.12 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            37.61             27.62 
[1] "4.1 - 153.6 (37.6)" "4.9 - 128.1 (27.6)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         2       20         8       12
  7Q GAIN WILD-TYPE       6       14         9        5
D13V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 2                 6
  STAGE II               20                14
  STAGE III               8                 9
  STAGE IV               12                 5
[1] 4 2
[1] 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    2 23  6 11
  7Q GAIN WILD-TYPE  6 16  5  7
D13V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               2                 6
  T2              23                16
  T3               6                 5
  T4              11                 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"
D13V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   35  7
  7Q GAIN WILD-TYPE 32  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     35    7
  7Q GAIN WILD-TYPE   32    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              35                32
  1               7                 3
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   28 14
  7Q GAIN WILD-TYPE 24 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     28   14
  7Q GAIN WILD-TYPE   24   14
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              28                24
  MALE                14                14
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 13
  7Q GAIN WILD-TYPE  1 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   13
  7Q GAIN WILD-TYPE    1   14
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              13                14
[1] 2 2
[1] FALSE

Clustering(14) Variable = 8P GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   22  8
  8P GAIN WILD-TYPE 30 19
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               30                49 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                19 
$`8P GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JH 
       15.45        12.00        79.82        38.89        57.53        40.34 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       41.26        18.48         4.90        22.16       121.25        16.04 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K9 
       50.66        31.23         6.94        89.52        17.36        11.31 
TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L5 TCGA-OR-A5L8 
       46.49       153.63        50.14         4.11        27.62        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LN TCGA-OR-A5LR 
       21.21        16.01         5.23        14.63        62.99        21.01 

$`8P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       44.55        55.13        63.85        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI 
       18.12        91.46        69.21        41.39        17.79        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW 
       10.16        22.03        29.23        12.59         9.50        63.25 
TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 
       18.15        33.83        32.68        93.44         8.32        37.15 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 
       87.88       120.30        35.87        12.85       128.12        23.80 
TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH 
       20.65        39.58        39.35        21.76        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        73.05        53.03        61.08        64.08        52.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       29.00        12.00        23.31        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             4.11              8.32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           153.63            128.12 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           21.685            35.870 
[1] "4.1 - 153.6 (21.7)" "8.3 - 128.1 (35.9)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         2       17         5        5
  8P GAIN WILD-TYPE       6       17        12       12
D14V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 2                 6
  STAGE II               17                17
  STAGE III               5                12
  STAGE IV                5                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                T1 T2 T3 T4
  8P GAIN MUTATED    2 18  3  6
  8P GAIN WILD-TYPE  6 21  8 12
D14V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               2                 6
  T2              18                21
  T3               3                 8
  T4               6                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"
D14V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   27  2
  8P GAIN WILD-TYPE 40  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     27    2
  8P GAIN WILD-TYPE   40    8
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              27                40
  1               2                 8
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   20 10
  8P GAIN WILD-TYPE 32 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     20   10
  8P GAIN WILD-TYPE   32   18
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              20                32
  MALE                10                18
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  9
  8P GAIN WILD-TYPE  4 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    9
  8P GAIN WILD-TYPE    4   18
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO               9                18
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   25  9
  8Q GAIN WILD-TYPE 27 18
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34                45 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                9                18 
$`8Q GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JF 
       15.45        12.00        79.82        38.89        57.53        41.39 
TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        10.16        41.26        18.48         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        16.04        50.66        31.23         6.94        89.52 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW 
       17.36         8.32        11.31        46.49       153.63        50.14 
TCGA-OR-A5KZ TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC 
        4.11        27.62        18.25        21.21        16.01         5.23 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LN TCGA-OR-A5LR 
       39.35        14.63        62.99        21.01 

$`8Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       44.55        55.13        63.85        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JL 
       18.12        91.46        69.21        17.79        46.82        22.03 
TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
       29.23        12.59         9.50        63.25        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       32.68        93.44        37.15        87.88       120.30        35.87 
TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LE 
       12.85       128.12        23.80        20.65        39.58        21.76 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       64.08        52.04        29.00        12.00        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             4.11              9.50 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           153.63            128.12 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           21.685            35.870 
[1] "4.1 - 153.6 (21.7)" "9.5 - 128.1 (35.9)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         2       18         7        6
  8Q GAIN WILD-TYPE       6       16        10       11
D15V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 2                 6
  STAGE II               18                16
  STAGE III               7                10
  STAGE IV                6                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                T1 T2 T3 T4
  8Q GAIN MUTATED    2 19  4  8
  8Q GAIN WILD-TYPE  6 20  7 10
D15V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               2                 6
  T2              19                20
  T3               4                 7
  T4               8                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"
D15V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   30  3
  8Q GAIN WILD-TYPE 37  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     30    3
  8Q GAIN WILD-TYPE   37    7
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              30                37
  1               3                 7
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   22 12
  8Q GAIN WILD-TYPE 30 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     22   12
  8Q GAIN WILD-TYPE   30   16
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              22                30
  MALE                12                16
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4 10
  8Q GAIN WILD-TYPE  4 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   10
  8Q GAIN WILD-TYPE    4   17
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              10                17
[1] 2 2
[1] FALSE

Clustering(16) Variable = 9P GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    8  8
  9P GAIN WILD-TYPE 44 19
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               16                63 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                19 
$`9P GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG 
       15.45        12.00        16.11        30.31        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JQ TCGA-OR-A5KO TCGA-OR-A5KY TCGA-OR-A5LJ 
       40.34        10.16        22.16        46.49        12.85        36.33 
TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       53.03        29.00        12.00        23.31 

$`9P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       44.55        55.13        63.85        79.82        19.04        38.89 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JI TCGA-OR-A5JK 
       18.12        57.53        91.46        69.21        46.82        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       22.03        18.48        29.23         4.90       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       16.04         9.50        50.66        63.25        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        37.15        11.31        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LK 
       39.35        21.76        14.63        52.24        78.41        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG 
       61.08        62.99        64.08        52.04        21.01        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            10.16              4.11 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            53.03            153.63 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           22.735            35.870 
[1] "10.2 - 53.0 (22.7)" "4.1 - 153.6 (35.9)"
[1] "hr=" "2.8"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         0        5         3        8
  9P GAIN WILD-TYPE       8       29        14        9
D16V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0                 8
  STAGE II                5                29
  STAGE III               3                14
  STAGE IV                8                 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                T1 T2 T3 T4
  9P GAIN MUTATED    0  7  3  6
  9P GAIN WILD-TYPE  8 32  8 12
D16V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0                 8
  T2               7                32
  T3               3                 8
  T4               6                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"
D16V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   10  6
  9P GAIN WILD-TYPE 57  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     10    6
  9P GAIN WILD-TYPE   57    4
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              10                57
  1               6                 4
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   12  4
  9P GAIN WILD-TYPE 40 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     12    4
  9P GAIN WILD-TYPE   40   24
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              12                40
  MALE                 4                24
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  4
  9P GAIN WILD-TYPE  5 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    4
  9P GAIN WILD-TYPE    5   23
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9Q GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   10 13
  9Q GAIN WILD-TYPE 42 14
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               23                56 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               13                14 
$`9Q GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE 
       15.45        12.00        16.11        38.89        30.31        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JQ TCGA-OR-A5JY 
       41.39        17.79        40.34        10.16        22.16        18.15 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5LB 
       33.83        32.68        46.49        12.85         4.11        39.58 
TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       36.33        53.03        29.00        12.00        23.31 

$`9Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JB 
       44.55        55.13        63.85        79.82        19.04        18.12 
TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM 
       57.53        91.46        46.82        41.26        22.03        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
       29.23         4.90       121.25        12.59        16.04         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
       50.66        63.25        31.23         6.94        89.52        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36         8.32        37.15        11.31        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
      120.30        50.14        35.87       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD 
       20.65        18.25        21.21        16.01         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LM 
       21.76        14.63        52.24        78.41        73.05        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 
       62.99        64.08        52.04        21.01        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             4.11              4.90 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            69.21            153.63 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            29.00             36.51 
[1] "4.1 - 69.2 (29.0)"  "4.9 - 153.6 (36.5)"
[1] "hr=" "3.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1        8         4       11
  9Q GAIN WILD-TYPE       7       26        13        6
D17V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                 7
  STAGE II                8                26
  STAGE III               4                13
  STAGE IV               11                 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                T1 T2 T3 T4
  9Q GAIN MUTATED    1 10  3 10
  9Q GAIN WILD-TYPE  7 29  8  8
D17V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                 7
  T2              10                29
  T3               3                 8
  T4              10                 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"
D17V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   17  7
  9Q GAIN WILD-TYPE 50  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     17    7
  9Q GAIN WILD-TYPE   50    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              17                50
  1               7                 3
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   18  6
  9Q GAIN WILD-TYPE 34 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     18    6
  9Q GAIN WILD-TYPE   34   22
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              18                34
  MALE                 6                22
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4  7
  9Q GAIN WILD-TYPE  4 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4    7
  9Q GAIN WILD-TYPE    4   20
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO               7                20
[1] 2 2
[1] FALSE

Clustering(18) Variable = 10P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   11 11
  10P GAIN WILD-TYPE 41 16
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                22                 57 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                11                 16 
$`10P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JF 
       55.13        12.00        16.11        38.89        57.53        41.39 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5KO TCGA-OR-A5KY 
       41.26         4.90        31.23        32.68        46.49        12.85 
TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LO 
       18.25        39.58         5.23        39.35        36.33        64.08 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       29.00        12.00        23.31        12.59 

$`10P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA 
       44.55        63.85        15.45        79.82        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        91.46        69.21        17.79        40.34        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       10.16        22.03        18.48        29.23        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       12.59        16.04         9.50        50.66        63.25        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        33.83        89.52        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       37.15        11.31        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       21.21        16.01        21.76        14.63        52.24        78.41 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        61.08        62.99        52.04        21.01 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              4.90               4.11 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             64.08             153.63 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            31.955             30.310 
[1] "4.9 - 64.1 (32.0)"  "4.1 - 153.6 (30.3)"
[1] "hr=" "2.5"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0        6         6        9
  10P GAIN WILD-TYPE       8       28        11        8
D18V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 6                 28
  STAGE III                6                 11
  STAGE IV                 9                  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                 T1 T2 T3 T4
  10P GAIN MUTATED    0  8  4  9
  10P GAIN WILD-TYPE  8 31  7  9
D18V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  8
  T2                8                 31
  T3                4                  7
  T4                9                  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"
D18V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   18  3
  10P GAIN WILD-TYPE 49  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     18    3
  10P GAIN WILD-TYPE   49    7
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               18                 49
  1                3                  7
[1] 2 2
[1] FALSE
D18V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   14  8
  10P GAIN WILD-TYPE 38 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     14    8
  10P GAIN WILD-TYPE   38   20
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               14                 38
  MALE                  8                 20
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  9
  10P GAIN WILD-TYPE  4 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    9
  10P GAIN WILD-TYPE    4   18
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO                9                 18
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED   10 12
  10Q GAIN WILD-TYPE 42 15
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                 57 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                12                 15 
$`10Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JF 
       55.13        12.00        16.11        38.89        57.53        41.39 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5KY 
       41.26        18.48         4.90        31.23        32.68        12.85 
TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LJ TCGA-OR-A5LO 
       18.25        39.58         5.23        39.35        36.33        64.08 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       29.00        12.00        23.31        12.59 

$`10Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA 
       44.55        63.85        15.45        79.82        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        91.46        69.21        17.79        40.34        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       10.16        22.03        29.23        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       16.04         9.50        50.66        63.25        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       33.83        89.52        93.44        17.36         8.32        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       35.87         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       21.21        16.01        21.76        14.63        52.24        78.41 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        61.08        62.99        52.04        21.01 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              4.90               4.11 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             64.08             153.63 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            30.115             33.830 
[1] "4.9 - 64.1 (30.1)"  "4.1 - 153.6 (33.8)"
[1] "hr=" "3.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        6         6       10
  10Q GAIN WILD-TYPE       8       28        11        7
D19V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 6                 28
  STAGE III                6                 11
  STAGE IV                10                  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                 T1 T2 T3 T4
  10Q GAIN MUTATED    0  8  4 10
  10Q GAIN WILD-TYPE  8 31  7  8
D19V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  8
  T2                8                 31
  T3                4                  7
  T4               10                  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"
D19V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   19  3
  10Q GAIN WILD-TYPE 48  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     19    3
  10Q GAIN WILD-TYPE   48    7
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               19                 48
  1                3                  7
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   15  8
  10Q GAIN WILD-TYPE 37 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     15    8
  10Q GAIN WILD-TYPE   37   20
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               15                 37
  MALE                  8                 20
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    4  9
  10Q GAIN WILD-TYPE  4 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4    9
  10Q GAIN WILD-TYPE    4   18
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO                9                 18
[1] 2 2
[1] FALSE

Clustering(20) Variable = 11P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    0  2
  11P GAIN WILD-TYPE 52 25
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 77 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 25 
$`11P GAIN MUTATED`
TCGA-OR-A5LD TCGA-P6-A5OG 
       39.35        12.59 

$`11P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        38.89        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       91.46        69.21        41.39        17.79        40.34        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       10.16        41.26        22.03        18.48        29.23         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       22.16       121.25        12.59        16.04         9.50        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       63.25        31.23        18.15         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       32.68        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE 
       18.25        21.21        16.01        39.58         5.23        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        64.08        52.04        21.01        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.00        23.31        10.09        27.29        42.51 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.59               4.11 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             39.35             153.63 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             25.97              31.23 
[1] "12.6 - 39.4 (26.0)" "4.1 - 153.6 (31.2)"
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0        0         1        2
  11P GAIN WILD-TYPE       8       34        16       15
D20V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 0                 34
  STAGE III                1                 16
  STAGE IV                 2                 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"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    0  0  0  3
  11P GAIN WILD-TYPE  8 39 11 15
D20V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                0                  8
  T2                0                 39
  T3                0                 11
  T4                3                 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"
D20V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  0
  11P GAIN WILD-TYPE 64 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    0
  11P GAIN WILD-TYPE   64   10
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                3                 64
  1                0                 10
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  1
  11P GAIN WILD-TYPE 50 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    1
  11P GAIN WILD-TYPE   50   27
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 50
  MALE                  1                 27
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    0  3
  11P GAIN WILD-TYPE  8 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    3
  11P GAIN WILD-TYPE    8   24
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                3                 24
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    1  3
  11Q GAIN WILD-TYPE 51 24
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 75 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 24 
$`11Q GAIN MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5K5 TCGA-OR-A5LD TCGA-P6-A5OG 
       16.11         8.32        39.35        12.59 

$`11Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.26        22.03        18.48        29.23         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        16.04         9.50        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15         6.94        33.83        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       93.44        17.36        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       16.01        39.58         5.23        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              8.32               4.11 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             39.35             153.63 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             14.35              32.68 
[1] "8.3 - 39.4 (14.3)"  "4.1 - 153.6 (32.7)"
[1] "hr=" "5.7"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0        0         3        1
  11Q GAIN WILD-TYPE       8       34        14       16
D21V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 0                 34
  STAGE III                3                 14
  STAGE IV                 1                 16
[1] 4 2
[1] 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    0  0  2  2
  11Q GAIN WILD-TYPE  8 39  9 16
D21V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                0                  8
  T2                0                 39
  T3                2                  9
  T4                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    4  0
  11Q GAIN WILD-TYPE 63 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4    0
  11Q GAIN WILD-TYPE   63   10
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                4                 63
  1                0                 10
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  1
  11Q GAIN WILD-TYPE 49 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    1
  11Q GAIN WILD-TYPE   49   27
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 49
  MALE                  1                 27
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  2
  11Q GAIN WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    2
  11Q GAIN WILD-TYPE    7   25
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(22) Variable = 12P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   36 19
  12P GAIN WILD-TYPE 16  8
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                55                 24 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                19                  8 
$`12P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        57.53        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       18.48         4.90        22.16       121.25        16.04        50.66 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23         6.94        89.52        32.68        93.44        17.36 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 
      153.63        50.14        12.85         4.11        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       39.35        14.63        78.41        36.33        73.05        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI 
       23.31 

$`12P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JU 
       44.55        18.12        91.46        29.23        12.59         9.50 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       63.25        18.15        33.83         8.32        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5LE 
       46.49        87.88       120.30        35.87       128.12        21.76 
TCGA-OR-A5LG TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       52.24        53.03        12.59        10.09        27.29        42.51 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              4.11               8.32 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            153.63             128.12 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             30.31              34.85 
[1] "4.1 - 153.6 (30.3)" "8.3 - 128.1 (34.8)"
[1] "hr=" "1"  
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         5       25        12       13
  12P GAIN WILD-TYPE       3        9         5        4
D22V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  5                  3
  STAGE II                25                  9
  STAGE III               12                  5
  STAGE IV                13                  4
[1] 4 2
[1] 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    5 28  8 14
  12P GAIN WILD-TYPE  3 11  3  4
D22V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                5                  3
  T2               28                 11
  T3                8                  3
  T4               14                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   48  7
  12P GAIN WILD-TYPE 19  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     48    7
  12P GAIN WILD-TYPE   19    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               48                 19
  1                7                  3
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   35 21
  12P GAIN WILD-TYPE 17  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     35   21
  12P GAIN WILD-TYPE   17    7
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               35                 17
  MALE                 21                  7
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8 17
  12P GAIN WILD-TYPE  0 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8   17
  12P GAIN WILD-TYPE    0   10
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO               17                 10
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   38 18
  12Q GAIN WILD-TYPE 14  9
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                56                 23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                  9 
$`12Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        57.53        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       17.79        40.34        46.82        10.16        41.26        22.03 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
        4.90        22.16       121.25        16.04        50.66        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 
      153.63        50.14        35.87        12.85         4.11        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
        5.23        39.35        14.63        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        64.08        52.04        21.01        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI 
       12.00        23.31 

$`12Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JS 
       44.55        18.12        91.46        18.48        29.23        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K6 TCGA-OR-A5K9 
        9.50        63.25        18.15        33.83        37.15        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LG 
       46.49        87.88       120.30       128.12        21.76        52.24 
TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       53.03        12.59        10.09        27.29        42.51 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              4.11               9.50 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            153.63             128.12 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             30.77              33.83 
[1] "4.1 - 153.6 (30.8)" "9.5 - 128.1 (33.8)"
[1] "hr=" "1.2"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         5       25        14       12
  12Q GAIN WILD-TYPE       3        9         3        5
D23V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  5                  3
  STAGE II                25                  9
  STAGE III               14                  3
  STAGE IV                12                  5
[1] 4 2
[1] 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    5 29  9 13
  12Q GAIN WILD-TYPE  3 10  2  5
D23V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                5                  3
  T2               29                 10
  T3                9                  2
  T4               13                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   48  8
  12Q GAIN WILD-TYPE 19  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     48    8
  12Q GAIN WILD-TYPE   19    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               48                 19
  1                8                  2
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   36 21
  12Q GAIN WILD-TYPE 16  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     36   21
  12Q GAIN WILD-TYPE   16    7
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               36                 16
  MALE                 21                  7
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8 18
  12Q GAIN WILD-TYPE  0  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8   18
  12Q GAIN WILD-TYPE    0    9
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO               18                  9
[1] 2 2
[1] FALSE

Clustering(24) Variable = 13Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    3  2
  13Q GAIN WILD-TYPE 49 25
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 5                 74 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 25 
$`13Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JL TCGA-OR-A5KW TCGA-OR-A5LC TCGA-OR-A5LM 
       55.13        22.03        50.14         5.23        61.08 

$`13Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       41.26        18.48        29.23         4.90        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       17.36         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      153.63       120.30        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       39.58        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        73.05        53.03        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       21.01        29.00        12.00        23.31        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              5.23               4.11 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             61.08             153.63 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             50.14              30.77 
[1] "5.2 - 61.1 (50.1)"  "4.1 - 153.6 (30.8)"
[1] "hr=" "1.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         1        1         1        2
  13Q GAIN WILD-TYPE       7       33        16       15
D24V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                  7
  STAGE II                 1                 33
  STAGE III                1                 16
  STAGE IV                 2                 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"
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    1  2  1  1
  13Q GAIN WILD-TYPE  7 37 10 17
D24V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                  7
  T2                2                 37
  T3                1                 10
  T4                1                 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"
D24V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  1
  13Q GAIN WILD-TYPE 63  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    1
  13Q GAIN WILD-TYPE   63    9
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                4                 63
  1                1                  9
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  1
  13Q GAIN WILD-TYPE 48 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    1
  13Q GAIN WILD-TYPE   48   27
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 48
  MALE                  1                 27
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  2
  13Q GAIN WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    2
  13Q GAIN WILD-TYPE    7   25
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(25) Variable = 14Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   11  7
  14Q GAIN WILD-TYPE 41 20
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                18                 61 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                 20 
$`14Q GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG 
       63.85        15.45        12.00        30.31        69.21        17.79 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5KO TCGA-OR-A5L4 TCGA-OR-A5L8 
       10.16        22.03         4.90        46.49        23.80        18.25 
TCGA-OR-A5LB TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI 
       39.58        53.03        61.08        64.08        29.00        23.31 

$`14Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 
       44.55        55.13        79.82        16.11        19.04        38.89 
TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI 
       18.12        57.53        91.46        41.39        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       41.26        18.48        29.23        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       16.04         9.50        50.66        63.25        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
        8.32        37.15        11.31        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L5 
       50.14        35.87        12.85         4.11       128.12        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       20.65        21.21        16.01         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN 
       14.63        52.24        78.41        36.33        73.05        62.99 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       52.04        21.01        12.00        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              4.90               4.11 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             69.21             153.63 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             26.40              33.83 
[1] "4.9 - 69.2 (26.4)"  "4.1 - 153.6 (33.8)"
[1] "hr=" "1.3"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         2        6         3        7
  14Q GAIN WILD-TYPE       6       28        14       10
D25V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  2                  6
  STAGE II                 6                 28
  STAGE III                3                 14
  STAGE IV                 7                 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                 T1 T2 T3 T4
  14Q GAIN MUTATED    2  7  2  7
  14Q GAIN WILD-TYPE  6 32  9 11
D25V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                2                  6
  T2                7                 32
  T3                2                  9
  T4                7                 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"
D25V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   14  4
  14Q GAIN WILD-TYPE 53  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     14    4
  14Q GAIN WILD-TYPE   53    6
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               14                 53
  1                4                  6
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   12  6
  14Q GAIN WILD-TYPE 40 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     12    6
  14Q GAIN WILD-TYPE   40   22
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               12                 40
  MALE                  6                 22
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    3  5
  14Q GAIN WILD-TYPE  5 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    5
  14Q GAIN WILD-TYPE    5   22
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO                5                 22
[1] 2 2
[1] FALSE

Clustering(26) Variable = 15Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    6  4
  15Q GAIN WILD-TYPE 46 23
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                10                 69 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 23 
$`15Q GAIN MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5KU TCGA-OR-A5KW 
       30.31        57.53        41.26        22.03       153.63        50.14 
TCGA-OR-A5LB TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       39.58        53.03        61.08        64.08 

$`15Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE 
       16.11        19.04        38.89        18.12        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM 
       41.39        17.79        40.34        46.82        10.16        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       29.23         4.90        22.16       121.25        12.59        16.04 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
        9.50        50.66        63.25        31.23        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       37.15        11.31        46.49        87.88       120.30        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       18.25        21.21        16.01         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN 
       14.63        52.24        78.41        36.33        73.05        62.99 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       52.04        21.01        29.00        12.00        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             22.03               4.11 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            153.63             128.12 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            51.585             27.620 
[1] "22.0 - 153.6 (51.6)" "4.1 - 128.1 (27.6)" 
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         1        4         1        3
  15Q GAIN WILD-TYPE       7       30        16       14
D26V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  1                  7
  STAGE II                 4                 30
  STAGE III                1                 16
  STAGE IV                 3                 14
[1] 4 2
[1] 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    1  5  0  3
  15Q GAIN WILD-TYPE  7 34 11 15
D26V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                1                  7
  T2                5                 34
  T3                0                 11
  T4                3                 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"
D26V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    8  1
  15Q GAIN WILD-TYPE 59  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      8    1
  15Q GAIN WILD-TYPE   59    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                8                 59
  1                1                  9
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    6  4
  15Q GAIN WILD-TYPE 46 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      6    4
  15Q GAIN WILD-TYPE   46   24
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                6                 46
  MALE                  4                 24
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    0  3
  15Q GAIN WILD-TYPE  8 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    3
  15Q GAIN WILD-TYPE    8   24
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                3                 24
[1] 2 2
[1] FALSE

Clustering(27) Variable = 16P GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   32 10
  16P GAIN WILD-TYPE 20 17
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                42                 37 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                 17 
$`16P GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JF 
       63.85        12.00        38.89        30.31        57.53        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JQ 
       17.79        40.34        46.82        10.16        41.26        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        16.04        50.66        31.23         6.94        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW 
       93.44        17.36         8.32        46.49       153.63        50.14 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       12.85         4.11        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LL 
       21.21        16.01        39.58         5.23        14.63        53.03 
TCGA-OR-A5LM TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       61.08        52.04        21.01        29.00        12.00        23.31 

$`16P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        55.13        15.45        79.82        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       18.12        91.46        69.21        22.03        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
        4.90        12.59         9.50        63.25        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       32.68        37.15        11.31        87.88       120.30        35.87 
TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
      128.12        39.35        21.76        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LO TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       73.05        62.99        64.08        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              4.11               4.90 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            153.63             128.12 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             28.31              35.87 
[1] "4.1 - 153.6 (28.3)" "4.9 - 128.1 (35.9)"
[1] "hr=" "1.6"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         3       20         9       10
  16P GAIN WILD-TYPE       5       14         8        7
D27V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  3                  5
  STAGE II                20                 14
  STAGE III                9                  8
  STAGE IV                10                  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                 T1 T2 T3 T4
  16P GAIN MUTATED    3 22  5 12
  16P GAIN WILD-TYPE  5 17  6  6
D27V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                  5
  T2               22                 17
  T3                5                  6
  T4               12                  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"
D27V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   37  5
  16P GAIN WILD-TYPE 30  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     37    5
  16P GAIN WILD-TYPE   30    5
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               37                 30
  1                5                  5
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   26 17
  16P GAIN WILD-TYPE 26 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     26   17
  16P GAIN WILD-TYPE   26   11
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               26                 26
  MALE                 17                 11
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3 15
  16P GAIN WILD-TYPE  5 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   15
  16P GAIN WILD-TYPE    5   12
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               15                 12
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16Q GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   31 11
  16Q GAIN WILD-TYPE 21 16
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                 37 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                11                 16 
$`16Q GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       63.85        12.00        38.89        30.31        57.53        69.21 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JQ 
       17.79        40.34        46.82        10.16        41.26        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        16.04        50.66        31.23         6.94        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       93.44        17.36        46.49       153.63        50.14        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       16.01         5.23        14.63        53.03        61.08        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       52.04        21.01        29.00        12.00        23.31        12.59 

$`16Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        55.13        15.45        79.82        16.11        19.04 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       18.12        91.46        41.39        22.03        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
        4.90        12.59         9.50        63.25        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV 
       32.68         8.32        37.15        11.31        87.88       120.30 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
       35.87       128.12        39.58        39.35        21.76        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-PK-A5H9 TCGA-PK-A5HA 
       78.41        36.33        73.05        62.99        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              4.11               4.90 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            153.63             128.12 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             28.31              35.87 
[1] "4.1 - 153.6 (28.3)" "4.9 - 128.1 (35.9)"
[1] "hr=" "1.5"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         4       20         8       10
  16Q GAIN WILD-TYPE       4       14         9        7
D28V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  4                  4
  STAGE II                20                 14
  STAGE III                8                  9
  STAGE IV                10                  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                 T1 T2 T3 T4
  16Q GAIN MUTATED    4 22  4 12
  16Q GAIN WILD-TYPE  4 17  7  6
D28V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                4                  4
  T2               22                 17
  T3                4                  7
  T4               12                  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"
D28V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   37  5
  16Q GAIN WILD-TYPE 30  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     37    5
  16Q GAIN WILD-TYPE   30    5
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               37                 30
  1                5                  5
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   27 16
  16Q GAIN WILD-TYPE 25 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     27   16
  16Q GAIN WILD-TYPE   25   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               27                 25
  MALE                 16                 12
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3 15
  16Q GAIN WILD-TYPE  5 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   15
  16Q GAIN WILD-TYPE    5   12
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               15                 12
[1] 2 2
[1] FALSE

Clustering(29) Variable = 17P GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    2  1
  17P GAIN WILD-TYPE 50 26
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 26 
$`17P GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JQ TCGA-OR-A5LT 
       19.04        22.16        12.00 

$`17P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       41.26        22.03        18.48        29.23         4.90       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       17.36         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       16.01        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI 
       62.99        64.08        52.04        21.01        29.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        10.09        27.29        42.51 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             12.00               4.11 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             22.16             153.63 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            19.040             33.255 
[1] "12.0 - 22.2 (19.0)" "4.1 - 153.6 (33.3)"
[1] "hr=" "1.9"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         0        1         2        1
  17P GAIN WILD-TYPE       8       33        15       16
D29V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 1                 33
  STAGE III                2                 15
  STAGE IV                 1                 16
[1] 4 2
[1] 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    0  1  2  1
  17P GAIN WILD-TYPE  8 38  9 17
D29V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                  8
  T2                1                 38
  T3                2                  9
  T4                1                 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"
D29V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  0
  17P GAIN WILD-TYPE 63 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    0
  17P GAIN WILD-TYPE   63   10
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                4                 63
  1                0                 10
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2  2
  17P GAIN WILD-TYPE 50 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    2
  17P GAIN WILD-TYPE   50   26
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 50
  MALE                  2                 26
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    1  1
  17P GAIN WILD-TYPE  7 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    1
  17P GAIN WILD-TYPE    7   26
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                1                 26
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17Q GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    3  1
  17Q GAIN WILD-TYPE 49 26
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 75 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 26 
$`17Q GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5LT 
       19.04        40.34        22.16        12.00 

$`17Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       69.21        41.39        17.79        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS 
       22.03        18.48        29.23         4.90       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       16.04         9.50        50.66        63.25        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
        8.32        37.15        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       39.58         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG 
       64.08        52.04        21.01        29.00        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.00               4.11 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             40.34             153.63 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             20.60              32.68 
[1] "12.0 - 40.3 (20.6)" "4.1 - 153.6 (32.7)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         0        2         2        1
  17Q GAIN WILD-TYPE       8       32        15       16
D30V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 2                 32
  STAGE III                2                 15
  STAGE IV                 1                 16
[1] 4 2
[1] 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    0  2  2  1
  17Q GAIN WILD-TYPE  8 37  9 17
D30V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                0                  8
  T2                2                 37
  T3                2                  9
  T4                1                 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"
D30V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  0
  17Q GAIN WILD-TYPE 62 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    0
  17Q GAIN WILD-TYPE   62   10
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                5                 62
  1                0                 10
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  2
  17Q GAIN WILD-TYPE 49 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    2
  17Q GAIN WILD-TYPE   49   26
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 49
  MALE                  2                 26
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  1
  17Q GAIN WILD-TYPE  7 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    1
  17Q GAIN WILD-TYPE    7   26
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                1                 26
[1] 2 2
[1] FALSE

Clustering(31) Variable = 19P GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   29 19
  19P GAIN WILD-TYPE 23  8
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                48                 31 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                19                  8 
$`19P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       38.89        30.31        57.53        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       40.34        46.82        10.16        41.26        18.48         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K2 
       22.16       121.25        50.66        31.23        33.83        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KW 
       93.44         8.32        11.31        46.49       153.63        50.14 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC 
       12.85         4.11        23.80        18.25        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       39.35        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       62.99        64.08        52.04        29.00        12.00        23.31 

$`19P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JO 
       44.55        19.04        18.12        91.46        22.03        29.23 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       12.59        16.04         9.50        63.25        18.15         6.94 
TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       89.52        17.36        37.15        87.88       120.30        35.87 
TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE 
      128.12        27.62        20.65        21.21        16.01        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       14.63        52.24        21.01        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              4.11               6.94 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            153.63             128.12 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             39.12              21.76 
[1] "4.1 - 153.6 (39.1)" "6.9 - 128.1 (21.8)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         3       21        10       14
  19P GAIN WILD-TYPE       5       13         7        3
D31V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  3                  5
  STAGE II                21                 13
  STAGE III               10                  7
  STAGE IV                14                  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                 T1 T2 T3 T4
  19P GAIN MUTATED    3 24  7 14
  19P GAIN WILD-TYPE  5 15  4  4
D31V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                  5
  T2               24                 15
  T3                7                  4
  T4               14                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   41  7
  19P GAIN WILD-TYPE 26  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     41    7
  19P GAIN WILD-TYPE   26    3
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               41                 26
  1                7                  3
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   32 17
  19P GAIN WILD-TYPE 20 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     32   17
  19P GAIN WILD-TYPE   20   11
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               32                 20
  MALE                 17                 11
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    7 14
  19P GAIN WILD-TYPE  1 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   14
  19P GAIN WILD-TYPE    1   13
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO               14                 13
[1] 2 2
[1] FALSE

Clustering(32) Variable = 19Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   27 17
  19Q GAIN WILD-TYPE 25 10
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                44                 35 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                17                 10 
$`19Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       38.89        30.31        57.53        69.21        41.39        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       40.34        46.82        10.16        41.26         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 
      121.25        50.66        31.23        32.68        93.44         8.32 
TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       11.31       153.63        50.14        35.87        12.85         4.11 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LH 
       23.80        18.25        39.58         5.23        39.35        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS 
       36.33        73.05        61.08        64.08        52.04        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI 
       12.00        23.31 

$`19Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J8 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JM 
       44.55        19.04        18.12        91.46        22.03        18.48 
TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY 
       29.23        12.59        16.04         9.50        63.25        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KO 
        6.94        33.83        89.52        17.36        37.15        46.49 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       87.88       120.30       128.12        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LN 
       16.01        21.76        14.63        52.24        53.03        62.99 
TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       21.01        12.59        10.09        27.29        42.51 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              4.11               6.94 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            153.63             128.12 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             37.61              22.03 
[1] "4.1 - 153.6 (37.6)" "6.9 - 128.1 (22.0)"
[1] "hr=" "1.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         3       18        11       12
  19Q GAIN WILD-TYPE       5       16         6        5
D32V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                  5
  STAGE II                18                 16
  STAGE III               11                  6
  STAGE IV                12                  5
[1] 4 2
[1] 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 22  7 12
  19Q GAIN WILD-TYPE  5 17  4  6
D32V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                  5
  T2               22                 17
  T3                7                  4
  T4               12                  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"
D32V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   36  8
  19Q GAIN WILD-TYPE 31  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     36    8
  19Q GAIN WILD-TYPE   31    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               36                 31
  1                8                  2
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   28 17
  19Q GAIN WILD-TYPE 24 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     28   17
  19Q GAIN WILD-TYPE   24   11
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               28                 24
  MALE                 17                 11
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    7 14
  19Q GAIN WILD-TYPE  1 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7   14
  19Q GAIN WILD-TYPE    1   13
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO               14                 13
[1] 2 2
[1] FALSE

Clustering(33) Variable = 20P GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   29 11
  20P GAIN WILD-TYPE 23 16
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                40                 39 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 16 
$`20P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JE 
       55.13        15.45        79.82        38.89        57.53        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JQ 
       41.39        17.79        40.34        46.82        41.26        22.16 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        16.04        50.66        31.23         6.94        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       93.44        17.36       153.63        35.87        12.85         4.11 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        20.65        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
        5.23        14.63        36.33        73.05        61.08        62.99 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       52.04        21.01        29.00        12.00 

$`20P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       44.55        63.85        12.00        16.11        19.04        30.31 
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       18.12        91.46        10.16        22.03        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
        4.90        12.59         9.50        63.25        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LD TCGA-OR-A5LE 
      120.30        50.14       128.12        18.25        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OU-A5PI TCGA-P6-A5OG 
       52.24        78.41        53.03        64.08        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              4.11               4.90 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            153.63             128.12 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             36.10              29.23 
[1] "4.1 - 153.6 (36.1)" "4.9 - 128.1 (29.2)"
[1] "hr=" "1.6"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         4       21         6        9
  20P GAIN WILD-TYPE       4       13        11        8
D33V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  4                  4
  STAGE II                21                 13
  STAGE III                6                 11
  STAGE IV                 9                  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                 T1 T2 T3 T4
  20P GAIN MUTATED    4 23  5  8
  20P GAIN WILD-TYPE  4 16  6 10
D33V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                4                  4
  T2               23                 16
  T3                5                  6
  T4                8                 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"
D33V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   35  5
  20P GAIN WILD-TYPE 32  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     35    5
  20P GAIN WILD-TYPE   32    5
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               35                 32
  1                5                  5
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   25 16
  20P GAIN WILD-TYPE 27 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     25   16
  20P GAIN WILD-TYPE   27   12
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               25                 27
  MALE                 16                 12
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    4 13
  20P GAIN WILD-TYPE  4 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   13
  20P GAIN WILD-TYPE    4   14
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               13                 14
[1] 2 2
[1] FALSE

Clustering(34) Variable = 20Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   31 12
  20Q GAIN WILD-TYPE 21 15
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                43                 36 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                 15 
$`20Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC 
       55.13        15.45        79.82        19.04        38.89        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       41.26        22.16       121.25        16.04        50.66        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KU TCGA-OR-A5KX 
        6.94        89.52        93.44        17.36       153.63        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       12.85         4.11        23.80        27.62        20.65        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.58         5.23        14.63        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       61.08        62.99        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI 
       23.31 

$`20Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       44.55        63.85        12.00        16.11        30.31        18.12 
TCGA-OR-A5JD TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       91.46        22.03        18.48        29.23         4.90        12.59 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
        9.50        63.25        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW 
       37.15        11.31        46.49        87.88       120.30        50.14 
TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH 
      128.12        18.25        39.35        21.76        52.24        78.41 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       53.03        64.08        12.59        10.09        27.29        42.51 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              4.11               4.90 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            153.63             128.12 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            31.230             31.495 
[1] "4.1 - 153.6 (31.2)" "4.9 - 128.1 (31.5)"
[1] "hr=" "1.5"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         4       21         7       11
  20Q GAIN WILD-TYPE       4       13        10        6
D34V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  4                  4
  STAGE II                21                 13
  STAGE III                7                 10
  STAGE IV                11                  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                 T1 T2 T3 T4
  20Q GAIN MUTATED    4 24  6  9
  20Q GAIN WILD-TYPE  4 15  5  9
D34V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                4                  4
  T2               24                 15
  T3                6                  5
  T4                9                  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"
D34V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   36  7
  20Q GAIN WILD-TYPE 31  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     36    7
  20Q GAIN WILD-TYPE   31    3
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               36                 31
  1                7                  3
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   26 18
  20Q GAIN WILD-TYPE 26 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     26   18
  20Q GAIN WILD-TYPE   26   10
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               26                 26
  MALE                 18                 10
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5 14
  20Q GAIN WILD-TYPE  3 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5   14
  20Q GAIN WILD-TYPE    3   13
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  3
  NOT HISPANIC OR LATINO               14                 13
[1] 2 2
[1] FALSE

Clustering(35) Variable = 21Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   17  9
  21Q GAIN WILD-TYPE 35 18
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                26                 53 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 9                 18 
$`21Q GAIN MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JC 
       44.55        63.85        79.82        16.11        38.89        57.53 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       69.21        17.79        46.82        10.16        41.26        22.03 
TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX 
       31.23        33.83        11.31       153.63        50.14        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LM TCGA-OR-A5LO 
       12.85         4.11        16.01        39.58        61.08        64.08 
TCGA-OR-A5LS TCGA-OU-A5PI 
       29.00        23.31 

$`21Q GAIN WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JB 
       55.13        15.45        12.00        19.04        30.31        18.12 
TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       91.46        41.39        40.34        18.48        29.23         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       22.16       121.25        12.59        16.04         9.50        50.66 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       63.25        18.15         6.94        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KV 
       17.36         8.32        37.15        46.49        87.88       120.30 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
        5.23        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        62.99        52.04        21.01 
TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.00        12.59        10.09        27.29        42.51 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.11               4.90 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            153.63             128.12 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             37.38              27.62 
[1] "4.1 - 153.6 (37.4)" "4.9 - 128.1 (27.6)"
[1] "hr=" "1"  
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         3       11         5        6
  21Q GAIN WILD-TYPE       5       23        12       11
D35V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  3                  5
  STAGE II                11                 23
  STAGE III                5                 12
  STAGE IV                 6                 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                 T1 T2 T3 T4
  21Q GAIN MUTATED    3 14  3  5
  21Q GAIN WILD-TYPE  5 25  8 13
D35V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                  5
  T2               14                 25
  T3                3                  8
  T4                5                 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"
D35V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   19  6
  21Q GAIN WILD-TYPE 48  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     19    6
  21Q GAIN WILD-TYPE   48    4
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               19                 48
  1                6                  4
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   16 10
  21Q GAIN WILD-TYPE 36 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     16   10
  21Q GAIN WILD-TYPE   36   18
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               16                 36
  MALE                 10                 18
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    4  8
  21Q GAIN WILD-TYPE  4 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4    8
  21Q GAIN WILD-TYPE    4   19
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO                8                 19
[1] 2 2
[1] FALSE

Clustering(36) Variable = XQ GAIN MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   24 11
  XQ GAIN WILD-TYPE 28 16
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               35                44 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               11                16 
$`XQ GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       55.13        63.85        12.00        79.82        19.04        38.89 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JR TCGA-OR-A5JT 
       69.21        41.39        10.16        22.03       121.25        16.04 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5KO TCGA-OR-A5KU 
        6.94        89.52        93.44        17.36        46.49       153.63 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       12.85         4.11        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       16.01        39.58        39.35        14.63        78.41        36.33 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       61.08        64.08        52.04        21.01        12.00 

$`XQ GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       44.55        15.45        16.11        30.31        18.12        57.53 
TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JM 
       91.46        17.79        40.34        46.82        41.26        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV 
       29.23         4.90        22.16        12.59         9.50        50.66 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
       63.25        31.23        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       37.15        11.31        87.88       120.30        50.14        35.87 
TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LK 
      128.12        20.65         5.23        21.76        52.24        73.05 
TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       53.03        62.99        29.00        23.31        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             4.11              4.90 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           153.63            128.12 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            36.33             30.77 
[1] "4.1 - 153.6 (36.3)" "4.9 - 128.1 (30.8)"
[1] "hr=" "1.3"
D36V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         4       17         8        6
  XQ GAIN WILD-TYPE       4       17         9       11
D36V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 4                 4
  STAGE II               17                17
  STAGE III               8                 9
  STAGE IV                6                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                T1 T2 T3 T4
  XQ GAIN MUTATED    4 18  5  8
  XQ GAIN WILD-TYPE  4 21  6 10
D36V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               4                 4
  T2              18                21
  T3               5                 6
  T4               8                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"
D36V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   32  3
  XQ GAIN WILD-TYPE 35  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     32    3
  XQ GAIN WILD-TYPE   35    7
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              32                35
  1               3                 7
[1] 2 2
[1] FALSE
D36V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   23 12
  XQ GAIN WILD-TYPE 29 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     23   12
  XQ GAIN WILD-TYPE   29   16
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              23                29
  MALE                12                16
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    6 13
  XQ GAIN WILD-TYPE  2 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   13
  XQ GAIN WILD-TYPE    2   14
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO              13                14
[1] 2 2
[1] FALSE

Clustering(37) Variable = 1P LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   20  7
  1P LOSS WILD-TYPE 32 20
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               27                52 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                20 
$`1P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       16.11        57.53        91.46        40.34        46.82        41.26 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       18.48        22.16        12.59        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KX 
       18.15        33.83        32.68         8.32        37.15        35.87 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       20.65         5.23        52.24        53.03        61.08        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       29.00        23.31        27.29 

$`1P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        18.12        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       17.79        10.16        22.03        29.23         4.90       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       16.04         9.50         6.94        89.52        93.44        17.36 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       12.85         4.11       128.12        23.80        27.62        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       21.21        16.01        39.58        39.35        21.76        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       78.41        36.33        73.05        64.08        52.04        21.01 
TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       12.00        12.59        10.09        42.51 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             5.23              4.11 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            91.46            153.63 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           33.830            28.425 
[1] "5.2 - 91.5 (33.8)"  "4.1 - 153.6 (28.4)"
[1] "hr=" "1.5"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         1       13         6        5
  1P LOSS WILD-TYPE       7       21        11       12
D37V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II               13                21
  STAGE III               6                11
  STAGE IV                5                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                T1 T2 T3 T4
  1P LOSS MUTATED    1 15  4  5
  1P LOSS WILD-TYPE  7 24  7 13
D37V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               1                 7
  T2              15                24
  T3               4                 7
  T4               5                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"
D37V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   23  3
  1P LOSS WILD-TYPE 44  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     23    3
  1P LOSS WILD-TYPE   44    7
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              23                44
  1               3                 7
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   17 10
  1P LOSS WILD-TYPE 35 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     17   10
  1P LOSS WILD-TYPE   35   18
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              17                35
  MALE                10                18
[1] 2 2
[1] FALSE
D37V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  6
  1P LOSS WILD-TYPE  7 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    6
  1P LOSS WILD-TYPE    7   21
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               6                21
[1] 2 2
[1] FALSE

Clustering(38) Variable = 1Q LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   12  6
  1Q LOSS WILD-TYPE 40 21
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               18                61 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                6                21 
$`1Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK 
       16.11        57.53        91.46        40.34        46.82        41.26 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       18.48        22.16        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5KX TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM TCGA-OU-A5PI 
       32.68        35.87        20.65         5.23        61.08        23.31 

$`1Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        18.12        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       17.79        10.16        22.03        29.23         4.90       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       12.59        16.04         9.50         6.94        33.83        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO 
       93.44        17.36         8.32        37.15        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       39.58        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        73.05        53.03        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       21.01        29.00        12.00        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             5.23              4.11 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            91.46            153.63 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           34.275            29.230 
[1] "5.2 - 91.5 (34.3)"  "4.1 - 153.6 (29.2)"
[1] "hr=" "1.1"
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         1        7         4        5
  1Q LOSS WILD-TYPE       7       27        13       12
D38V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                7                27
  STAGE III               4                13
  STAGE IV                5                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                T1 T2 T3 T4
  1Q LOSS MUTATED    1  9  2  5
  1Q LOSS WILD-TYPE  7 30  9 13
D38V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               1                 7
  T2               9                30
  T3               2                 9
  T4               5                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"
D38V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   14  3
  1Q LOSS WILD-TYPE 53  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     14    3
  1Q LOSS WILD-TYPE   53    7
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              14                53
  1               3                 7
[1] 2 2
[1] FALSE
D38V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   10  8
  1Q LOSS WILD-TYPE 42 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     10    8
  1Q LOSS WILD-TYPE   42   20
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              10                42
  MALE                 8                20
[1] 2 2
[1] FALSE
D38V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    1  4
  1Q LOSS WILD-TYPE  7 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    4
  1Q LOSS WILD-TYPE    7   23
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(39) Variable = 2P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   15  2
  2P LOSS WILD-TYPE 37 25
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17                62 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                25 
$`2P LOSS MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       30.31        57.53        91.46        40.34        41.26        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5KX 
       22.16        12.59        50.66        63.25        31.23        35.87 
TCGA-OR-A5LG TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       52.24        62.99        29.00        23.31        27.29 

$`2P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        38.89        18.12        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       17.79        46.82        10.16        18.48        29.23         4.90 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
      121.25        16.04         9.50        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       89.52        32.68        93.44        17.36         8.32        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11       128.12        23.80        27.62        20.65 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       18.25        21.21        16.01        39.58         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       21.76        14.63        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG 
       61.08        64.08        52.04        21.01        12.00        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HB 
       10.09        42.51 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            12.59              4.11 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            91.46            153.63 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           35.870            28.425 
[1] "12.6 - 91.5 (35.9)" "4.1 - 153.6 (28.4)"
[1] "hr=" "3.9"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         1        8         3        3
  2P LOSS WILD-TYPE       7       26        14       14
D39V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                8                26
  STAGE III               3                14
  STAGE IV                3                14
[1] 4 2
[1] 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    1 10  2  2
  2P LOSS WILD-TYPE  7 29  9 16
D39V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               1                 7
  T2              10                29
  T3               2                 9
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   14  2
  2P LOSS WILD-TYPE 53  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14    2
  2P LOSS WILD-TYPE   53    8
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              14                53
  1               2                 8
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   10  7
  2P LOSS WILD-TYPE 42 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10    7
  2P LOSS WILD-TYPE   42   21
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              10                42
  MALE                 7                21
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    0  3
  2P LOSS WILD-TYPE  8 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    3
  2P LOSS WILD-TYPE    8   24
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                24
[1] 2 2
[1] FALSE

Clustering(40) Variable = 2Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   13  2
  2Q LOSS WILD-TYPE 39 25
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                64 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                25 
$`2Q LOSS MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JL 
       30.31        57.53        91.46        40.34        41.26        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5LN 
       22.16        12.59        50.66        63.25        31.23        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       29.00        23.31        27.29 

$`2Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        38.89        18.12        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       17.79        46.82        10.16        18.48        29.23         4.90 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
      121.25        16.04         9.50        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       89.52        32.68        93.44        17.36         8.32        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       35.87        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        61.08        64.08        52.04        21.01 
TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       12.00        12.59        10.09        42.51 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            12.59              4.11 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            91.46            153.63 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           31.230            30.955 
[1] "12.6 - 91.5 (31.2)" "4.1 - 153.6 (31.0)"
[1] "hr=" "3.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         1        8         1        3
  2Q LOSS WILD-TYPE       7       26        16       14
D40V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                8                26
  STAGE III               1                16
  STAGE IV                3                14
[1] 4 2
[1] 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    1  9  1  2
  2Q LOSS WILD-TYPE  7 30 10 16
D40V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               1                 7
  T2               9                30
  T3               1                10
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   13  1
  2Q LOSS WILD-TYPE 54  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     13    1
  2Q LOSS WILD-TYPE   54    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              13                54
  1               1                 9
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    9  6
  2Q LOSS WILD-TYPE 43 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    6
  2Q LOSS WILD-TYPE   43   22
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               9                43
  MALE                 6                22
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    0  1
  2Q LOSS WILD-TYPE  8 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    1
  2Q LOSS WILD-TYPE    8   26
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(41) Variable = 3P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    9  9
  3P LOSS WILD-TYPE 43 18
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               18                61 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                9                18 
$`3P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JH 
       16.11        30.31        18.12        57.53        17.79        40.34 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K9 
       41.26        22.03         4.90        63.25        18.15        11.31 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LS TCGA-PK-A5HB 
       20.65         5.23        53.03        61.08        29.00        42.51 

$`3P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI 
       19.04        38.89        91.46        69.21        41.39        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       10.16        18.48        29.23        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 
       16.04         9.50        50.66        31.23         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       89.52        32.68        93.44        17.36         8.32        37.15 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       12.85         4.11       128.12        23.80        27.62        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       21.21        16.01        39.58        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LO 
       52.24        78.41        36.33        73.05        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       52.04        21.01        12.00        23.31        12.59        10.09 
TCGA-PK-A5HA 
       27.29 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             4.90              4.11 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            63.25            153.63 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           25.515            33.830 
[1] "4.9 - 63.2 (25.5)"  "4.1 - 153.6 (33.8)"
[1] "hr=" "2.1"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         1        8         1        6
  3P LOSS WILD-TYPE       7       26        16       11
D41V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                8                26
  STAGE III               1                16
  STAGE IV                6                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                T1 T2 T3 T4
  3P LOSS MUTATED    1  8  1  6
  3P LOSS WILD-TYPE  7 31 10 12
D41V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               1                 7
  T2               8                31
  T3               1                10
  T4               6                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"
D41V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   14  2
  3P LOSS WILD-TYPE 53  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     14    2
  3P LOSS WILD-TYPE   53    8
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              14                53
  1               2                 8
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    9  9
  3P LOSS WILD-TYPE 43 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      9    9
  3P LOSS WILD-TYPE   43   19
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               9                43
  MALE                 9                19
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    1  2
  3P LOSS WILD-TYPE  7 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    2
  3P LOSS WILD-TYPE    7   25
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(42) Variable = 3Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    9  9
  3Q LOSS WILD-TYPE 43 18
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               18                61 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9                18 
$`3Q LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JH 
       79.82        16.11        30.31        57.53        17.79        40.34 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
       41.26        22.03         4.90        63.25        18.15        33.83 
TCGA-OR-A5K9 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LL TCGA-OR-A5LM TCGA-PK-A5HB 
       11.31         5.23        21.76        53.03        61.08        42.51 

$`3Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI 
       38.89        18.12        91.46        69.21        41.39        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       10.16        18.48        29.23        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       16.04         9.50        50.66        31.23         6.94        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KO 
       32.68        93.44        17.36         8.32        37.15        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG 
       21.21        16.01        39.58        39.35        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       78.41        36.33        73.05        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       21.01        29.00        12.00        23.31        12.59        10.09 
TCGA-PK-A5HA 
       27.29 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             4.90              4.11 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            79.82            153.63 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            32.07             31.23 
[1] "4.9 - 79.8 (32.1)"  "4.1 - 153.6 (31.2)"
[1] "hr=" "1.8"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         1        9         1        5
  3Q LOSS WILD-TYPE       7       25        16       12
D42V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                9                25
  STAGE III               1                16
  STAGE IV                5                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                T1 T2 T3 T4
  3Q LOSS MUTATED    1  9  1  5
  3Q LOSS WILD-TYPE  7 30 10 13
D42V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               1                 7
  T2               9                30
  T3               1                10
  T4               5                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"
D42V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   14  2
  3Q LOSS WILD-TYPE 53  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     14    2
  3Q LOSS WILD-TYPE   53    8
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              14                53
  1               2                 8
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   10  8
  3Q LOSS WILD-TYPE 42 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     10    8
  3Q LOSS WILD-TYPE   42   20
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              10                42
  MALE                 8                20
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  2
  3Q LOSS WILD-TYPE  6 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    2
  3Q LOSS WILD-TYPE    6   25
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(43) Variable = 4P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    3  6
  4P LOSS WILD-TYPE 49 21
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                70 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                6                21 
$`4P LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5KO 
       18.12        18.48        12.59        18.15        32.68        46.49 
TCGA-OR-A5KZ TCGA-OR-A5LC TCGA-PK-A5HA 
        4.11         5.23        27.29 

$`4P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        38.89        30.31        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       41.26        22.03        29.23         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
       16.04         9.50        50.66        63.25        31.23         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       33.83        89.52        93.44        17.36         8.32        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       11.31        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       12.85       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       21.21        16.01        39.58        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       23.31        12.59        10.09        42.51 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             4.11              4.90 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            46.49            153.63 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            18.15             36.10 
[1] "4.1 - 46.5 (18.1)"  "4.9 - 153.6 (36.1)"
[1] "hr=" "4.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         0        2         1        5
  4P LOSS WILD-TYPE       8       32        16       12
D43V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                2                32
  STAGE III               1                16
  STAGE IV                5                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                T1 T2 T3 T4
  4P LOSS MUTATED    0  2  0  6
  4P LOSS WILD-TYPE  8 37 11 12
D43V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               0                 8
  T2               2                37
  T3               0                11
  T4               6                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"
D43V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    8  1
  4P LOSS WILD-TYPE 59  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    1
  4P LOSS WILD-TYPE   59    9
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               8                59
  1               1                 9
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    6  3
  4P LOSS WILD-TYPE 46 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6    3
  4P LOSS WILD-TYPE   46   25
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               6                46
  MALE                 3                25
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    0  3
  4P LOSS WILD-TYPE  8 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    3
  4P LOSS WILD-TYPE    8   24
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                24
[1] 2 2
[1] FALSE

Clustering(44) Variable = 4Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  7
  4Q LOSS WILD-TYPE 49 20
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               10                69 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                7                20 
$`4Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JY TCGA-OR-A5K2 
       16.11        18.12        18.48        12.59        18.15        32.68 
TCGA-OR-A5KO TCGA-OR-A5KZ TCGA-OR-A5LC TCGA-PK-A5HA 
       46.49         4.11         5.23        27.29 

$`4Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        38.89        30.31        57.53        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       22.03        29.23         4.90        22.16       121.25        16.04 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 
        9.50        50.66        63.25        31.23         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       89.52        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       16.01        39.58        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HB 
       12.59        10.09        42.51 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             4.11              4.90 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            46.49            153.63 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           18.135            36.330 
[1] "4.1 - 46.5 (18.1)"  "4.9 - 153.6 (36.3)"
[1] "hr=" "5.4"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         0        2         2        5
  4Q LOSS WILD-TYPE       8       32        15       12
D44V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                2                32
  STAGE III               2                15
  STAGE IV                5                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                T1 T2 T3 T4
  4Q LOSS MUTATED    0  2  1  6
  4Q LOSS WILD-TYPE  8 37 10 12
D44V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               0                 8
  T2               2                37
  T3               1                10
  T4               6                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"
D44V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    9  1
  4Q LOSS WILD-TYPE 58  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      9    1
  4Q LOSS WILD-TYPE   58    9
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               9                58
  1               1                 9
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    7  3
  4Q LOSS WILD-TYPE 45 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      7    3
  4Q LOSS WILD-TYPE   45   25
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               7                45
  MALE                 3                25
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  3
  4Q LOSS WILD-TYPE  7 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    3
  4Q LOSS WILD-TYPE    7   24
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               3                24
[1] 2 2
[1] FALSE

Clustering(45) Variable = 5P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    3  4
  5P LOSS WILD-TYPE 49 23
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                7                72 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                23 
$`5P LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5JM TCGA-OR-A5JX TCGA-OR-A5KX TCGA-OR-A5LG 
       44.55        55.13        18.48        31.23        35.87        52.24 
TCGA-OR-A5LL 
       53.03 

$`5P LOSS WILD-TYPE`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       63.85        15.45        12.00        79.82        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       38.89        30.31        18.12        57.53        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       22.03        29.23         4.90        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       16.04         9.50        50.66        63.25        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       37.15        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        21.76        14.63        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        64.08        52.04        21.01        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.00        23.31        12.59        10.09        27.29        42.51 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            18.48              4.11 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            55.13            153.63 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           44.550            29.115 
[1] "18.5 - 55.1 (44.5)" "4.1 - 153.6 (29.1)"
[1] "hr=" "1.6"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        2         3        2
  5P LOSS WILD-TYPE       8       32        14       15
D45V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                2                32
  STAGE III               3                14
  STAGE IV                2                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"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    0  3  3  1
  5P LOSS WILD-TYPE  8 36  8 17
D45V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                 8
  T2               3                36
  T3               3                 8
  T4               1                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"
D45V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    6  1
  5P LOSS WILD-TYPE 61  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      6    1
  5P LOSS WILD-TYPE   61    9
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               6                61
  1               1                 9
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    4  3
  5P LOSS WILD-TYPE 48 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      4    3
  5P LOSS WILD-TYPE   48   25
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               4                48
  MALE                 3                25
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  2
  5P LOSS WILD-TYPE  7 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    2
  5P LOSS WILD-TYPE    7   25
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(46) Variable = 5Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    4  2
  5Q LOSS WILD-TYPE 48 25
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                6                73 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                25 
$`5Q LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JX TCGA-OR-A5KX TCGA-OR-A5LG 
       44.55        41.26        18.48        31.23        35.87        52.24 

$`5Q LOSS WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       22.03        29.23         4.90        22.16       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       16.04         9.50        50.66        63.25        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       37.15        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        21.76        14.63        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       53.03        61.08        62.99        64.08        52.04        21.01 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       29.00        12.00        23.31        12.59        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            18.48              4.11 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            52.24            153.63 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           38.565            29.230 
[1] "18.5 - 52.2 (38.6)" "4.1 - 153.6 (29.2)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        1         3        2
  5Q LOSS WILD-TYPE       8       33        14       15
D46V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                1                33
  STAGE III               3                14
  STAGE IV                2                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"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    0  2  2  2
  5Q LOSS WILD-TYPE  8 37  9 16
D46V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0                 8
  T2               2                37
  T3               2                 9
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    5  1
  5Q LOSS WILD-TYPE 62  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5    1
  5Q LOSS WILD-TYPE   62    9
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               5                62
  1               1                 9
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  4
  5Q LOSS WILD-TYPE 50 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    4
  5Q LOSS WILD-TYPE   50   24
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               2                50
  MALE                 4                24
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    0  2
  5Q LOSS WILD-TYPE  8 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    2
  5Q LOSS WILD-TYPE    8   25
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               2                25
[1] 2 2
[1] FALSE

Clustering(47) Variable = 6P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   10  7
  6P LOSS WILD-TYPE 42 20
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               17                62 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                20 
$`6P LOSS MUTATED`
TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       91.46        17.79        40.34        41.26         4.90        22.16 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5LC TCGA-OR-A5LE 
       12.59        50.66        18.15        32.68         5.23        21.76 
TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       53.03        29.00        12.00        23.31        12.59 

$`6P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        38.89        30.31        18.12        57.53 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM 
       69.21        41.39        46.82        10.16        22.03        18.48 
TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
       29.23       121.25        16.04         9.50        63.25        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        33.83        89.52        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       37.15        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14        35.87        12.85         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        52.24        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5H9 
       61.08        62.99        64.08        52.04        21.01        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             4.90              4.11 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            91.46            153.63 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            22.16             36.10 
[1] "4.9 - 91.5 (22.2)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.8"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         0        9         2        6
  6P LOSS WILD-TYPE       8       25        15       11
D47V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                9                25
  STAGE III               2                15
  STAGE IV                6                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                T1 T2 T3 T4
  6P LOSS MUTATED    0 10  1  6
  6P LOSS WILD-TYPE  8 29 10 12
D47V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 8
  T2              10                29
  T3               1                10
  T4               6                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"
D47V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   14  3
  6P LOSS WILD-TYPE 53  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     14    3
  6P LOSS WILD-TYPE   53    7
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              14                53
  1               3                 7
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   11  6
  6P LOSS WILD-TYPE 41 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     11    6
  6P LOSS WILD-TYPE   41   22
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              11                41
  MALE                 6                22
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    0  4
  6P LOSS WILD-TYPE  8 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    4
  6P LOSS WILD-TYPE    8   23
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(48) Variable = 6Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   11  8
  6Q LOSS WILD-TYPE 41 19
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19                60 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8                19 
$`6Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JK 
       16.11        18.12        91.46        17.79        40.34        41.26 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 
        4.90        22.16        12.59        50.66        18.15        32.68 
TCGA-OR-A5KO TCGA-OR-A5LC TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       46.49         5.23        53.03        29.00        12.00        23.31 
TCGA-P6-A5OG 
       12.59 

$`6Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        30.31        57.53        69.21        41.39 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR 
       46.82        10.16        22.03        18.48        29.23       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 
       16.04         9.50        63.25        31.23         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       89.52        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       21.21        16.01        39.58        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       52.24        78.41        36.33        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       64.08        52.04        21.01        10.09        27.29        42.51 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             4.90              4.11 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            91.46            153.63 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            22.16             36.10 
[1] "4.9 - 91.5 (22.2)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.9"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         0        8         3        9
  6Q LOSS WILD-TYPE       8       26        14        8
D48V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                8                26
  STAGE III               3                14
  STAGE IV                9                 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                T1 T2 T3 T4
  6Q LOSS MUTATED    0  9  2  9
  6Q LOSS WILD-TYPE  8 30  9  9
D48V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               0                 8
  T2               9                30
  T3               2                 9
  T4               9                 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"
D48V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   17  3
  6Q LOSS WILD-TYPE 50  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     17    3
  6Q LOSS WILD-TYPE   50    7
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              17                50
  1               3                 7
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   14  6
  6Q LOSS WILD-TYPE 38 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     14    6
  6Q LOSS WILD-TYPE   38   22
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              14                38
  MALE                 6                22
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    1  5
  6Q LOSS WILD-TYPE  7 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    5
  6Q LOSS WILD-TYPE    7   22
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               5                22
[1] 2 2
[1] FALSE

Clustering(49) Variable = 7P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    2  2
  7P LOSS WILD-TYPE 50 25
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                75 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2                25 
$`7P LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JP TCGA-OR-A5LD TCGA-OR-A5LT 
       57.53         4.90        39.35        12.00 

$`7P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        38.89        30.31        18.12        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       41.26        22.03        18.48        29.23        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       17.36         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       16.01        39.58         5.23        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG 
       64.08        52.04        21.01        29.00        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             4.90              4.11 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            57.53            153.63 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           25.675            31.230 
[1] "4.9 - 57.5 (25.7)"  "4.1 - 153.6 (31.2)"
[1] "hr=" "2"  
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         0        1         2        0
  7P LOSS WILD-TYPE       8       33        15       17
D49V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                1                33
  STAGE III               2                15
  STAGE IV                0                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"
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    0  1  1  1
  7P LOSS WILD-TYPE  8 38 10 17
D49V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               0                 8
  T2               1                38
  T3               1                10
  T4               1                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"
D49V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    3  0
  7P LOSS WILD-TYPE 64 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE   64   10
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               3                64
  1               0                10
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    0  4
  7P LOSS WILD-TYPE 52 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    4
  7P LOSS WILD-TYPE   52   24
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               0                52
  MALE                 4                24
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    0  1
  7P LOSS WILD-TYPE  8 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    1
  7P LOSS WILD-TYPE    8   26
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(50) Variable = 7Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    2  3
  7Q LOSS WILD-TYPE 50 24
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5                74 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3                24 
$`7Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5K5 TCGA-OR-A5LD TCGA-OR-A5LT 
       57.53        69.21         8.32        39.35        12.00 

$`7Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        38.89        30.31        18.12        91.46 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       22.03        18.48        29.23         4.90        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       17.36        37.15        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       39.58         5.23        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       36.33        73.05        53.03        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       52.04        21.01        29.00        23.31        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             8.32              4.11 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            69.21            153.63 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            39.35             30.77 
[1] "8.3 - 69.2 (39.4)"  "4.1 - 153.6 (30.8)"
[1] "hr=" "1.9"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         1        0         3        0
  7Q LOSS WILD-TYPE       7       34        14       17
D50V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                0                34
  STAGE III               3                14
  STAGE IV                0                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"
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    1  0  2  1
  7Q LOSS WILD-TYPE  7 39  9 17
D50V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               1                 7
  T2               0                39
  T3               2                 9
  T4               1                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"
D50V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    4  0
  7Q LOSS WILD-TYPE 63 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    0
  7Q LOSS WILD-TYPE   63   10
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               4                63
  1               0                10
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    2  3
  7Q LOSS WILD-TYPE 50 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    3
  7Q LOSS WILD-TYPE   50   25
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2                50
  MALE                 3                25
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    0  1
  7Q LOSS WILD-TYPE  8 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    1
  7Q LOSS WILD-TYPE    8   26
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               1                26
[1] 2 2
[1] FALSE

Clustering(51) Variable = 8P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    8  5
  8P LOSS WILD-TYPE 44 22
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                66 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                22 
$`8P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JG TCGA-OR-A5JL TCGA-OR-A5JW 
       16.11        30.31        18.12        17.79        22.03        63.25 
TCGA-OR-A5K6 TCGA-OR-A5KX TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OU-A5PI 
       37.15        35.87        52.24        53.03        29.00        23.31 
TCGA-PK-A5HB 
       42.51 

$`8P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        57.53        91.46        69.21        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO 
       40.34        46.82        10.16        41.26        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
        4.90        22.16       121.25        12.59        16.04         9.50 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       50.66        31.23        18.15         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KO 
       32.68        93.44        17.36         8.32        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       16.01        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        36.33        73.05        61.08        62.99        64.08 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       52.04        21.01        12.00        12.59        10.09        27.29 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            16.11              4.11 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            63.25            153.63 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           30.310            31.955 
[1] "16.1 - 63.2 (30.3)" "4.1 - 153.6 (32.0)"
[1] "hr=" "1.3"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         1        4         3        4
  8P LOSS WILD-TYPE       7       30        14       13
D51V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                4                30
  STAGE III               3                14
  STAGE IV                4                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                T1 T2 T3 T4
  8P LOSS MUTATED    1  6  2  3
  8P LOSS WILD-TYPE  7 33  9 15
D51V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1                 7
  T2               6                33
  T3               2                 9
  T4               3                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"
D51V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    9  3
  8P LOSS WILD-TYPE 58  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9    3
  8P LOSS WILD-TYPE   58    7
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               9                58
  1               3                 7
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    8  5
  8P LOSS WILD-TYPE 44 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8    5
  8P LOSS WILD-TYPE   44   23
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               8                44
  MALE                 5                23
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  4
  8P LOSS WILD-TYPE  7 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    4
  8P LOSS WILD-TYPE    7   23
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(52) Variable = 8Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    7  3
  8Q LOSS WILD-TYPE 45 24
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10                69 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                24 
$`8Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JG TCGA-OR-A5JL TCGA-OR-A5JW TCGA-OR-A5K6 
       16.11        30.31        17.79        22.03        63.25        37.15 
TCGA-OR-A5KX TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HB 
       35.87        29.00        23.31        42.51 

$`8Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        38.89        18.12        57.53        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM 
       41.39        40.34        46.82        10.16        41.26        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       29.23         4.90        22.16       121.25        12.59        16.04 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
        9.50        50.66        31.23        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 
       89.52        32.68        93.44        17.36         8.32        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       46.49        87.88       153.63       120.30        50.14        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       21.21        16.01        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       61.08        62.99        64.08        52.04        21.01        12.00 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       12.59        10.09        27.29 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            16.11              4.11 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            63.25            153.63 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           29.655            32.680 
[1] "16.1 - 63.2 (29.7)" "4.1 - 153.6 (32.7)"
[1] "hr=" "1"  
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1        3         2        3
  8Q LOSS WILD-TYPE       7       31        15       14
D52V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                3                31
  STAGE III               2                15
  STAGE IV                3                14
[1] 4 2
[1] 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    1  5  1  2
  8Q LOSS WILD-TYPE  7 34 10 16
D52V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1                 7
  T2               5                34
  T3               1                10
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    6  3
  8Q LOSS WILD-TYPE 61  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6    3
  8Q LOSS WILD-TYPE   61    7
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               6                61
  1               3                 7
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    7  3
  8Q LOSS WILD-TYPE 45 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      7    3
  8Q LOSS WILD-TYPE   45   25
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               7                45
  MALE                 3                25
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  3
  8Q LOSS WILD-TYPE  7 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    3
  8Q LOSS WILD-TYPE    7   24
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               3                24
[1] 2 2
[1] FALSE

Clustering(53) Variable = 9P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   11  8
  9P LOSS WILD-TYPE 41 19
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               19                60 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                8                19 
$`9P LOSS MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       19.04        38.89        57.53        41.26        18.48         4.90 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
       12.59        50.66        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LM 
       37.15       128.12         5.23        21.76        52.24        61.08 
TCGA-P6-A5OG 
       12.59 

$`9P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        30.31        18.12        91.46        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO 
       17.79        40.34        46.82        10.16        22.03        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
       22.16       121.25        16.04         9.50        63.25        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K9 TCGA-OR-A5KO 
        6.94        89.52        93.44        17.36        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
        4.11        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
       16.01        39.58        39.35        14.63        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        62.99        64.08        52.04        21.01 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       29.00        12.00        23.31        10.09        27.29        42.51 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             4.90              4.11 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           128.12            153.63 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            32.68             30.77 
[1] "4.9 - 128.1 (32.7)" "4.1 - 153.6 (30.8)"
[1] "hr=" "1.6"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         1        8         4        5
  9P LOSS WILD-TYPE       7       26        13       12
D53V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                8                26
  STAGE III               4                13
  STAGE IV                5                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                T1 T2 T3 T4
  9P LOSS MUTATED    1  8  3  6
  9P LOSS WILD-TYPE  7 31  8 12
D53V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               1                 7
  T2               8                31
  T3               3                 8
  T4               6                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"
D53V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   17  1
  9P LOSS WILD-TYPE 50  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     17    1
  9P LOSS WILD-TYPE   50    9
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              17                50
  1               1                 9
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   11  8
  9P LOSS WILD-TYPE 41 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     11    8
  9P LOSS WILD-TYPE   41   20
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              11                41
  MALE                 8                20
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    2  6
  9P LOSS WILD-TYPE  6 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    6
  9P LOSS WILD-TYPE    6   21
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               6                21
[1] 2 2
[1] FALSE

Clustering(54) Variable = 9Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    6  4
  9Q LOSS WILD-TYPE 46 23
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               10                69 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                23 
$`9Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5K6 
       57.53        41.26        18.48        12.59        50.66        37.15 
TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LM TCGA-P6-A5OG 
      128.12         5.23        61.08        12.59 

$`9Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        38.89        30.31        18.12        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       22.03        29.23         4.90        22.16       121.25        16.04 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
        9.50        63.25        31.23        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 
       89.52        32.68        93.44        17.36         8.32        11.31 
TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       46.49        87.88       153.63       120.30        50.14        35.87 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       12.85         4.11        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       21.21        16.01        39.58        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN 
       52.24        78.41        36.33        73.05        53.03        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             5.23              4.11 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           128.12            153.63 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           39.205            30.310 
[1] "5.2 - 128.1 (39.2)" "4.1 - 153.6 (30.3)"
[1] "hr=" "1.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         1        4         0        4
  9Q LOSS WILD-TYPE       7       30        17       13
D54V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 1                 7
  STAGE II                4                30
  STAGE III               0                17
  STAGE IV                4                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                T1 T2 T3 T4
  9Q LOSS MUTATED    1  4  0  4
  9Q LOSS WILD-TYPE  7 35 11 14
D54V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               1                 7
  T2               4                35
  T3               0                11
  T4               4                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    9  0
  9Q LOSS WILD-TYPE 58 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9    0
  9Q LOSS WILD-TYPE   58   10
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               9                58
  1               0                10
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6  4
  9Q LOSS WILD-TYPE 46 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    4
  9Q LOSS WILD-TYPE   46   24
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               6                46
  MALE                 4                24
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    0  4
  9Q LOSS WILD-TYPE  8 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0    4
  9Q LOSS WILD-TYPE    8   23
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               4                23
[1] 2 2
[1] FALSE

Clustering(55) Variable = 10P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    6  5
  10P LOSS WILD-TYPE 46 22
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                 68 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                 22 
$`10P LOSS MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JQ 
       15.45        30.31        69.21        17.79        40.34        22.16 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L6 TCGA-OR-A5LM 
       12.59        50.66        18.15        20.65        61.08 

$`10P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        55.13        63.85        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        38.89        18.12        57.53        91.46        41.39 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       46.82        10.16        41.26        22.03        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX 
        4.90       121.25        16.04         9.50        63.25        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
        8.32        37.15        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        18.25        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
        5.23        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        73.05        53.03        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       21.01        29.00        12.00        23.31        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.59               4.11 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             69.21             153.63 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            22.160             33.255 
[1] "12.6 - 69.2 (22.2)" "4.1 - 153.6 (33.3)"
[1] "hr=" "1.6"
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         1        6         0        4
  10P LOSS WILD-TYPE       7       28        17       13
D55V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  1                  7
  STAGE II                 6                 28
  STAGE III                0                 17
  STAGE IV                 4                 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                 T1 T2 T3 T4
  10P LOSS MUTATED    1  6  1  3
  10P LOSS WILD-TYPE  7 33 10 15
D55V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  7
  T2                6                 33
  T3                1                 10
  T4                3                 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"
D55V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    8  3
  10P LOSS WILD-TYPE 59  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    3
  10P LOSS WILD-TYPE   59    7
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                8                 59
  1                3                  7
[1] 2 2
[1] FALSE
D55V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    7  4
  10P LOSS WILD-TYPE 45 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      7    4
  10P LOSS WILD-TYPE   45   24
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                7                 45
  MALE                  4                 24
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  1
  10P LOSS WILD-TYPE  7 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    1
  10P LOSS WILD-TYPE    7   26
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                1                 26
[1] 2 2
[1] FALSE

Clustering(56) Variable = 10Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    5  4
  10Q LOSS WILD-TYPE 47 23
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 70 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 4                 23 
$`10Q LOSS MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5JS 
       30.31        69.21        17.79        40.34        22.16        12.59 
TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L6 
       50.66        18.15        20.65 

$`10Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        38.89        18.12        57.53        91.46 
TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM 
       41.39        46.82        10.16        41.26        22.03        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
       29.23         4.90       121.25        16.04         9.50        63.25 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       17.36         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       39.58         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       78.41        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        10.09        27.29        42.51 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             12.59               4.11 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             69.21             153.63 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            22.160             33.255 
[1] "12.6 - 69.2 (22.2)" "4.1 - 153.6 (33.3)"
[1] "hr=" "1.6"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         1        5         0        3
  10Q LOSS WILD-TYPE       7       29        17       14
D56V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  7
  STAGE II                 5                 29
  STAGE III                0                 17
  STAGE IV                 3                 14
[1] 4 2
[1] 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    1  5  0  3
  10Q LOSS WILD-TYPE  7 34 11 15
D56V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  7
  T2                5                 34
  T3                0                 11
  T4                3                 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"
D56V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    7  2
  10Q LOSS WILD-TYPE 60  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7    2
  10Q LOSS WILD-TYPE   60    8
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                7                 60
  1                2                  8
[1] 2 2
[1] FALSE
D56V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    6  3
  10Q LOSS WILD-TYPE 46 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6    3
  10Q LOSS WILD-TYPE   46   25
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 46
  MALE                  3                 25
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    0  1
  10Q LOSS WILD-TYPE  8 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    1
  10Q LOSS WILD-TYPE    8   26
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                1                 26
[1] 2 2
[1] FALSE

Clustering(57) Variable = 11P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   16  7
  11P LOSS WILD-TYPE 36 20
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                23                 56 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 20 
$`11P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH 
       16.11        30.31        57.53        91.46        17.79        40.34 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW 
       46.82        41.26        22.03        22.16        50.66        63.25 
TCGA-OR-A5JY TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM 
       18.15        37.15        11.31        20.65         5.23        61.08 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA TCGA-PK-A5HB 
       62.99        29.00        23.31        27.29        42.51 

$`11P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       19.04        38.89        18.12        69.21        41.39        10.16 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       18.48        29.23         4.90       121.25        12.59        16.04 
TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
        9.50        31.23         6.94        33.83        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       93.44        17.36         8.32        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       23.80        27.62        18.25        21.21        16.01        39.58 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       73.05        53.03        64.08        52.04        21.01        12.00 
TCGA-P6-A5OG TCGA-PK-A5H9 
       12.59        10.09 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              5.23               4.11 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             91.46             153.63 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            30.310             31.955 
[1] "5.2 - 91.5 (30.3)"  "4.1 - 153.6 (32.0)"
[1] "hr=" "1.2"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         2       11         1        6
  11P LOSS WILD-TYPE       6       23        16       11
D57V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  2                  6
  STAGE II                11                 23
  STAGE III                1                 16
  STAGE IV                 6                 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                 T1 T2 T3 T4
  11P LOSS MUTATED    2 12  1  5
  11P LOSS WILD-TYPE  6 27 10 13
D57V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                2                  6
  T2               12                 27
  T3                1                 10
  T4                5                 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"
D57V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   18  3
  11P LOSS WILD-TYPE 49  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18    3
  11P LOSS WILD-TYPE   49    7
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               18                 49
  1                3                  7
[1] 2 2
[1] FALSE
D57V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   13 10
  11P LOSS WILD-TYPE 39 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13   10
  11P LOSS WILD-TYPE   39   18
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               13                 39
  MALE                 10                 18
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1  4
  11P LOSS WILD-TYPE  7 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    4
  11P LOSS WILD-TYPE    7   23
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                4                 23
[1] 2 2
[1] FALSE

Clustering(58) Variable = 11Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   17  5
  11Q LOSS WILD-TYPE 35 22
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                22                 57 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 22 
$`11Q LOSS MUTATED`
TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI 
       30.31        57.53        91.46        17.79        40.34        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       41.26        22.03        22.16        12.59        50.66        63.25 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM TCGA-OR-A5LN 
       37.15        11.31        20.65         5.23        61.08        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA TCGA-PK-A5HB 
       29.00        23.31        27.29        42.51 

$`11Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        38.89        18.12        69.21        41.39 
TCGA-OR-A5JJ TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JT 
       10.16        18.48        29.23         4.90       121.25        16.04 
TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
        9.50        31.23        18.15         6.94        33.83        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        93.44        17.36         8.32        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       39.58        39.35        21.76        14.63        52.24        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        64.08        52.04        21.01 
TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 
       12.00        12.59        10.09 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              5.23               4.11 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             91.46             153.63 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             33.73              31.23 
[1] "5.2 - 91.5 (33.7)"  "4.1 - 153.6 (31.2)"
[1] "hr=" "1.7"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         2       12         0        5
  11Q LOSS WILD-TYPE       6       22        17       12
D58V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  2                  6
  STAGE II                12                 22
  STAGE III                0                 17
  STAGE IV                 5                 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                 T1 T2 T3 T4
  11Q LOSS MUTATED    2 13  0  4
  11Q LOSS WILD-TYPE  6 26 11 14
D58V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                2                  6
  T2               13                 26
  T3                0                 11
  T4                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   18  2
  11Q LOSS WILD-TYPE 49  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     18    2
  11Q LOSS WILD-TYPE   49    8
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               18                 49
  1                2                  8
[1] 2 2
[1] FALSE
D58V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   12 10
  11Q LOSS WILD-TYPE 40 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     12   10
  11Q LOSS WILD-TYPE   40   18
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               12                 40
  MALE                 10                 18
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  4
  11Q LOSS WILD-TYPE  8 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    4
  11Q LOSS WILD-TYPE    8   23
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                4                 23
[1] 2 2
[1] FALSE

Clustering(59) Variable = 12P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    2  3
  12P LOSS WILD-TYPE 50 24
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 74 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 24 
$`12P LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5LG TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5HB 
       18.12        52.24        53.03        12.59        42.51 

$`12P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        38.89        30.31        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.26        22.03        18.48        29.23         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        16.04         9.50        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15         6.94        33.83        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO 
       93.44        17.36         8.32        37.15        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       21.21        16.01        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        78.41        36.33        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       10.09        27.29 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             12.59               4.11 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             53.03             153.63 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             42.51              30.77 
[1] "12.6 - 53.0 (42.5)" "4.1 - 153.6 (30.8)"
[1] "hr=" "2.1"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         0        1         1        2
  12P LOSS WILD-TYPE       8       33        16       15
D59V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 1                 33
  STAGE III                1                 16
  STAGE IV                 2                 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"
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    0  1  1  2
  12P LOSS WILD-TYPE  8 38 10 16
D59V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                0                  8
  T2                1                 38
  T3                1                 10
  T4                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 63 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    0
  12P LOSS WILD-TYPE   63   10
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                4                 63
  1                0                 10
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  3
  12P LOSS WILD-TYPE 50 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    3
  12P LOSS WILD-TYPE   50   25
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 50
  MALE                  3                 25
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    0  2
  12P LOSS WILD-TYPE  8 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    2
  12P LOSS WILD-TYPE    8   25
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(60) Variable = 12Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    1  3
  12Q LOSS WILD-TYPE 51 24
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 75 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 24 
$`12Q LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5LG TCGA-OR-A5LL TCGA-P6-A5OG 
       18.12        52.24        53.03        12.59 

$`12Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        38.89        30.31        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.26        22.03        18.48        29.23         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        16.04         9.50        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15         6.94        33.83        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO 
       93.44        17.36         8.32        37.15        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       21.21        16.01        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        78.41        36.33        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       64.08        52.04        21.01        29.00        12.00        23.31 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       10.09        27.29        42.51 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             12.59               4.11 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             53.03             153.63 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             35.18              31.23 
[1] "12.6 - 53.0 (35.2)" "4.1 - 153.6 (31.2)"
[1] "hr=" "2.8"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         0        1         1        2
  12Q LOSS WILD-TYPE       8       33        16       15
D60V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 1                 33
  STAGE III                1                 16
  STAGE IV                 2                 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"
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    0  1  1  2
  12Q LOSS WILD-TYPE  8 38 10 16
D60V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                0                  8
  T2                1                 38
  T3                1                 10
  T4                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    4  0
  12Q LOSS WILD-TYPE 63 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    0
  12Q LOSS WILD-TYPE   63   10
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                4                 63
  1                0                 10
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  2
  12Q LOSS WILD-TYPE 50 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    2
  12Q LOSS WILD-TYPE   50   26
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                2                 50
  MALE                  2                 26
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    0  2
  12Q LOSS WILD-TYPE  8 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE    8   25
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(61) Variable = 13Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   18 14
  13Q LOSS WILD-TYPE 34 13
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                32                 47 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                14                 13 
$`13Q LOSS MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       15.45        16.11        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP 
       69.21        17.79        40.34        46.82        41.26         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 
       22.16        12.59         9.50        50.66        63.25        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LD 
        8.32        11.31       153.63         4.11        20.65        39.35 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG 
       73.05        53.03        62.99        29.00        23.31        12.59 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

$`13Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 
       44.55        55.13        63.85        12.00        79.82        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       38.89        41.39        10.16        22.03        18.48        29.23 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
      121.25        16.04        31.23        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT 
       89.52        93.44        17.36        37.15        46.49        87.88 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 
      120.30        50.14        35.87        12.85       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       27.62        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LM 
       21.76        14.63        52.24        78.41        36.33        61.08 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PK-A5H9 
       64.08        52.04        21.01        12.00        10.09 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              4.11               5.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            153.63             128.12 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            29.655             33.830 
[1] "4.1 - 153.6 (29.7)" "5.2 - 128.1 (33.8)"
[1] "hr=" "1.8"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         2       15         5        8
  13Q LOSS WILD-TYPE       6       19        12        9
D61V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  2                  6
  STAGE II                15                 19
  STAGE III                5                 12
  STAGE IV                 8                  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                 T1 T2 T3 T4
  13Q LOSS MUTATED    2 16  4  8
  13Q LOSS WILD-TYPE  6 23  7 10
D61V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                2                  6
  T2               16                 23
  T3                4                  7
  T4                8                 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"
D61V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   28  3
  13Q LOSS WILD-TYPE 39  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     28    3
  13Q LOSS WILD-TYPE   39    7
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               28                 39
  1                3                  7
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   19 14
  13Q LOSS WILD-TYPE 33 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     19   14
  13Q LOSS WILD-TYPE   33   14
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               19                 33
  MALE                 14                 14
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2  7
  13Q LOSS WILD-TYPE  6 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2    7
  13Q LOSS WILD-TYPE    6   20
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO                7                 20
[1] 2 2
[1] FALSE

Clustering(62) Variable = 14Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   10  7
  14Q LOSS WILD-TYPE 42 20
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                17                 62 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 20 
$`14Q LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK 
       79.82        16.11        19.04        91.46        40.34        41.26 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5KZ TCGA-OR-A5L6 
       18.48        22.16        50.66        18.15         4.11        20.65 
TCGA-OR-A5LC TCGA-OR-A5LN TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5HA 
        5.23        62.99        12.00        12.59        27.29 

$`14Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J9 
       44.55        55.13        63.85        15.45        12.00        38.89 
TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       30.31        18.12        57.53        69.21        41.39        17.79 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       46.82        10.16        22.03        29.23         4.90       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
       12.59        16.04         9.50        63.25        31.23         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       37.15        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87        12.85       128.12        23.80        27.62 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE 
       18.25        21.21        16.01        39.58        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        78.41        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OU-A5PI 
       61.08        64.08        52.04        21.01        29.00        23.31 
TCGA-PK-A5H9 TCGA-PK-A5HB 
       10.09        42.51 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              4.11               4.90 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             91.46             153.63 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             20.65              34.85 
[1] "4.1 - 91.5 (20.6)"  "4.9 - 153.6 (34.8)"
[1] "hr=" "1.5"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         0        8         3        5
  14Q LOSS WILD-TYPE       8       26        14       12
D62V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 8                 26
  STAGE III                3                 14
  STAGE IV                 5                 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                 T1 T2 T3 T4
  14Q LOSS MUTATED    0  8  3  5
  14Q LOSS WILD-TYPE  8 31  8 13
D62V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                0                  8
  T2                8                 31
  T3                3                  8
  T4                5                 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"
D62V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   16  1
  14Q LOSS WILD-TYPE 51  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     16    1
  14Q LOSS WILD-TYPE   51    9
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               16                 51
  1                1                  9
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   10  7
  14Q LOSS WILD-TYPE 42 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10    7
  14Q LOSS WILD-TYPE   42   21
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               10                 42
  MALE                  7                 21
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    3  4
  14Q LOSS WILD-TYPE  5 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    4
  14Q LOSS WILD-TYPE    5   23
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO                4                 23
[1] 2 2
[1] FALSE

Clustering(63) Variable = 15Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   12  7
  15Q LOSS WILD-TYPE 40 20
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                19                 60 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 20 
$`15Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JM TCGA-OR-A5JQ 
       16.11        91.46        40.34        46.82        18.48        22.16 
TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KT TCGA-OR-A5KX TCGA-OR-A5L6 
       50.66        32.68        11.31        87.88        35.87        20.65 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
        5.23        39.35        29.00        12.00        23.31        12.59 
TCGA-PK-A5HA 
       27.29 

$`15Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE 
       19.04        38.89        30.31        18.12        57.53        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO 
       41.39        17.79        10.16        41.26        22.03        29.23 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JW 
        4.90       121.25        12.59        16.04         9.50        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 
       31.23        18.15         6.94        33.83        89.52        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36         8.32        37.15        46.49       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LF 
       18.25        21.21        16.01        39.58        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5H9 TCGA-PK-A5HB 
       62.99        64.08        52.04        21.01        10.09        42.51 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              5.23               4.11 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             91.46             153.63 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             27.29              35.08 
[1] "5.2 - 91.5 (27.3)"  "4.1 - 153.6 (35.1)"
[1] "hr=" "1.3"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         2        7         5        5
  15Q LOSS WILD-TYPE       6       27        12       12
D63V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  2                  6
  STAGE II                 7                 27
  STAGE III                5                 12
  STAGE IV                 5                 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                 T1 T2 T3 T4
  15Q LOSS MUTATED    2  9  2  6
  15Q LOSS WILD-TYPE  6 30  9 12
D63V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                2                  6
  T2                9                 30
  T3                2                  9
  T4                6                 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"
D63V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   18  2
  15Q LOSS WILD-TYPE 49  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     18    2
  15Q LOSS WILD-TYPE   49    8
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               18                 49
  1                2                  8
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   14  6
  15Q LOSS WILD-TYPE 38 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     14    6
  15Q LOSS WILD-TYPE   38   22
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               14                 38
  MALE                  6                 22
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  8
  15Q LOSS WILD-TYPE  7 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    8
  15Q LOSS WILD-TYPE    7   19
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                8                 19
[1] 2 2
[1] FALSE

Clustering(64) Variable = 16P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  5
  16P LOSS WILD-TYPE 51 22
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 73 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 22 
$`16P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5LD TCGA-P6-A5OG 
       16.11        18.12        18.15        33.83        39.35        12.59 

$`16P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        38.89        30.31        57.53        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       22.03        18.48        29.23         4.90        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        89.52        32.68        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       37.15        11.31        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
       50.14        35.87        12.85         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
        5.23        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       73.05        53.03        61.08        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA 
       21.01        29.00        12.00        23.31        10.09        27.29 
TCGA-PK-A5HB 
       42.51 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             12.59               4.11 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             39.35             153.63 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            18.135             32.680 
[1] "12.6 - 39.4 (18.1)" "4.1 - 153.6 (32.7)"
[1] "hr=" "5"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         0        1         2        3
  16P LOSS WILD-TYPE       8       33        15       14
D64V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 1                 33
  STAGE III                2                 15
  STAGE IV                 3                 14
[1] 4 2
[1] 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  1  1  4
  16P LOSS WILD-TYPE  8 38 10 14
D64V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                  8
  T2                1                 38
  T3                1                 10
  T4                4                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    5  1
  16P LOSS WILD-TYPE 62  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    1
  16P LOSS WILD-TYPE   62    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                 62
  1                1                  9
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  2
  16P LOSS WILD-TYPE 48 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    2
  16P LOSS WILD-TYPE   48   26
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                4                 48
  MALE                  2                 26
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  2
  16P LOSS WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    2
  16P LOSS WILD-TYPE    7   25
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(65) Variable = 16Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    1  4
  16Q LOSS WILD-TYPE 51 23
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 74 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 23 
$`16Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5LB TCGA-OR-A5LD 
       16.11        18.15        33.83        39.58        39.35 

$`16Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.26        22.03        18.48        29.23         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        16.04         9.50        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23         6.94        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
        8.32        37.15        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
        5.23        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       73.05        53.03        61.08        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       21.01        29.00        12.00        23.31        12.59        10.09 
TCGA-PK-A5HA TCGA-PK-A5HB 
       27.29        42.51 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             16.11               4.11 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             39.58             153.63 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             33.83              30.77 
[1] "16.1 - 39.6 (33.8)" "4.1 - 153.6 (30.8)"
[1] "hr=" "3.3"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         0        1         2        2
  16Q LOSS WILD-TYPE       8       33        15       15
D65V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 1                 33
  STAGE III                2                 15
  STAGE IV                 2                 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"
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    0  1  1  3
  16Q LOSS WILD-TYPE  8 38 10 15
D65V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                  8
  T2                1                 38
  T3                1                 10
  T4                3                 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"
D65V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  1
  16Q LOSS WILD-TYPE 63  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    1
  16Q LOSS WILD-TYPE   63    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                4                 63
  1                1                  9
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  2
  16Q LOSS WILD-TYPE 49 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    2
  16Q LOSS WILD-TYPE   49   26
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 49
  MALE                  2                 26
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  2
  16Q LOSS WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    2
  16Q LOSS WILD-TYPE    7   25
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 25
[1] 2 2
[1] FALSE

Clustering(66) Variable = 17P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   14 15
  17P LOSS WILD-TYPE 38 12
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                29                 50 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                15                 12 
$`17P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JG 
       16.11        30.31        18.12        57.53        69.21        17.79 
TCGA-OR-A5JH TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JS TCGA-OR-A5JV 
       40.34        41.26        18.48         4.90        12.59        50.66 
TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KX TCGA-OR-A5KY 
       63.25        32.68         8.32        11.31        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LM 
        4.11        20.65        39.58         5.23        21.76        61.08 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       29.00        23.31        12.59        27.29        42.51 

$`17P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ 
       19.04        38.89        91.46        41.39        46.82        10.16 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU 
       22.03        29.23        22.16       121.25        16.04         9.50 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 
       31.23        18.15         6.94        33.83        89.52        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       17.36        37.15        46.49        87.88       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       50.14       128.12        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       16.01        39.35        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        53.03        62.99        64.08        52.04        21.01 
TCGA-OR-A5LT TCGA-PK-A5H9 
       12.00        10.09 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              4.11               6.94 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             69.21             153.63 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             23.31              38.02 
[1] "4.1 - 69.2 (23.3)"  "6.9 - 153.6 (38.0)"
[1] "hr=" "3.4"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         1       11         4       10
  17P LOSS WILD-TYPE       7       23        13        7
D66V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  1                  7
  STAGE II                11                 23
  STAGE III                4                 13
  STAGE IV                10                  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                 T1 T2 T3 T4
  17P LOSS MUTATED    1 13  2 10
  17P LOSS WILD-TYPE  7 26  9  8
D66V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                1                  7
  T2               13                 26
  T3                2                  9
  T4               10                  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"
D66V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   23  4
  17P LOSS WILD-TYPE 44  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     23    4
  17P LOSS WILD-TYPE   44    6
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               23                 44
  1                4                  6
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   15 14
  17P LOSS WILD-TYPE 37 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     15   14
  17P LOSS WILD-TYPE   37   14
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               15                 37
  MALE                 14                 14
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1  9
  17P LOSS WILD-TYPE  7 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1    9
  17P LOSS WILD-TYPE    7   18
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                9                 18
[1] 2 2
[1] FALSE

Clustering(67) Variable = 17Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   12 12
  17Q LOSS WILD-TYPE 40 15
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                 55 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 15 
$`17Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JK TCGA-OR-A5JP 
       16.11        30.31        57.53        17.79        41.26         4.90 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KY 
       12.59        50.66        63.25        32.68        11.31        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
        4.11        20.65        39.58         5.23        21.76        52.24 
TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       61.08        29.00        23.31        12.59        27.29        42.51 

$`17Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        38.89        18.12        91.46        69.21        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       40.34        46.82        10.16        22.03        18.48        29.23 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JX TCGA-OR-A5JY 
       22.16       121.25        16.04         9.50        31.23        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        33.83        89.52        93.44        17.36         8.32 
TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       37.15        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       35.87       128.12        23.80        27.62        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       16.01        39.35        14.63        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       53.03        62.99        64.08        52.04        21.01        12.00 
TCGA-PK-A5H9 
       10.09 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              4.11               6.94 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             63.25             153.63 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             25.30              36.33 
[1] "4.1 - 63.2 (25.3)"  "6.9 - 153.6 (36.3)"
[1] "hr=" "2.8"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         0       10         3        8
  17Q LOSS WILD-TYPE       8       24        14        9
D67V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                10                 24
  STAGE III                3                 14
  STAGE IV                 8                  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                 T1 T2 T3 T4
  17Q LOSS MUTATED    0 11  2  8
  17Q LOSS WILD-TYPE  8 28  9 10
D67V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  8
  T2               11                 28
  T3                2                  9
  T4                8                 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"
D67V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   19  3
  17Q LOSS WILD-TYPE 48  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     19    3
  17Q LOSS WILD-TYPE   48    7
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               19                 48
  1                3                  7
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10 14
  17Q LOSS WILD-TYPE 42 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10   14
  17Q LOSS WILD-TYPE   42   14
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               10                 42
  MALE                 14                 14
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  9
  17Q LOSS WILD-TYPE  7 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    9
  17Q LOSS WILD-TYPE    7   18
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                9                 18
[1] 2 2
[1] FALSE

Clustering(68) Variable = 18P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   23 12
  18P LOSS WILD-TYPE 29 15
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                35                 44 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                12                 15 
$`18P LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       79.82        16.11        30.31        18.12        57.53        91.46 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       17.79        40.34        46.82        41.26         4.90        22.16 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       12.59        16.04        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KY TCGA-OR-A5L6 
       32.68         8.32        46.49        87.88        12.85        20.65 
TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS 
        5.23        21.76        53.03        61.08        62.99        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       12.00        23.31        12.59        27.29        42.51 

$`18P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM 
       38.89        69.21        41.39        10.16        22.03        18.48 
TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       29.23       121.25         9.50         6.94        33.83        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KU TCGA-OR-A5KV 
       93.44        17.36        37.15        11.31       153.63       120.30 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        35.87         4.11       128.12        23.80        27.62 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF 
       18.25        21.21        16.01        39.58        39.35        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP 
       52.24        78.41        36.33        73.05        64.08        52.04 
TCGA-OR-A5LR TCGA-PK-A5H9 
       21.01        10.09 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              4.90               4.11 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             91.46             153.63 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              29.0               36.1 
[1] "4.9 - 91.5 (29.0)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "1.1"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         2       15         5       11
  18P LOSS WILD-TYPE       6       19        12        6
D68V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  2                  6
  STAGE II                15                 19
  STAGE III                5                 12
  STAGE IV                11                  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                 T1 T2 T3 T4
  18P LOSS MUTATED    2 16  4 11
  18P LOSS WILD-TYPE  6 23  7  7
D68V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                2                  6
  T2               16                 23
  T3                4                  7
  T4               11                  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"
D68V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   30  4
  18P LOSS WILD-TYPE 37  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     30    4
  18P LOSS WILD-TYPE   37    6
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               30                 37
  1                4                  6
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   21 15
  18P LOSS WILD-TYPE 31 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     21   15
  18P LOSS WILD-TYPE   31   13
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               21                 31
  MALE                 15                 13
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  9
  18P LOSS WILD-TYPE  6 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    9
  18P LOSS WILD-TYPE    6   18
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO                9                 18
[1] 2 2
[1] FALSE

Clustering(69) Variable = 18Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   22 11
  18Q LOSS WILD-TYPE 30 16
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                33                 46 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 16 
$`18Q LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       79.82        16.11        18.12        57.53        91.46        17.79 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS 
       40.34        46.82        41.26         4.90        22.16        12.59 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       16.04        50.66        63.25        31.23        18.15        32.68 
TCGA-OR-A5KO TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       46.49        12.85        20.65         5.23        21.76        52.24 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       53.03        61.08        62.99        29.00        12.00        23.31 
TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        27.29        42.51 

$`18Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J8 
       44.55        55.13        63.85        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       38.89        30.31        69.21        41.39        10.16        22.03 
TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JZ TCGA-OR-A5K0 
       18.48        29.23       121.25         9.50         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 
       89.52        93.44        17.36         8.32        37.15        11.31 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ 
       87.88       153.63       120.30        50.14        35.87         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      128.12        23.80        27.62        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.58        39.35        14.63        78.41        36.33        73.05 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5H9 
       64.08        52.04        21.01        10.09 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              4.90               4.11 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             91.46             153.63 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             29.00              34.85 
[1] "4.9 - 91.5 (29.0)"  "4.1 - 153.6 (34.8)"
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         1       15         5       10
  18Q LOSS WILD-TYPE       7       19        12        7
D69V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  1                  7
  STAGE II                15                 19
  STAGE III                5                 12
  STAGE IV                10                  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                 T1 T2 T3 T4
  18Q LOSS MUTATED    1 16  4 10
  18Q LOSS WILD-TYPE  7 23  7  8
D69V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                1                  7
  T2               16                 23
  T3                4                  7
  T4               10                  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"
D69V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   28  4
  18Q LOSS WILD-TYPE 39  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     28    4
  18Q LOSS WILD-TYPE   39    6
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               28                 39
  1                4                  6
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   18 16
  18Q LOSS WILD-TYPE 34 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     18   16
  18Q LOSS WILD-TYPE   34   12
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               18                 34
  MALE                 16                 12
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2  9
  18Q LOSS WILD-TYPE  6 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2    9
  18Q LOSS WILD-TYPE    6   18
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO                9                 18
[1] 2 2
[1] FALSE

Clustering(70) Variable = 19P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    0  3
  19P LOSS WILD-TYPE 52 24
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 76 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 24 
$`19P LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-P6-A5OG 
       44.55        18.12        12.59 

$`19P LOSS WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        38.89        30.31        57.53        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       22.03        18.48        29.23         4.90        22.16       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        16.04         9.50        50.66        63.25        31.23 
TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       18.15         6.94        33.83        89.52        32.68        93.44 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT 
       17.36         8.32        37.15        11.31        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       120.30        50.14        35.87        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      128.12        23.80        27.62        20.65        18.25        21.21 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       16.01        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        36.33        73.05        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        10.09        27.29        42.51 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             12.59               4.11 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             44.55             153.63 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            18.120             31.955 
[1] "12.6 - 44.5 (18.1)" "4.1 - 153.6 (32.0)"
[1] "hr=" "4.9"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0        1         0        2
  19P LOSS WILD-TYPE       8       33        17       15
D70V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 1                 33
  STAGE III                0                 17
  STAGE IV                 2                 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"
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    0  1  0  2
  19P LOSS WILD-TYPE  8 38 11 16
D70V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  8
  T2                1                 38
  T3                0                 11
  T4                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3  0
  19P LOSS WILD-TYPE 64 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    0
  19P LOSS WILD-TYPE   64   10
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                3                 64
  1                0                 10
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    1  2
  19P LOSS WILD-TYPE 51 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1    2
  19P LOSS WILD-TYPE   51   26
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                1                 51
  MALE                  2                 26
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    0  1
  19P LOSS WILD-TYPE  8 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    1
  19P LOSS WILD-TYPE    8   26
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                1                 26
[1] 2 2
[1] FALSE

Clustering(71) Variable = 19Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    0  3
  19Q LOSS WILD-TYPE 52 24
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 76 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 24 
$`19Q LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5LL TCGA-P6-A5OG 
       44.55        53.03        12.59 

$`19Q LOSS WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        63.85        15.45        12.00        79.82        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        38.89        30.31        18.12        57.53        91.46 
TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ 
       69.21        41.39        17.79        40.34        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       41.26        22.03        18.48        29.23         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        16.04         9.50        50.66        63.25 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 
       31.23        18.15         6.94        33.83        89.52        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO 
       93.44        17.36         8.32        37.15        11.31        46.49 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       87.88       153.63       120.30        50.14        35.87        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       128.12        23.80        27.62        20.65        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       21.21        16.01        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        52.24        78.41        36.33        73.05        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        64.08        52.04        21.01        29.00        12.00 
TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        10.09        27.29        42.51 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             12.59               4.11 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             53.03             153.63 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             44.55              30.77 
[1] "12.6 - 53.0 (44.5)" "4.1 - 153.6 (30.8)"
[1] "hr=" "3.4"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0        2         0        1
  19Q LOSS WILD-TYPE       8       32        17       16
D71V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 2                 32
  STAGE III                0                 17
  STAGE IV                 1                 16
[1] 4 2
[1] 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    0  2  0  1
  19Q LOSS WILD-TYPE  8 37 11 17
D71V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  8
  T2                2                 37
  T3                0                 11
  T4                1                 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"
D71V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  0
  19Q LOSS WILD-TYPE 64 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    0
  19Q LOSS WILD-TYPE   64   10
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                3                 64
  1                0                 10
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  1
  19Q LOSS WILD-TYPE 50 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    1
  19Q LOSS WILD-TYPE   50   27
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                2                 50
  MALE                  1                 27
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    0  1
  19Q LOSS WILD-TYPE  8 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    1
  19Q LOSS WILD-TYPE    8   26
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                1                 26
[1] 2 2
[1] FALSE

Clustering(72) Variable = 20P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    4  3
  20P LOSS WILD-TYPE 48 24
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 7                 72 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 24 
$`20P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5K0 TCGA-OU-A5PI 
       16.11        30.31        18.48        12.59        33.83        23.31 
TCGA-PK-A5HB 
       42.51 

$`20P LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        38.89        18.12        57.53        91.46        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       22.03        29.23         4.90        22.16       121.25        16.04 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
        9.50        50.66        63.25        31.23        18.15         6.94 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       89.52        32.68        93.44        17.36         8.32        37.15 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       11.31        46.49        87.88       153.63       120.30        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       35.87        12.85         4.11       128.12        23.80        27.62 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       20.65        18.25        21.21        16.01        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       39.35        21.76        14.63        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       73.05        53.03        61.08        62.99        64.08        52.04 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       21.01        29.00        12.00        12.59        10.09        27.29 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             12.59               4.11 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             42.51             153.63 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            23.310             34.275 
[1] "12.6 - 42.5 (23.3)" "4.1 - 153.6 (34.3)"
[1] "hr=" "1.9"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0        2         1        3
  20P LOSS WILD-TYPE       8       32        16       14
D72V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 2                 32
  STAGE III                1                 16
  STAGE IV                 3                 14
[1] 4 2
[1] 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    0  3  1  2
  20P LOSS WILD-TYPE  8 36 10 16
D72V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                  8
  T2                3                 36
  T3                1                 10
  T4                2                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    5  1
  20P LOSS WILD-TYPE 62  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    1
  20P LOSS WILD-TYPE   62    9
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                5                 62
  1                1                  9
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    6  1
  20P LOSS WILD-TYPE 46 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    1
  20P LOSS WILD-TYPE   46   27
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                6                 46
  MALE                  1                 27
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  1
  20P LOSS WILD-TYPE  7 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    1
  20P LOSS WILD-TYPE    7   26
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                1                 26
[1] 2 2
[1] FALSE

Clustering(73) Variable = 21Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    6  9
  21Q LOSS WILD-TYPE 46 18
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 64 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                 18 
$`21Q LOSS MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JM TCGA-OR-A5JQ 
       19.04        30.31        91.46        40.34        18.48        22.16 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF 
        9.50        50.66        18.15         5.23        21.76        14.63 
TCGA-OR-A5LN TCGA-P6-A5OG TCGA-PK-A5HA 
       62.99        12.59        27.29 

$`21Q LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        38.89        18.12        57.53        69.21        41.39 
TCGA-OR-A5JG TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO 
       17.79        46.82        10.16        41.26        22.03        29.23 
TCGA-OR-A5JP TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JW TCGA-OR-A5JX 
        4.90       121.25        12.59        16.04        63.25        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        89.52        32.68        93.44        17.36 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
        8.32        37.15        11.31        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 
      120.30        50.14        35.87        12.85         4.11       128.12 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       23.80        27.62        20.65        18.25        21.21        16.01 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.58        39.35        52.24        78.41        36.33        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       53.03        61.08        64.08        52.04        21.01        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5H9 TCGA-PK-A5HB 
       12.00        23.31        10.09        42.51 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              5.23               4.11 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             91.46             153.63 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             21.76              36.10 
[1] "5.2 - 91.5 (21.8)"  "4.1 - 153.6 (36.1)"
[1] "hr=" "2.8"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         0        6         3        5
  21Q LOSS WILD-TYPE       8       28        14       12
D73V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  0                  8
  STAGE II                 6                 28
  STAGE III                3                 14
  STAGE IV                 5                 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                 T1 T2 T3 T4
  21Q LOSS MUTATED    0  6  3  5
  21Q LOSS WILD-TYPE  8 33  8 13
D73V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                0                  8
  T2                6                 33
  T3                3                  8
  T4                5                 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"
D73V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   14  1
  21Q LOSS WILD-TYPE 53  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14    1
  21Q LOSS WILD-TYPE   53    9
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               14                 53
  1                1                  9
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   11  4
  21Q LOSS WILD-TYPE 41 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11    4
  21Q LOSS WILD-TYPE   41   24
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               11                 41
  MALE                  4                 24
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1  3
  21Q LOSS WILD-TYPE  7 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1    3
  21Q LOSS WILD-TYPE    7   24
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 24
[1] 2 2
[1] FALSE

Clustering(74) Variable = 22Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   23 21
  22Q LOSS WILD-TYPE 29  6
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                44                 35 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                21                  6 
$`22Q LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       44.55        55.13        63.85        79.82        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       38.89        30.31        18.12        57.53        91.46        69.21 
TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JQ 
       17.79        40.34        46.82        41.26         4.90        22.16 
TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25         9.50        50.66        63.25        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
       32.68         8.32        11.31        35.87        12.85         4.11 
TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LL 
       20.65        39.58         5.23        39.35        14.63        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       61.08        62.99        29.00        12.00        23.31        12.59 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       10.09        27.29 

$`22Q LOSS WILD-TYPE`
TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM 
       15.45        12.00        41.39        10.16        22.03        18.48 
TCGA-OR-A5JO TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       29.23        12.59        16.04         6.94        33.83        89.52 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KO TCGA-OR-A5KT TCGA-OR-A5KU 
       93.44        17.36        37.15        46.49        87.88       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
      120.30        50.14       128.12        23.80        27.62        18.25 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ 
       21.21        16.01        21.76        52.24        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PK-A5HB 
       73.05        64.08        52.04        21.01        42.51 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              4.11               6.94 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            121.25             153.63 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             30.77              33.83 
[1] "4.1 - 121.2 (30.8)" "6.9 - 153.6 (33.8)"
[1] "hr=" "3.3"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         3       16        11       12
  22Q LOSS WILD-TYPE       5       18         6        5
D74V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  3                  5
  STAGE II                16                 18
  STAGE III               11                  6
  STAGE IV                12                  5
[1] 4 2
[1] 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    3 18  9 12
  22Q LOSS WILD-TYPE  5 21  2  6
D74V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                3                  5
  T2               18                 21
  T3                9                  2
  T4               12                  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"
D74V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   38  5
  22Q LOSS WILD-TYPE 29  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     38    5
  22Q LOSS WILD-TYPE   29    5
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               38                 29
  1                5                  5
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   26 19
  22Q LOSS WILD-TYPE 26  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     26   19
  22Q LOSS WILD-TYPE   26    9
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               26                 26
  MALE                 19                  9
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    6 11
  22Q LOSS WILD-TYPE  2 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   11
  22Q LOSS WILD-TYPE    2   16
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO               11                 16
[1] 2 2
[1] FALSE

Clustering(75) Variable = XQ LOSS MUTATION ANALYSIS
D75V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   10  5
  XQ LOSS WILD-TYPE 42 22
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                64 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                5                22 
$`XQ LOSS MUTATED`
TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JS TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
       18.12        91.46        12.59        63.25        18.15        33.83 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5LE TCGA-OR-A5LG 
       37.15        11.31       120.30        50.14        21.76        52.24 
TCGA-OR-A5LL TCGA-PK-A5HA TCGA-PK-A5HB 
       53.03        27.29        42.51 

$`XQ LOSS WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 
       44.55        55.13        63.85        15.45        12.00        79.82 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       16.11        19.04        38.89        30.31        57.53        69.21 
TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK 
       41.39        17.79        40.34        46.82        10.16        41.26 
TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       22.03        18.48        29.23         4.90        22.16       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       16.04         9.50        50.66        31.23         6.94        89.52 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KT 
       32.68        93.44        17.36         8.32        46.49        87.88 
TCGA-OR-A5KU TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 
      153.63        35.87        12.85         4.11       128.12        23.80 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       27.62        20.65        18.25        21.21        16.01        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
        5.23        39.35        14.63        78.41        36.33        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        64.08        52.04        21.01        29.00 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 
       12.00        23.31        12.59        10.09 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            11.31              4.11 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           120.30            153.63 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            37.15             29.77 
[1] "11.3 - 120.3 (37.1)" "4.1 - 153.6 (29.8)" 
[1] "hr=" "1.1"
D75V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         0        8         3        2
  XQ LOSS WILD-TYPE       8       26        14       15
D75V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 0                 8
  STAGE II                8                26
  STAGE III               3                14
  STAGE IV                2                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"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    0 10  1  2
  XQ LOSS WILD-TYPE  8 29 10 16
D75V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0                 8
  T2              10                29
  T3               1                10
  T4               2                16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   11  3
  XQ LOSS WILD-TYPE 56  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11    3
  XQ LOSS WILD-TYPE   56    7
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              11                56
  1               3                 7
[1] 2 2
[1] FALSE
D75V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    9  6
  XQ LOSS WILD-TYPE 43 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      9    6
  XQ LOSS WILD-TYPE   43   22
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               9                43
  MALE                 6                22
[1] 2 2
[1] FALSE
D75V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  5
  XQ LOSS WILD-TYPE  8 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    5
  XQ LOSS WILD-TYPE    8   22
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               5                22
[1] 2 2
[1] FALSE
