[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/11541222/ACC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/ACC-TP/11562192/transformed.cor.cli.txt"

nPatients in clinical file=92, in cluster file=90, common to both=90
[1] 80 90
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                86 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                86 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                82 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                82 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                77 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               13                77 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12                78 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               12                78 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13                77 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13                77 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15                75 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15                75 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               37                53 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               37                53 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33                57 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33                57 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57                33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               57                33 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               53                37 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               53                37 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                72 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                72 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                74 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                74 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48                42 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48                42 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                42 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                42 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                58 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                58 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               38                52 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               38                52 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               20                70 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               20                70 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               29                61 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               29                61 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                 65 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                 65 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                 64 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                26                 64 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 85 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 5                 85 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 84 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 84 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                 26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                 26 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                64                 26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                64                 26 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 84 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 84 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 69 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 69 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 79 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                49                 41 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                49                 41 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                47                 43 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                47                 43 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 85 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 5                 85 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 83 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 83 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 84 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 84 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 85 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 85 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                 34 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                56                 34 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                52                 38 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                52                 38 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                46                 44 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                46                 44 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                49                 41 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                49                 41 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                 59 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                 59 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 87 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 87 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               40                50 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               40                50 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29                61 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29                61 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20                70 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20                70 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17                73 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17                73 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                75 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                75 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20                70 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20                70 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               20                70 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               20                70 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                80 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                80 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11                79 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11                79 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8                82 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8                82 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                83 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                83 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19                71 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19                71 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                68 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22                68 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                85 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                85 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                84 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                84 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                74 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                74 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12                78 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12                78 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20                70 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20                70 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                79 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                79 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 78 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 78 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 80 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 80 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                 66 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                 66 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                 67 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                 67 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 85 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 85 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 86 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 86 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                39                 51 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                39                 51 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 72 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 72 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 69 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                21                 69 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 84 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 84 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 85 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 85 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                 58 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                 58 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                 66 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                 66 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 53 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                37                 53 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 55 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 55 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 85 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 85 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 86 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 86 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 81 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 81 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 87 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 87 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 75 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 75 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                48                 42 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                48                 42 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17                73 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17                73 
[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 90 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         2091           NA           NA         2703 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
          NA           NA         1352           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         2110         1424 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
         309         1497          670           NA          889          149 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
        1103         3688          383          907           NA         2023 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
        2202          950           NA          211         1029         2938 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
          NA         3047          699          253         1493          749 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
          NA          741         1414         2777         2677         2549 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
        2895         4673         3878         1525         1364           NA 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
          NA         1781           NA         4628          967         1317 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
         861          885          871          719           NA           NA 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
          NA           NA           NA         1589           NA           NA 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
          NA         2222           NA         1858         1916         2102 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
        1857          853         1096          549          709           NA 
TCGA-P6-A5OH TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
          NA          470          616         1201         1293          679 
Variable 1:'AGE':	nDistinctValues=50,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=31,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=60,	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=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                   "NEOPLASM.DISEASESTAGE" "PATHOLOGY.T.STAGE"    
[4] "PATHOLOGY.N.STAGE"     "GENDER"                "RACE"                 
[7] "ETHNICITY"            
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 90 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=50, 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 
 9 48 11 20 
[1] "table(vv)"
vv
T1 T2 T3 T4 
 9 48 11 20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 9 48 11 20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
 9 48 11 20 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    2  2
  1P GAIN WILD-TYPE 56 29
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                85 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                29 
$`1P GAIN MUTATED`
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-P6-A5OG TCGA-PK-A5HC 
       11.31        24.36        12.59        22.32 

$`1P 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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        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        69.37        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       10.16        49.22        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 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       72.39        31.23        18.15         6.94        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        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        69.11        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       36.03        18.05        23.31        15.45        20.25        39.48 
TCGA-PK-A5HB 
       42.51 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            11.31              4.11 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            24.36            153.63 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           17.455            39.350 
[1] "11.3 - 24.4 (17.5)" "4.1 - 153.6 (39.4)"
[1] "hr=" "3.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         0        2         1        1
  1P GAIN WILD-TYPE       9       41        17       17
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 0                 9
  STAGE II                2                41
  STAGE III               1                17
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  1P GAIN MUTATED    0  2  0  2
  1P GAIN WILD-TYPE  9 46 11 18
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               0                 9
  T2               2                46
  T3               0                11
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  0
  1P GAIN WILD-TYPE 74 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    0
  1P GAIN WILD-TYPE   74   10
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               4                74
  1               0                10
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  0
  1P GAIN WILD-TYPE 55 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    0
  1P GAIN WILD-TYPE   55   31
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                55
  MALE                 0                31
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       1                         0     3
  1P GAIN WILD-TYPE     1                         1    73
D1V7, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   3                73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    0  3
  1P GAIN WILD-TYPE  8 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0    3
  1P GAIN WILD-TYPE    8   34
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                34
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    3  5
  1Q GAIN WILD-TYPE 55 26
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                81 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                5                26 
$`1Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JE TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5LS 
       55.13        69.21         8.32        11.31        24.36        36.03 
TCGA-P6-A5OG TCGA-PK-A5HC 
       12.59        22.32 

$`1Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       44.55        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        46.82        10.16        49.22 
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        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        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        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       22.98        49.08        24.62        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       14.33        36.33        73.05        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG 
       69.11        61.05        28.04        18.05        23.31        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       20.25        39.48        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 
            23.34             39.35 
[1] "8.3 - 69.2 (23.3)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "2.7"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED         1        3         2        2
  1Q GAIN WILD-TYPE       8       40        16       16
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                3                40
  STAGE III               2                16
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    1  3  2  2
  1Q GAIN WILD-TYPE  8 45  9 18
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               1                 8
  T2               3                45
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    8  0
  1Q GAIN WILD-TYPE 70 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    0
  1Q GAIN WILD-TYPE   70   10
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               8                70
  1               0                10
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    8  0
  1Q GAIN WILD-TYPE 51 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      8    0
  1Q GAIN WILD-TYPE   51   31
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 0                31
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         0     6
  1Q GAIN WILD-TYPE     1                         1    70
D2V7, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   6                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    1  3
  1Q GAIN WILD-TYPE  7 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      1    3
  1Q GAIN WILD-TYPE    7   34
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               3                34
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    3  9
  2P GAIN WILD-TYPE 55 22
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12                77 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                9                22 
$`2P GAIN MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JU 
       88.87        16.11        69.21        18.48         4.90         9.50 
TCGA-OR-A5K5 TCGA-OR-A5KP TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LL 
        8.32        91.30         5.23        39.35        14.33        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        68.75        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       44.45        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        69.37        46.82        10.16        49.22        22.03 
TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV 
       29.23        36.26       121.25        12.59        29.82        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       72.39        31.23        18.15         6.94        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
       32.68       100.18        22.98        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       28.64        23.64        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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       61.05        28.04        36.03        18.05        23.31        12.59 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       15.45        20.25        39.48        42.51        22.32 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             4.90              4.11 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            91.30            153.63 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           17.295            36.330 
[1] "4.9 - 91.3 (17.3)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "3.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED         1        4         4        4
  2P GAIN WILD-TYPE       8       39        14       14
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                4                39
  STAGE III               4                14
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    1  4  3  5
  2P GAIN WILD-TYPE  8 44  8 15
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               1                 8
  T2               4                44
  T3               3                 8
  T4               5                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
  2P GAIN MUTATED   13  0
  2P GAIN WILD-TYPE 65 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     13    0
  2P GAIN WILD-TYPE   65   10
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              13                65
  1               0                10
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   11  2
  2P GAIN WILD-TYPE 48 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     11    2
  2P GAIN WILD-TYPE   48   29
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              11                48
  MALE                 2                29
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         1    11
  2P GAIN WILD-TYPE     2                         0    65
D3V7, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  5
  2P GAIN WILD-TYPE  6 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    5
  2P GAIN WILD-TYPE    6   32
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               5                32
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    4  7
  2Q GAIN WILD-TYPE 54 24
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11                78 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                24 
$`2Q GAIN MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JE TCGA-OR-A5JU TCGA-OR-A5K5 TCGA-OR-A5KB 
       88.87        16.11        69.21         9.50         8.32        24.36 
TCGA-OR-A5KP TCGA-OR-A5KX TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LI 
       91.30        44.84         5.23        39.35        14.33 

$`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        68.75        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       44.45        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        69.37        46.82        10.16        49.22        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        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82        66.51        72.39        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        96.59        32.68       100.18        22.98        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        11.31        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       28.64        23.64        39.58        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 
       69.11        61.05        28.04        36.03        18.05        23.31 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59        15.45        20.25        39.48        42.51        22.32 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             5.23              4.11 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            91.30            153.63 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           24.360            36.295 
[1] "5.2 - 91.3 (24.4)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "2.5"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED         1        3         5        3
  2Q GAIN WILD-TYPE       8       40        13       15
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                3                40
  STAGE III               5                13
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    1  4  3  4
  2Q GAIN WILD-TYPE  8 44  8 16
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               1                 8
  T2               4                44
  T3               3                 8
  T4               4                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
  2Q GAIN MUTATED   11  1
  2Q GAIN WILD-TYPE 67  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11    1
  2Q GAIN WILD-TYPE   67    9
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              11                67
  1               1                 9
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   11  1
  2Q GAIN WILD-TYPE 48 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     11    1
  2Q GAIN WILD-TYPE   48   30
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              11                48
  MALE                 1                30
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         1    11
  2Q GAIN WILD-TYPE     2                         0    65
D4V7, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  7
  2Q GAIN WILD-TYPE  6 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    7
  2Q GAIN WILD-TYPE    6   30
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               7                30
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   10  3
  3P GAIN WILD-TYPE 48 28
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               13                76 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                28 
$`3P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5KB TCGA-OR-A5KO 
       55.13        36.26       121.25        66.51        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5L2 TCGA-OR-A5L8 TCGA-OR-A5LK TCGA-OR-A5LT TCGA-OU-A5PI 
       83.80        60.89        29.10        73.05        18.05        23.31 
TCGA-P6-A5OG 
       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        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       49.22        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 
       29.82         9.50        72.39        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        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT 
       49.08        24.62        11.31        91.30        88.01        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       23.64        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LM 
       52.24        78.41        14.33        36.33        53.03        61.08 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-PA-A5YG 
       62.99        69.11        61.05        28.04        36.03        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            12.59              4.11 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           121.25            153.63 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            46.49             34.93 
[1] "12.6 - 121.2 (46.5)" "4.1 - 153.6 (34.9)" 
[1] "hr=" "1.9"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED         1        7         1        4
  3P GAIN WILD-TYPE       8       36        17       14
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                7                36
  STAGE III               1                17
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    1  8  2  2
  3P GAIN WILD-TYPE  8 40  9 18
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1                 8
  T2               8                40
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   12  1
  3P GAIN WILD-TYPE 66  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     12    1
  3P GAIN WILD-TYPE   66    9
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              12                66
  1               1                 9
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    8  5
  3P GAIN WILD-TYPE 51 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      8    5
  3P GAIN WILD-TYPE   51   26
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               8                51
  MALE                 5                26
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0    11
  3P GAIN WILD-TYPE     2                         1    65
D5V7, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  11                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  7
  3P GAIN WILD-TYPE  7 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    7
  3P GAIN WILD-TYPE    7   30
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               7                30
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   11  4
  3Q GAIN WILD-TYPE 47 27
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15                74 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                27 
$`3Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5KB TCGA-OR-A5KO 
       55.13        36.26       121.25        66.51        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5L2 TCGA-OR-A5L8 TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LS 
       83.80        60.89        29.10        36.33        73.05        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       18.05        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        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JS 
       49.22        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 
       29.82         9.50        72.39        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        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT 
       49.08        24.62        11.31        91.30        88.01        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       58.55       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       23.64        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       52.24        78.41        14.33        53.03        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       69.11        61.05        28.04        15.45        20.25        39.48 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.59              4.11 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           121.25            153.63 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           36.330            33.255 
[1] "12.6 - 121.2 (36.3)" "4.1 - 153.6 (33.3)" 
[1] "hr=" "1.6"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED         1        8         1        5
  3Q GAIN WILD-TYPE       8       35        17       13
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II                8                35
  STAGE III               1                17
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    1 10  2  2
  3Q GAIN WILD-TYPE  8 38  9 18
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               1                 8
  T2              10                38
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   13  2
  3Q GAIN WILD-TYPE 65  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     13    2
  3Q GAIN WILD-TYPE   65    8
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              13                65
  1               2                 8
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   10  5
  3Q GAIN WILD-TYPE 49 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     10    5
  3Q GAIN WILD-TYPE   49   26
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              10                49
  MALE                 5                26
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0    12
  3Q GAIN WILD-TYPE     2                         1    64
D6V7, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  12                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    1  8
  3Q GAIN WILD-TYPE  7 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    8
  3Q GAIN WILD-TYPE    7   29
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               8                29
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   26 11
  4P GAIN WILD-TYPE 32 20
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               37                52 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11                20 
$`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        44.45        30.31        57.53 
TCGA-OR-A5JF TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL 
       41.39        69.37        46.82        10.16        49.22        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K3 TCGA-OR-A5K4 
       36.26       121.25        29.82        66.51       100.18        22.98 
TCGA-OR-A5K8 TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5L2 
       24.62        83.80       153.63        50.14        58.55        60.89 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK TCGA-OR-A5LL 
       23.64        39.58        14.63        78.41        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       61.08        62.99        69.11        36.03        18.05        23.31 
TCGA-PK-A5HC 
       22.32 

$`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        68.75        88.87        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        72.39        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        96.59        32.68         8.32        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       24.36        46.49        91.30        88.01        95.18       127.50 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       44.84        12.85         4.11       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.31        29.10        28.64         5.23        39.35        21.76 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG 
       52.24        14.33        36.33        61.05        28.04        12.59 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       15.45        20.25        39.48        42.51 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            10.16              4.11 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           153.63            152.15 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            44.45             31.51 
[1] "10.2 - 153.6 (44.5)" "4.1 - 152.2 (31.5)" 
[1] "hr=" "1.6"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED         3       20         7        6
  4P GAIN WILD-TYPE       6       23        11       12
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 3                 6
  STAGE II               20                23
  STAGE III               7                11
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  4P GAIN MUTATED    3 22  4  7
  4P GAIN WILD-TYPE  6 26  7 13
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               3                 6
  T2              22                26
  T3               4                 7
  T4               7                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"
D7V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   32  4
  4P GAIN WILD-TYPE 46  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     32    4
  4P GAIN WILD-TYPE   46    6
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              32                46
  1               4                 6
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   23 14
  4P GAIN WILD-TYPE 36 17
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     23   14
  4P GAIN WILD-TYPE   36   17
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              23                36
  MALE                14                17
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       1                         0    29
  4P GAIN WILD-TYPE     1                         1    47
D7V7, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  29                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    4 11
  4P GAIN WILD-TYPE  4 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      4   11
  4P GAIN WILD-TYPE    4   26
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              11                26
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   25  8
  4Q GAIN WILD-TYPE 33 23
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               33                56 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                8                23 
$`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        44.45        30.31        57.53        41.39 
TCGA-OR-A5JH TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ 
       69.37        46.82        10.16        49.22        22.03        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KS 
      121.25        29.82        66.51        22.98        24.62        83.80 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5L1 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LF 
      153.63        50.14        58.55        23.64        39.58        14.63 
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        69.11        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5HC 
       18.05        23.31        22.32 

$`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        68.75        88.87        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        72.39        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        96.59        32.68       100.18         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       49.08        11.31        24.36        46.49        91.30        88.01 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L2 
       95.18       127.50        44.84        12.85         4.11        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
        5.23        39.35        21.76        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       36.33        61.05        28.04        12.59        15.45        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        42.51 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            10.16              4.11 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           153.63            152.15 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           41.390            32.235 
[1] "10.2 - 153.6 (41.4)" "4.1 - 152.2 (32.2)" 
[1] "hr=" "1.9"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED         3       17         6        6
  4Q GAIN WILD-TYPE       6       26        12       12
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                 3                 6
  STAGE II               17                26
  STAGE III               6                12
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  4Q GAIN MUTATED    3 19  3  7
  4Q GAIN WILD-TYPE  6 29  8 13
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               3                 6
  T2              19                29
  T3               3                 8
  T4               7                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"
D8V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   28  4
  4Q GAIN WILD-TYPE 50  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     28    4
  4Q GAIN WILD-TYPE   50    6
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              28                50
  1               4                 6
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   20 13
  4Q GAIN WILD-TYPE 39 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     20   13
  4Q GAIN WILD-TYPE   39   18
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              20                39
  MALE                13                18
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         0    25
  4Q GAIN WILD-TYPE     1                         1    51
D8V7, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  25                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    3  9
  4Q GAIN WILD-TYPE  5 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3    9
  4Q GAIN WILD-TYPE    5   28
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO               9                28
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   39 17
  5P GAIN WILD-TYPE 19 14
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               56                33 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               17                14 
$`5P GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        15.45        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        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 
       69.37        46.82        10.16        49.22        22.03        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        18.15         6.94        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
      100.18        22.98         8.32        24.62        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       83.80       153.63        58.55        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF 
       29.10        28.64        23.64        39.58         5.23        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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       61.05        28.04        36.03        18.05        23.31        12.59 
TCGA-PA-A5YG TCGA-PK-A5HC 
       15.45        22.32 

$`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        72.39        31.23        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT 
       32.68        49.08        11.31        91.30        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L2 
      127.50        50.14        44.84        12.85         4.11        60.89 
TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL 
      152.15        39.35        21.76        52.24        14.33        53.03 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       20.25        39.48        42.51 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             5.23              4.11 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           153.63            152.15 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            33.91             39.48 
[1] "5.2 - 153.6 (33.9)" "4.1 - 152.2 (39.5)"
[1] "hr=" "1.4"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED         5       28        10       13
  5P GAIN WILD-TYPE       4       15         8        5
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 5                 4
  STAGE II               28                15
  STAGE III              10                 8
  STAGE IV               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"
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    5 30  7 14
  5P GAIN WILD-TYPE  4 18  4  6
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               5                 4
  T2              30                18
  T3               7                 4
  T4              14                 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"
D9V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   50  6
  5P GAIN WILD-TYPE 28  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     50    6
  5P GAIN WILD-TYPE   28    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              50                28
  1               6                 4
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   37 20
  5P GAIN WILD-TYPE 22 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     37   20
  5P GAIN WILD-TYPE   22   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              37                22
  MALE                20                11
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       1                         1    47
  5P GAIN WILD-TYPE     1                         0    29
D9V7, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  47                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7 21
  5P GAIN WILD-TYPE  1 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7   21
  5P GAIN WILD-TYPE    1   16
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              21                16
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   35 17
  5Q GAIN WILD-TYPE 23 14
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               52                37 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               17                14 
$`5Q GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        15.45        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        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 
       69.37        46.82        10.16        22.03        36.26        29.82 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 
       66.51        72.39        18.15        96.59       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KY 
        8.32        24.62        46.49        83.80       153.63        12.85 
TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       58.55        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LK 
       23.64        39.58         5.23        14.63        78.41        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG 
       18.05        23.31        12.59        15.45 

$`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        49.22        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-A5KB 
        6.94        33.83        32.68        49.08        11.31        24.36 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       91.30        88.01        95.18       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG 
        4.11        60.89       152.15        39.35        21.76        52.24 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       14.33        36.33        53.03        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             5.23              4.11 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           153.63            152.15 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            33.91             39.35 
[1] "5.2 - 153.6 (33.9)" "4.1 - 152.2 (39.4)"
[1] "hr=" "1.2"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED         4       27         9       12
  5Q GAIN WILD-TYPE       5       16         9        6
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 4                 5
  STAGE II               27                16
  STAGE III               9                 9
  STAGE IV               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"
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    4 28  7 13
  5Q GAIN WILD-TYPE  5 20  4  7
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               4                 5
  T2              28                20
  T3               7                 4
  T4              13                 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"
D10V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   46  6
  5Q GAIN WILD-TYPE 32  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     46    6
  5Q GAIN WILD-TYPE   32    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              46                32
  1               6                 4
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   35 18
  5Q GAIN WILD-TYPE 24 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     35   18
  5Q GAIN WILD-TYPE   24   13
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              35                24
  MALE                18                13
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         1    44
  5Q GAIN WILD-TYPE     2                         0    32
D10V7, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  44                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7 19
  5Q GAIN WILD-TYPE  1 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7   19
  5Q GAIN WILD-TYPE    1   18
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              19                18
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   10  8
  6P GAIN WILD-TYPE 48 23
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               18                71 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8                23 
$`6P GAIN MUTATED`
TCGA-OR-A5J4 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC 
       15.45        88.87        16.11        19.04        30.31        57.53 
TCGA-OR-A5JE TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KT 
       69.21        22.03        18.48        24.36        46.49        95.18 
TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-PK-A5HC 
        4.11        31.79        73.05        61.08        62.99        22.32 

$`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        68.75        12.00        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       49.22        29.23         4.90        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        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        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ 
        8.32        49.08        24.62        11.31        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       83.80       153.63       127.50        50.14        44.84        12.85 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55        60.89       152.15        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL 
       14.63        52.24        78.41        14.33        36.33        53.03 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       69.11        61.05        28.04        36.03        18.05        23.31 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        15.45        20.25        39.48        42.51 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             4.11              4.90 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            95.18            153.63 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            31.05             36.33 
[1] "4.1 - 95.2 (31.0)"  "4.9 - 153.6 (36.3)"
[1] "hr=" "1.3"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         3        6         4        4
  6P GAIN WILD-TYPE       6       37        14       14
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 3                 6
  STAGE II                6                37
  STAGE III               4                14
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    3  6  3  5
  6P GAIN WILD-TYPE  6 42  8 15
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               3                 6
  T2               6                42
  T3               3                 8
  T4               5                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"
D11V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   16  1
  6P GAIN WILD-TYPE 62  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16    1
  6P GAIN WILD-TYPE   62    9
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              16                62
  1               1                 9
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   13  5
  6P GAIN WILD-TYPE 46 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     13    5
  6P GAIN WILD-TYPE   46   26
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              13                46
  MALE                 5                26
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         1    13
  6P GAIN WILD-TYPE     1                         0    63
D11V7, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  13                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    4  6
  6P GAIN WILD-TYPE  4 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    6
  6P GAIN WILD-TYPE    4   31
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO               6                31
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   10  6
  6Q GAIN WILD-TYPE 48 25
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16                73 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                6                25 
$`6Q GAIN MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JL 
       88.87        19.04        30.31        57.53        69.21        22.03 
TCGA-OR-A5KB TCGA-OR-A5KT TCGA-OR-A5KZ TCGA-OR-A5L4 TCGA-OR-A5LE TCGA-OR-A5LK 
       24.36        95.18         4.11        31.79        21.76        73.05 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-PK-A5HA TCGA-PK-A5HC 
       61.08        62.99        39.48        22.32 

$`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        68.75        15.45        12.00        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH 
       44.45        18.12        91.46        41.39        17.79        69.37 
TCGA-OR-A5JI TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       46.82        10.16        49.22        18.48        29.23         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       72.39        31.23        18.15         6.94        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU 
       11.31        46.49        91.30        88.01        83.80       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84        12.85        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        43.30        28.31        29.10        28.64        23.64 
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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       14.33        36.33        53.03        69.11        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        23.31        12.59        15.45        20.25 
TCGA-PK-A5HB 
       42.51 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             4.11              4.90 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            95.18            153.63 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           35.635            36.260 
[1] "4.1 - 95.2 (35.6)"  "4.9 - 153.6 (36.3)"
[1] "hr=" "1.1"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         4        7         3        1
  6Q GAIN WILD-TYPE       5       36        15       17
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 4                 5
  STAGE II                7                36
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    4  7  1  3
  6Q GAIN WILD-TYPE  5 41 10 17
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               4                 5
  T2               7                41
  T3               1                10
  T4               3                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"
D12V5, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   15  0
  6Q GAIN WILD-TYPE 63 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     15    0
  6Q GAIN WILD-TYPE   63   10
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0              15                63
  1               0                10
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    9  7
  6Q GAIN WILD-TYPE 50 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      9    7
  6Q GAIN WILD-TYPE   50   24
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               9                50
  MALE                 7                24
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         1    10
  6Q GAIN WILD-TYPE     1                         0    66
D12V7, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED    2  6
  6Q GAIN WILD-TYPE  6 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    6
  6Q GAIN WILD-TYPE    6   31
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               6                31
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   31 17
  7P GAIN WILD-TYPE 27 14
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               48                41 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               17                14 
$`7P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       55.13        68.75        12.00        88.87        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        69.37        10.16        49.22 
TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       22.03        36.26       121.25        29.82        66.51        31.23 
TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KB 
       18.15        96.59       100.18         8.32        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       46.49        83.80       153.63        50.14        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LA TCGA-OR-A5LB 
       58.55        60.89        31.79        29.10        23.64        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-A5LS TCGA-OU-A5PI TCGA-PA-A5YG 
       62.99        69.11        61.05        36.03        23.31        15.45 

$`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        44.45        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        72.39         6.94        33.83        32.68        22.98 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       49.08        11.31        91.30        88.01        95.18       127.50 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LD 
       44.84       152.15        43.30        28.31        28.64        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LR TCGA-OR-A5LT 
       21.76        52.24        14.33        53.03        28.04        18.05 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59        20.25        39.48        42.51        22.32 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             4.11              4.90 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           153.63            152.15 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           36.295            33.830 
[1] "4.1 - 153.6 (36.3)" "4.9 - 152.2 (33.8)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED         2       25         9       12
  7P GAIN WILD-TYPE       7       18         9        6
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               25                18
  STAGE III               9                 9
  STAGE IV               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"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    2 28  7 11
  7P GAIN WILD-TYPE  7 20  4  9
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               2                 7
  T2              28                20
  T3               7                 4
  T4              11                 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"
D13V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   41  7
  7P GAIN WILD-TYPE 37  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     41    7
  7P GAIN WILD-TYPE   37    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0              41                37
  1               7                 3
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   31 17
  7P GAIN WILD-TYPE 28 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     31   17
  7P GAIN WILD-TYPE   28   14
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              31                28
  MALE                17                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       0                         1    41
  7P GAIN WILD-TYPE     2                         0    35
D13V7, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  41                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    6 19
  7P GAIN WILD-TYPE  2 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      6   19
  7P GAIN WILD-TYPE    2   18
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO              19                18
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   32 16
  7Q GAIN WILD-TYPE 26 15
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               48                41 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16                15 
$`7Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       55.13        68.75        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JF TCGA-OR-A5JG TCGA-OR-A5JH TCGA-OR-A5JJ 
       44.45        30.31        41.39        17.79        69.37        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       49.22        22.03        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K8 TCGA-OR-A5KB 
       31.23        18.15        96.59       100.18        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ 
       46.49        83.80       153.63        50.14        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LA TCGA-OR-A5LB 
       58.55        60.89        31.79        29.10        23.64        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-A5LS TCGA-OU-A5PI TCGA-PA-A5YG 
       62.99        69.11        61.05        36.03        23.31        15.45 

$`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 
       72.39         6.94        33.83        32.68        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       49.08        11.31        91.30        88.01        95.18       127.50 
TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LD 
       44.84       152.15        43.30        28.31        28.64        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LR TCGA-OR-A5LT 
       21.76        52.24        14.33        53.03        28.04        18.05 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59        20.25        39.48        42.51        22.32 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             4.11              4.90 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           153.63            152.15 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           37.955            32.680 
[1] "4.1 - 153.6 (38.0)" "4.9 - 152.2 (32.7)"
[1] "hr=" "1.2"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED         2       26         8       12
  7Q GAIN WILD-TYPE       7       17        10        6
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               26                17
  STAGE III               8                10
  STAGE IV               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"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    2 29  6 11
  7Q GAIN WILD-TYPE  7 19  5  9
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               2                 7
  T2              29                19
  T3               6                 5
  T4              11                 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"
D14V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   41  7
  7Q GAIN WILD-TYPE 37  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     41    7
  7Q GAIN WILD-TYPE   37    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0              41                37
  1               7                 3
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   31 17
  7Q GAIN WILD-TYPE 28 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     31   17
  7Q GAIN WILD-TYPE   28   14
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              31                28
  MALE                17                14
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       0                         1    41
  7Q GAIN WILD-TYPE     2                         0    35
D14V7, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  41                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    7 19
  7Q GAIN WILD-TYPE  1 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      7   19
  7Q GAIN WILD-TYPE    1   18
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                 1
  NOT HISPANIC OR LATINO              19                18
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   24  8
  8P GAIN WILD-TYPE 34 23
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               32                57 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                8                23 
$`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        88.87        44.45        57.53        69.37 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       49.22        18.48         4.90        36.26       121.25        29.82 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K9 
       66.51        31.23         6.94        96.59        22.98        11.31 
TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 
       46.49        83.80       153.63        50.14         4.11        58.55 
TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF 
       43.30        29.10        28.64        23.64         5.23        14.63 
TCGA-OR-A5LN TCGA-OR-A5LR 
       62.99        28.04 

$`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        68.75        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        72.39 
TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K6 
       18.15        33.83        32.68       100.18         8.32        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV 
       24.62        24.36        91.30        88.01        95.18       127.50 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L6 
       44.84        12.85        60.89       152.15        31.79        28.31 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.58        39.35        21.76        52.24        78.41        14.33 
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        69.11        61.05 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        23.31        12.59        15.45        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             4.11              8.32 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           153.63            152.15 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           33.745            36.330 
[1] "4.1 - 153.6 (33.7)" "8.3 - 152.2 (36.3)"
[1] "hr=" "1.5"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED         2       19         5        5
  8P GAIN WILD-TYPE       7       24        13       13
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               19                24
  STAGE III               5                13
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    2 20  3  6
  8P GAIN WILD-TYPE  7 28  8 14
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               2                 7
  T2              20                28
  T3               3                 8
  T4               6                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"
D15V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   29  2
  8P GAIN WILD-TYPE 49  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     29    2
  8P GAIN WILD-TYPE   49    8
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              29                49
  1               2                 8
[1] 2 2
[1] FALSE
D15V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   21 11
  8P GAIN WILD-TYPE 38 20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     21   11
  8P GAIN WILD-TYPE   38   20
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              21                38
  MALE                11                20
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         1    29
  8P GAIN WILD-TYPE     2                         0    47
D15V7, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  29                47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V8, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4 11
  8P GAIN WILD-TYPE  4 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4   11
  8P GAIN WILD-TYPE    4   26
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              11                26
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   26 12
  8Q GAIN WILD-TYPE 32 19
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               38                51 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                19 
$`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        88.87        44.45        57.53        41.39 
TCGA-OR-A5JH TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ 
       69.37        10.16        49.22        18.48         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        31.23         6.94        96.59 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KS 
       22.98         8.32        11.31        24.36        46.49        83.80 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L5 
      153.63        50.14         4.11        58.55        60.89        43.30 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LF 
       29.10        28.64        23.64         5.23        39.35        14.63 
TCGA-OR-A5LN TCGA-OR-A5LR 
       62.99        28.04 

$`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        68.75        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        72.39        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KP TCGA-OR-A5KQ 
       32.68       100.18        49.08        24.62        91.30        88.01 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L3 TCGA-OR-A5L4 
       95.18       127.50        44.84        12.85       152.15        31.79 
TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       28.31        39.58        21.76        52.24        78.41        14.33 
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        69.11        61.05 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        23.31        12.59        15.45        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             4.11              9.50 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           153.63            152.15 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           33.745            36.330 
[1] "4.1 - 153.6 (33.7)" "9.5 - 152.2 (36.3)"
[1] "hr=" "1"  
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED         2       22         7        6
  8Q GAIN WILD-TYPE       7       21        11       12
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 2                 7
  STAGE II               22                21
  STAGE III               7                11
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    2 23  4  8
  8Q GAIN WILD-TYPE  7 25  7 12
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               2                 7
  T2              23                25
  T3               4                 7
  T4               8                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
  8Q GAIN MUTATED   34  3
  8Q GAIN WILD-TYPE 44  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     34    3
  8Q GAIN WILD-TYPE   44    7
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              34                44
  1               3                 7
[1] 2 2
[1] FALSE
D16V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   25 13
  8Q GAIN WILD-TYPE 34 18
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     25   13
  8Q GAIN WILD-TYPE   34   18
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              25                34
  MALE                13                18
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         1    35
  8Q GAIN WILD-TYPE     2                         0    41
D16V7, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  35                41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    4 14
  8Q GAIN WILD-TYPE  4 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   14
  8Q GAIN WILD-TYPE    4   23
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              14                23
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   11  9
  9P GAIN WILD-TYPE 47 22
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               20                69 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                9                22 
$`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-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP 
       69.37        10.16        36.26        24.62        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5LJ TCGA-OR-A5LL TCGA-OR-A5LS 
       83.80        12.85        58.55        36.33        53.03        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI 
       18.05        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        68.75        88.87        19.04        44.45 
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        49.22 
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 
       29.82         9.50        66.51        72.39        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        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT 
        8.32        49.08        11.31        24.36        88.01        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L2 
      153.63       127.50        50.14        44.84         4.11        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       23.64        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       52.24        78.41        14.33        73.05        61.08        62.99 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       69.11        61.05        28.04        12.59        15.45        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            10.16              4.11 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            91.30            153.63 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            33.17             39.48 
[1] "10.2 - 91.3 (33.2)" "4.1 - 153.6 (39.5)"
[1] "hr=" "1.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         0        9         3        8
  9P GAIN WILD-TYPE       9       34        15       10
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 0                 9
  STAGE II                9                34
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    0 11  3  6
  9P GAIN WILD-TYPE  9 37  8 14
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               0                 9
  T2              11                37
  T3               3                 8
  T4               6                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"
D17V5, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   14  6
  9P GAIN WILD-TYPE 64  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14    6
  9P GAIN WILD-TYPE   64    4
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              14                64
  1               6                 4
[1] 2 2
[1] FALSE
D17V6, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   14  6
  9P GAIN WILD-TYPE 45 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     14    6
  9P GAIN WILD-TYPE   45   25
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              14                45
  MALE                 6                25
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         0    17
  9P GAIN WILD-TYPE     2                         1    59
D17V7, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  17                59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V8, binary
                   cls
clus                 0  1
  9P GAIN MUTATED    3  8
  9P GAIN WILD-TYPE  5 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      3    8
  9P GAIN WILD-TYPE    5   29
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                 5
  NOT HISPANIC OR LATINO               8                29
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   14 14
  9Q GAIN WILD-TYPE 44 17
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               28                61 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               14                17 
$`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        44.45        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        69.37        10.16        36.26        18.15 
TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KS 
       33.83        32.68        24.62        46.49        91.30        83.80 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5LB TCGA-OR-A5LJ TCGA-OR-A5LL 
       12.85         4.11        58.55        39.58        36.33        53.03 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PK-A5HC 
       36.03        18.05        23.31        22.32 

$`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        68.75        88.87        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        49.22        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        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 
       66.51        72.39        31.23         6.94        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ 
       22.98         8.32        49.08        11.31        24.36        88.01 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L2 
       95.18       153.63       127.50        50.14        44.84        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       23.64         5.23        39.35        21.76        14.63        52.24 
TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO 
       78.41        14.33        73.05        61.08        62.99        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       61.05        28.04        12.59        15.45        20.25        39.48 
TCGA-PK-A5HB 
       42.51 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             4.11              4.90 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            91.30            153.63 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           33.255            42.510 
[1] "4.1 - 91.3 (33.3)"  "4.9 - 153.6 (42.5)"
[1] "hr=" "2.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         1       12         5       11
  9Q GAIN WILD-TYPE       8       31        13        7
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 1                 8
  STAGE II               12                31
  STAGE III               5                13
  STAGE IV               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"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    1 14  3 11
  9Q GAIN WILD-TYPE  8 34  8  9
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                 8
  T2              14                34
  T3               3                 8
  T4              11                 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
  9Q GAIN MUTATED   22  7
  9Q GAIN WILD-TYPE 56  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     22    7
  9Q GAIN WILD-TYPE   56    3
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              22                56
  1               7                 3
[1] 2 2
[1] FALSE
D18V6, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   21  8
  9Q GAIN WILD-TYPE 38 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     21    8
  9Q GAIN WILD-TYPE   38   23
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              21                38
  MALE                 8                23
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       1                         0    25
  9Q GAIN WILD-TYPE     1                         1    51
D18V7, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  25                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V8, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    4 12
  9Q GAIN WILD-TYPE  4 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      4   12
  9Q GAIN WILD-TYPE    4   25
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                 4
  NOT HISPANIC OR LATINO              12                25
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED   13 12
  10P GAIN WILD-TYPE 45 19
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                25                 64 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                 19 
$`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        44.45        57.53        41.39 
TCGA-OR-A5JK TCGA-OR-A5JP TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K8 TCGA-OR-A5KB 
       49.22         4.90        31.23        32.68        24.62        24.36 
TCGA-OR-A5KO TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       46.49        12.85        29.10        39.58         5.23        39.35 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       14.33        36.33        69.11        36.03        18.05        23.31 
TCGA-P6-A5OG 
       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        68.75        15.45        88.87        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        69.37        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        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY 
       12.59        29.82         9.50        66.51        72.39        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        33.83        96.59       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       49.08        11.31        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LK 
       23.64        21.76        14.63        52.24        78.41        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       53.03        61.08        62.99        61.05        28.04        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              4.90               4.11 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             69.11             153.63 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            31.230             42.905 
[1] "4.9 - 69.1 (31.2)"  "4.1 - 153.6 (42.9)"
[1] "hr=" "2.5"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED         0        8         6       10
  10P GAIN WILD-TYPE       9       35        12        8
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 8                 35
  STAGE III                6                 12
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    0 10  4 10
  10P GAIN WILD-TYPE  9 38  7 10
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  9
  T2               10                 38
  T3                4                  7
  T4               10                 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"
D19V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   21  3
  10P GAIN WILD-TYPE 57  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     21    3
  10P GAIN WILD-TYPE   57    7
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               21                 57
  1                3                  7
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED   16  9
  10P GAIN WILD-TYPE 43 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     16    9
  10P GAIN WILD-TYPE   43   22
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               16                 43
  MALE                  9                 22
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0    22
  10P GAIN WILD-TYPE     2                         1    54
D19V7, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   22                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V8, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4 12
  10P GAIN WILD-TYPE  4 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4   12
  10P GAIN WILD-TYPE    4   25
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               12                 25
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED   12 13
  10Q GAIN WILD-TYPE 46 18
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                25                 64 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                13                 18 
$`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        44.45        57.53        41.39 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K8 
       49.22        18.48         4.90        31.23        32.68        24.62 
TCGA-OR-A5KP TCGA-OR-A5KY TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       91.30        12.85        29.10        39.58         5.23        39.35 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       14.33        36.33        69.11        36.03        18.05        23.31 
TCGA-P6-A5OG 
       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        68.75        15.45        88.87        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        69.37        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        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82         9.50        66.51        72.39        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       33.83        96.59       100.18        22.98         8.32        49.08 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LK 
       23.64        21.76        14.63        52.24        78.41        73.05 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       53.03        61.08        62.99        61.05        28.04        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              4.90               4.11 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             91.30             153.63 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            31.230             42.905 
[1] "4.9 - 91.3 (31.2)"  "4.1 - 153.6 (42.9)"
[1] "hr=" "2.6"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED         0        8         6       11
  10Q GAIN WILD-TYPE       9       35        12        7
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 8                 35
  STAGE III                6                 12
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  10Q GAIN MUTATED    0 10  4 11
  10Q GAIN WILD-TYPE  9 38  7  9
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  9
  T2               10                 38
  T3                4                  7
  T4               11                  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"
D20V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   22  3
  10Q GAIN WILD-TYPE 56  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     22    3
  10Q GAIN WILD-TYPE   56    7
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               22                 56
  1                3                  7
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED   17  9
  10Q GAIN WILD-TYPE 42 22
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     17    9
  10Q GAIN WILD-TYPE   42   22
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               17                 42
  MALE                  9                 22
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0    23
  10Q GAIN WILD-TYPE     2                         1    53
D20V7, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   23                 53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V8, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    4 12
  10Q GAIN WILD-TYPE  4 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      4   12
  10Q GAIN WILD-TYPE    4   25
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               12                 25
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    0  4
  11P GAIN WILD-TYPE 58 27
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 85 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 27 
$`11P GAIN MUTATED`
TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-P6-A5OG 
       60.89        39.35        14.33        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        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        69.37        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       10.16        49.22        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 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       72.39        31.23        18.15         6.94        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
       11.31        24.36        46.49        91.30        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        50.14        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE 
       29.10        28.64        23.64        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       18.05        23.31        15.45        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.59               4.11 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             60.89             153.63 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             26.84              36.26 
[1] "12.6 - 60.9 (26.8)" "4.1 - 153.6 (36.3)"
[1] "hr=" "4.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED         0        1         1        3
  11P GAIN WILD-TYPE       9       42        17       15
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    0  1  0  4
  11P GAIN WILD-TYPE  9 47 11 16
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                0                 11
  T4                4                 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
  11P GAIN MUTATED    5  0
  11P GAIN WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      5    0
  11P GAIN WILD-TYPE   73   10
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  1
  11P GAIN WILD-TYPE 55 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    1
  11P GAIN WILD-TYPE   55   30
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  1                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0     5
  11P GAIN WILD-TYPE     2                         1    71
D21V7, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V8, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    0  5
  11P GAIN WILD-TYPE  8 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      0    5
  11P GAIN WILD-TYPE    8   32
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                5                 32
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    0  6
  11Q GAIN WILD-TYPE 58 25
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 83 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 6                 25 
$`11Q GAIN MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5K5 TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-P6-A5OG 
       16.11         8.32        60.89        39.35        14.33        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
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        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
      100.18        22.98        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       23.64        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 
       69.11        61.05        28.04        36.03        18.05        23.31 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       15.45        20.25        39.48        42.51        22.32 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              8.32               4.11 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             60.89             153.63 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             15.22              36.33 
[1] "8.3 - 60.9 (15.2)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "5.7"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED         0        1         3        2
  11Q GAIN WILD-TYPE       9       42        15       16
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                3                 15
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    0  1  2  3
  11Q GAIN WILD-TYPE  9 47  9 17
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                2                  9
  T4                3                 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"
D22V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    6  0
  11Q GAIN WILD-TYPE 72 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      6    0
  11Q GAIN WILD-TYPE   72   10
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                6                 72
  1                0                 10
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    5  1
  11Q GAIN WILD-TYPE 54 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      5    1
  11Q GAIN WILD-TYPE   54   30
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  1                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0     6
  11Q GAIN WILD-TYPE     2                         1    70
D22V7, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    6                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V8, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  4
  11Q GAIN WILD-TYPE  7 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    4
  11Q GAIN WILD-TYPE    7   33
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                4                 33
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   41 22
  12P GAIN WILD-TYPE 17  9
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                63                 26 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                  9 
$`12P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        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        69.37        46.82        10.16        49.22        22.03 
TCGA-OR-A5JM TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV 
       18.48         4.90        36.26       121.25        29.82        66.51 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23         6.94        96.59        32.68       100.18        22.98 
TCGA-OR-A5K8 TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY 
       24.62        91.30        83.80       153.63        50.14        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55        60.89        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       29.10        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM 
       14.63        78.41        14.33        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        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5HC 
       23.31        15.45        22.32 

$`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 
       72.39        18.15        33.83         8.32        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX 
       24.36        46.49        88.01        95.18       127.50        44.84 
TCGA-OR-A5L3 TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5H9 
      152.15        21.76        52.24        53.03        12.59        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        42.51 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              4.11               8.32 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            153.63             152.15 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            36.030             40.995 
[1] "4.1 - 153.6 (36.0)" "8.3 - 152.2 (41.0)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED         5       31        13       14
  12P GAIN WILD-TYPE       4       12         5        4
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  5                  4
  STAGE II                31                 12
  STAGE III               13                  5
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    5 34  8 16
  12P GAIN WILD-TYPE  4 14  3  4
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                5                  4
  T2               34                 14
  T3                8                  3
  T4               16                  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"
D23V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   56  7
  12P GAIN WILD-TYPE 22  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     56    7
  12P GAIN WILD-TYPE   22    3
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0               56                 22
  1                7                  3
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   40 24
  12P GAIN WILD-TYPE 19  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     40   24
  12P GAIN WILD-TYPE   19    7
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               40                 19
  MALE                 24                  7
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       1                         1    54
  12P GAIN WILD-TYPE     1                         0    22
D23V7, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   54                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V8, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8 25
  12P GAIN WILD-TYPE  0 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8   25
  12P GAIN WILD-TYPE    0   12
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO               25                 12
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   41 22
  12Q GAIN WILD-TYPE 17  9
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                63                 26 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                  9 
$`12Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        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        69.37        46.82        10.16        49.22        22.03 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
        4.90        36.26       121.25        29.82        66.51        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K8 TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KX 
       24.62        91.30        83.80       153.63        50.14        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 
       12.85         4.11        58.55        60.89        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       28.31        29.10        28.64        23.64        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       39.35        14.63        78.41        14.33        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG 
       18.05        23.31        15.45 

$`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        72.39        18.15        33.83        49.08        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 
       24.36        46.49        88.01        95.18       127.50       152.15 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LL TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       21.76        52.24        53.03        12.59        20.25        39.48 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              4.11               9.50 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            153.63             152.15 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            36.260             36.655 
[1] "4.1 - 153.6 (36.3)" "9.5 - 152.2 (36.7)"
[1] "hr=" "1"  
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED         5       31        14       13
  12Q GAIN WILD-TYPE       4       12         4        5
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  5                  4
  STAGE II                31                 12
  STAGE III               14                  4
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    5 35  9 14
  12Q GAIN WILD-TYPE  4 13  2  6
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                5                  4
  T2               35                 13
  T3                9                  2
  T4               14                  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"
D24V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   55  8
  12Q GAIN WILD-TYPE 23  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     55    8
  12Q GAIN WILD-TYPE   23    2
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0               55                 23
  1                8                  2
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   40 24
  12Q GAIN WILD-TYPE 19  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     40   24
  12Q GAIN WILD-TYPE   19    7
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               40                 19
  MALE                 24                  7
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         1    55
  12Q GAIN WILD-TYPE     2                         0    21
D24V7, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   55                 21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V8, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8 25
  12Q GAIN WILD-TYPE  0 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8   25
  12Q GAIN WILD-TYPE    0   12
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                  0
  NOT HISPANIC OR LATINO               25                 12
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    4  2
  13Q GAIN WILD-TYPE 54 29
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 83 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 2                 29 
$`13Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5JL TCGA-OR-A5K8 TCGA-OR-A5KW TCGA-OR-A5LC TCGA-OR-A5LM 
       55.13        22.03        24.62        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        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       49.22        18.48        29.23         4.90        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        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        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        49.08        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO 
       14.33        36.33        73.05        53.03        62.99        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       61.05        28.04        36.03        18.05        23.31        12.59 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       15.45        20.25        39.48        42.51        22.32 

  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 
             37.38              36.26 
[1] "5.2 - 61.1 (37.4)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "1.1"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED         1        2         1        2
  13Q GAIN WILD-TYPE       8       41        17       16
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 2                 41
  STAGE III                1                 17
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    1  3  1  1
  13Q GAIN WILD-TYPE  8 45 10 19
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                  8
  T2                3                 45
  T3                1                 10
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 73  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5    1
  13Q GAIN WILD-TYPE   73    9
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                5                 73
  1                1                  9
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  2
  13Q GAIN WILD-TYPE 55 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    2
  13Q GAIN WILD-TYPE   55   29
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0     5
  13Q GAIN WILD-TYPE     2                         1    71
D25V7, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V8, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  3
  13Q GAIN WILD-TYPE  7 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    3
  13Q GAIN WILD-TYPE    7   34
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 34
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   11 10
  14Q GAIN WILD-TYPE 47 21
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                21                 68 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                 21 
$`14Q GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JG 
       68.75        15.45        12.00        30.31        69.21        17.79 
TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5L2 
       10.16        22.03         4.90        46.49        91.30        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM 
       31.79        29.10        39.58        14.33        53.03        61.08 
TCGA-OR-A5LO TCGA-OR-A5LS TCGA-OU-A5PI 
       69.11        36.03        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        88.87        16.11        19.04        44.45 
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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       49.22        18.48        29.23        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       29.82         9.50        66.51        72.39        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        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ 
        8.32        49.08        24.62        11.31        24.36        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11        58.55       152.15        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-OR-A5LP 
       52.24        78.41        36.33        73.05        62.99        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       28.04        18.05        12.59        15.45        20.25        39.48 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              4.90               4.11 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             91.30             153.63 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             31.79              37.84 
[1] "4.9 - 91.3 (31.8)"  "4.1 - 153.6 (37.8)"
[1] "hr=" "1.7"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED         2        8         3        8
  14Q GAIN WILD-TYPE       7       35        15       10
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                  2                  7
  STAGE II                 8                 35
  STAGE III                3                 15
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  14Q GAIN MUTATED    2  9  2  8
  14Q GAIN WILD-TYPE  7 39  9 12
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                2                  7
  T2                9                 39
  T3                2                  9
  T4                8                 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"
D26V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   17  4
  14Q GAIN WILD-TYPE 61  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     17    4
  14Q GAIN WILD-TYPE   61    6
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               17                 61
  1                4                  6
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   15  6
  14Q GAIN WILD-TYPE 44 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15    6
  14Q GAIN WILD-TYPE   44   25
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               15                 44
  MALE                  6                 25
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    17
  14Q GAIN WILD-TYPE     2                         1    59
D26V7, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   17                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V8, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    3  8
  14Q GAIN WILD-TYPE  5 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      3    8
  14Q GAIN WILD-TYPE    5   29
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO                8                 29
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    6  5
  15Q GAIN WILD-TYPE 52 26
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                 78 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 26 
$`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        49.22        22.03       153.63        50.14 
TCGA-OR-A5L2 TCGA-OR-A5LB TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       60.89        39.58        53.03        61.08        69.11 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE 
       16.11        19.04        44.45        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        69.37        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        36.26       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
        9.50        66.51        72.39        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        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       49.08        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5KY 
       88.01        83.80        95.18       127.50        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
        4.11        58.55       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        36.33        73.05 
TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       62.99        61.05        28.04        36.03        18.05        23.31 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59        15.45        20.25        39.48        42.51        22.32 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             22.03               4.11 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            153.63             152.15 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            53.030             32.235 
[1] "22.0 - 153.6 (53.0)" "4.1 - 152.2 (32.2)" 
[1] "hr=" "1"  
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED         1        5         1        3
  15Q GAIN WILD-TYPE       8       38        17       15
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 5                 38
  STAGE III                1                 17
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  15Q GAIN MUTATED    1  6  0  3
  15Q GAIN WILD-TYPE  8 42 11 17
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                1                  8
  T2                6                 42
  T3                0                 11
  T4                3                 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"
D27V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    9  1
  15Q GAIN WILD-TYPE 69  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      9    1
  15Q GAIN WILD-TYPE   69    9
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                9                 69
  1                1                  9
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    7  4
  15Q GAIN WILD-TYPE 52 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      7    4
  15Q GAIN WILD-TYPE   52   27
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                7                 52
  MALE                  4                 27
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0     8
  15Q GAIN WILD-TYPE     2                         1    68
D27V7, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    8                 68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V8, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    0  4
  15Q GAIN WILD-TYPE  8 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    4
  15Q GAIN WILD-TYPE    8   33
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                4                 33
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   35 13
  16P GAIN WILD-TYPE 23 18
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                48                 41 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                13                 18 
$`16P GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JF 
       68.75        12.00        44.45        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        69.37        46.82        10.16        49.22        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        31.23         6.94        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS 
      100.18        22.98         8.32        24.62        46.49        83.80 
TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 
      153.63        50.14        12.85         4.11        58.55        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        39.58 
TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LP 
        5.23        14.63        14.33        53.03        61.08        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5HC 
       28.04        36.03        18.05        23.31        15.45        22.32 

$`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        88.87        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        72.39        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ 
       32.68        49.08        11.31        24.36        91.30        88.01 
TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5LD 
       95.18       127.50        44.84        60.89       152.15        39.35 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN 
       21.76        52.24        78.41        36.33        73.05        62.99 
TCGA-OR-A5LO TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       69.11        12.59        20.25        39.48        42.51 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              4.11               4.90 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            153.63             152.15 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             31.51              39.48 
[1] "4.1 - 153.6 (31.5)" "4.9 - 152.2 (39.5)"
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED         3       24        10       11
  16P GAIN WILD-TYPE       6       19         8        7
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                24                 19
  STAGE III               10                  8
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    3 26  5 14
  16P GAIN WILD-TYPE  6 22  6  6
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                  6
  T2               26                 22
  T3                5                  6
  T4               14                  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
  16P GAIN MUTATED   43  5
  16P GAIN WILD-TYPE 35  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     43    5
  16P GAIN WILD-TYPE   35    5
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0               43                 35
  1                5                  5
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   29 20
  16P GAIN WILD-TYPE 30 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     29   20
  16P GAIN WILD-TYPE   30   11
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               29                 30
  MALE                 20                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    42
  16P GAIN WILD-TYPE     1                         1    34
D28V7, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   42                 34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V8, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    3 21
  16P GAIN WILD-TYPE  5 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   21
  16P GAIN WILD-TYPE    5   16
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               21                 16
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   34 12
  16Q GAIN WILD-TYPE 24 19
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                46                 43 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                12                 19 
$`16Q GAIN MUTATED`
TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       68.75        12.00        44.45        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        69.37        46.82        10.16        49.22        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        31.23         6.94        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KS TCGA-OR-A5KU 
      100.18        22.98        24.62        46.49        83.80       153.63 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 
       50.14        12.85         4.11        58.55        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LF 
       28.31        29.10        28.64        23.64         5.23        14.63 
TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       53.03        61.08        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG 
       18.05        23.31        12.59        15.45 

$`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        88.87        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        72.39        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP 
       32.68         8.32        49.08        11.31        24.36        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L3 
       88.01        95.18       127.50        44.84        60.89       152.15 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.58        39.35        21.76        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LN TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       36.33        73.05        62.99        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              4.11               4.90 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            153.63             152.15 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             33.91              39.35 
[1] "4.1 - 153.6 (33.9)" "4.9 - 152.2 (39.4)"
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED         4       24         8       10
  16Q GAIN WILD-TYPE       5       19        10        8
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  4                  5
  STAGE II                24                 19
  STAGE III                8                 10
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    4 26  4 12
  16Q GAIN WILD-TYPE  5 22  7  8
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                4                  5
  T2               26                 22
  T3                4                  7
  T4               12                  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"
D29V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   41  5
  16Q GAIN WILD-TYPE 37  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     41    5
  16Q GAIN WILD-TYPE   37    5
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0               41                 37
  1                5                  5
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   28 19
  16Q GAIN WILD-TYPE 31 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     28   19
  16Q GAIN WILD-TYPE   31   12
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               28                 31
  MALE                 19                 12
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         0    40
  16Q GAIN WILD-TYPE     2                         1    36
D29V7, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   40                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V8, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    3 19
  16Q GAIN WILD-TYPE  5 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   19
  16Q GAIN WILD-TYPE    5   18
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO               19                 18
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    3  1
  17P GAIN WILD-TYPE 55 30
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                 85 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 1                 30 
$`17P GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JQ TCGA-OR-A5LT TCGA-PK-A5HC 
       19.04        36.26        18.05        22.32 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JR 
       49.22        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        29.82         9.50        66.51        72.39        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        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       22.98         8.32        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        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        69.11        61.05        28.04 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       36.03        23.31        12.59        15.45        20.25        39.48 
TCGA-PK-A5HB 
       42.51 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             18.05               4.11 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             36.26             153.63 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             20.68              39.35 
[1] "18.1 - 36.3 (20.7)" "4.1 - 153.6 (39.4)"
[1] "hr=" "1.1"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED         0        1         3        1
  17P GAIN WILD-TYPE       9       42        15       17
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                3                 15
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  17P GAIN MUTATED    0  1  2  2
  17P GAIN WILD-TYPE  9 47  9 18
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                2                  9
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    5  0
  17P GAIN WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5    0
  17P GAIN WILD-TYPE   73   10
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    3  2
  17P GAIN WILD-TYPE 56 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      3    2
  17P GAIN WILD-TYPE   56   29
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                3                 56
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       1                         0     3
  17P GAIN WILD-TYPE     1                         1    73
D30V7, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V8, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    1  2
  17P GAIN WILD-TYPE  7 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    2
  17P GAIN WILD-TYPE    7   35
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    3  3
  17Q GAIN WILD-TYPE 55 28
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 83 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 3                 28 
$`17Q GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5JH TCGA-OR-A5JQ TCGA-OR-A5L2 TCGA-OR-A5LI TCGA-OR-A5LT 
       19.04        69.37        36.26        60.89        14.33        18.05 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        44.45        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        49.22 
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 
       29.82         9.50        66.51        72.39        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        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
        8.32        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
       50.14        44.84        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
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 
       69.11        61.05        28.04        36.03        23.31        12.59 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       15.45        20.25        39.48        42.51        22.32 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             14.33               4.11 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             69.37             153.63 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             27.65              36.33 
[1] "14.3 - 69.4 (27.6)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.6"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED         0        3         2        2
  17Q GAIN WILD-TYPE       9       40        16       16
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 3                 40
  STAGE III                2                 16
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    0  3  2  2
  17Q GAIN WILD-TYPE  9 45  9 18
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                0                  9
  T2                3                 45
  T3                2                  9
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    7  0
  17Q GAIN WILD-TYPE 71 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    0
  17Q GAIN WILD-TYPE   71   10
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                7                 71
  1                0                 10
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  2
  17Q GAIN WILD-TYPE 54 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    2
  17Q GAIN WILD-TYPE   54   29
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                5                 54
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         0     6
  17Q GAIN WILD-TYPE     2                         1    70
D31V7, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    6                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V8, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    1  3
  17Q GAIN WILD-TYPE  7 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      1    3
  17Q GAIN WILD-TYPE    7   34
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 34
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    2  4
  18P GAIN WILD-TYPE 56 27
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 83 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 4                 27 
$`18P GAIN MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-PK-A5HC 
       19.04        58.55        60.89        39.35        14.33        22.32 

$`18P 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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
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        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      100.18        22.98         8.32        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.36        46.49        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       23.64        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 
       69.11        61.05        28.04        36.03        18.05        23.31 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        15.45        20.25        39.48        42.51 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             14.33               4.11 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             60.89             153.63 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            30.835             36.260 
[1] "14.3 - 60.9 (30.8)" "4.1 - 153.6 (36.3)"
[1] "hr=" "2.2"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED         0        2         3        1
  18P GAIN WILD-TYPE       9       41        15       17
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                3                 15
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  18P GAIN MUTATED    0  2  1  3
  18P GAIN WILD-TYPE  9 46 10 17
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                1                 10
  T4                3                 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"
D32V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6  0
  18P GAIN WILD-TYPE 72 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    0
  18P GAIN WILD-TYPE   72   10
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                6                 72
  1                0                 10
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  2
  18P GAIN WILD-TYPE 55 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    2
  18P GAIN WILD-TYPE   55   29
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0     5
  18P GAIN WILD-TYPE     1                         1    71
D32V7, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    1  5
  18P GAIN WILD-TYPE  7 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    5
  18P GAIN WILD-TYPE    7   32
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                5                 32
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    2  3
  18Q GAIN WILD-TYPE 56 28
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                 84 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 28 
$`18Q GAIN MUTATED`
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-PK-A5HC 
       58.55        60.89        39.35        14.33        22.32 

$`18Q 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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        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        69.37        46.82 
TCGA-OR-A5JJ TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP 
       10.16        49.22        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 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       72.39        31.23        18.15         6.94        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
       11.31        24.36        46.49        91.30        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        50.14        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
        4.11       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        39.58         5.23        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        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        12.59        15.45        20.25        39.48        42.51 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             14.33               4.11 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             60.89             153.63 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            39.350             36.145 
[1] "14.3 - 60.9 (39.4)" "4.1 - 153.6 (36.1)"
[1] "hr=" "1.8"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED         0        2         2        1
  18Q GAIN WILD-TYPE       9       41        16       17
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                2                 16
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  18Q GAIN MUTATED    0  2  0  3
  18Q GAIN WILD-TYPE  9 46 11 17
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                0                 11
  T4                3                 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"
D33V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  0
  18Q GAIN WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    0
  18Q GAIN WILD-TYPE   73   10
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    4  1
  18Q GAIN WILD-TYPE 55 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4    1
  18Q GAIN WILD-TYPE   55   30
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                4                 55
  MALE                  1                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         0     4
  18Q GAIN WILD-TYPE     1                         1    72
D33V7, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    4                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    0  5
  18Q GAIN WILD-TYPE  8 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    5
  18Q GAIN WILD-TYPE    8   32
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                5                 32
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   33 22
  19P GAIN WILD-TYPE 25  9
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                55                 34 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                22                  9 
$`19P GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        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 
       69.37        46.82        10.16        49.22        18.48         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K2 
       36.26       121.25        66.51        31.23        33.83        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP 
      100.18         8.32        24.62        11.31        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
       83.80       153.63        50.14        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L8 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       60.89        31.79        29.10        39.58         5.23        39.35 
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-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG 
       69.11        61.05        36.03        18.05        23.31        15.45 
TCGA-PK-A5HC 
       22.32 

$`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        29.82         9.50        72.39        18.15         6.94 
TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KT 
       96.59        22.98        49.08        24.36        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 
      127.50        44.84       152.15        43.30        28.31        28.64 
TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LR 
       23.64        21.76        14.63        52.24        14.33        28.04 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       12.59        20.25        39.48        42.51 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              4.11               6.94 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            153.63             152.15 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            39.580             28.475 
[1] "4.1 - 153.6 (39.6)" "6.9 - 152.2 (28.5)"
[1] "hr=" "1.4"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED         3       27        11       14
  19P GAIN WILD-TYPE       6       16         7        4
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                27                 16
  STAGE III               11                  7
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    3 30  7 15
  19P GAIN WILD-TYPE  6 18  4  5
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                3                  6
  T2               30                 18
  T3                7                  4
  T4               15                  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"
D34V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   48  7
  19P GAIN WILD-TYPE 30  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     48    7
  19P GAIN WILD-TYPE   30    3
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               48                 30
  1                7                  3
[1] 2 2
[1] FALSE
D34V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   36 20
  19P GAIN WILD-TYPE 23 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     36   20
  19P GAIN WILD-TYPE   23   11
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               36                 23
  MALE                 20                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       1                         1    46
  19P GAIN WILD-TYPE     1                         0    30
D34V7, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   46                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V8, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    7 21
  19P GAIN WILD-TYPE  1 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      7   21
  19P GAIN WILD-TYPE    1   16
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO               21                 16
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   31 20
  19Q GAIN WILD-TYPE 27 11
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                51                 38 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                20                 11 
$`19Q GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JG 
       44.45        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 
       69.37        46.82        10.16        49.22         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K5 
      121.25        66.51        31.23        32.68       100.18         8.32 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KW 
       24.62        11.31        91.30        83.80       153.63        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L8 
       44.84        12.85         4.11        58.55        31.79        29.10 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.58         5.23        39.35        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LS TCGA-OR-A5LT 
       73.05        61.08        69.11        61.05        36.03        18.05 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5HC 
       23.31        15.45        22.32 

$`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        29.82         9.50        72.39        18.15 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5KB 
        6.94        33.83        96.59        22.98        49.08        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L2 TCGA-OR-A5L3 
       46.49        88.01        95.18       127.50        60.89       152.15 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LF 
       43.30        28.31        28.64        23.64        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LR TCGA-P6-A5OG TCGA-PK-A5H9 
       52.24        53.03        62.99        28.04        12.59        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        42.51 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              4.11               6.94 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            153.63             152.15 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            39.350             29.525 
[1] "4.1 - 153.6 (39.4)" "6.9 - 152.2 (29.5)"
[1] "hr=" "1.3"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED         3       23        12       13
  19Q GAIN WILD-TYPE       6       20         6        5
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                23                 20
  STAGE III               12                  6
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    3 27  7 14
  19Q GAIN WILD-TYPE  6 21  4  6
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                3                  6
  T2               27                 21
  T3                7                  4
  T4               14                  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"
D35V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   43  8
  19Q GAIN WILD-TYPE 35  2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     43    8
  19Q GAIN WILD-TYPE   35    2
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               43                 35
  1                8                  2
[1] 2 2
[1] FALSE
D35V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   32 20
  19Q GAIN WILD-TYPE 27 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     32   20
  19Q GAIN WILD-TYPE   27   11
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               32                 27
  MALE                 20                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       1                         1    44
  19Q GAIN WILD-TYPE     1                         0    32
D35V7, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   44                 32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    7 21
  19Q GAIN WILD-TYPE  1 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      7   21
  19Q GAIN WILD-TYPE    1   16
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                  1
  NOT HISPANIC OR LATINO               21                 16
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   33 12
  20P GAIN WILD-TYPE 25 19
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                45                 44 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                 19 
$`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        88.87        44.45        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        69.37        46.82        49.22        36.26 
TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
      121.25        29.82        66.51        31.23         6.94        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KX 
      100.18        22.98        24.62        83.80       153.63        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       12.85         4.11        58.55        31.79        43.30        28.31 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LF TCGA-OR-A5LI 
       28.64        23.64        39.58         5.23        14.63        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        61.08        62.99        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-PA-A5YG 
       36.03        18.05        15.45 

$`20P GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JA 
       44.55        68.75        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        72.39        18.15        33.83 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       32.68         8.32        49.08        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L2 
       91.30        88.01        95.18       127.50        50.14        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L8 TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH 
      152.15        29.10        39.35        21.76        52.24        78.41 
TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       53.03        69.11        23.31        12.59        20.25        39.48 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              4.11               4.90 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            153.63             152.15 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            39.580             31.495 
[1] "4.1 - 153.6 (39.6)" "4.9 - 152.2 (31.5)"
[1] "hr=" "1.8"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED         4       25         6       10
  20P GAIN WILD-TYPE       5       18        12        8
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  4                  5
  STAGE II                25                 18
  STAGE III                6                 12
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    4 27  5  9
  20P GAIN WILD-TYPE  5 21  6 11
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                4                  5
  T2               27                 21
  T3                5                  6
  T4                9                 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"
D36V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   40  5
  20P GAIN WILD-TYPE 38  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     40    5
  20P GAIN WILD-TYPE   38    5
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0               40                 38
  1                5                  5
[1] 2 2
[1] FALSE
D36V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   27 19
  20P GAIN WILD-TYPE 32 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     27   19
  20P GAIN WILD-TYPE   32   12
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               27                 32
  MALE                 19                 12
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         1    38
  20P GAIN WILD-TYPE     2                         0    38
D36V7, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   38                 38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    4 18
  20P GAIN WILD-TYPE  4 19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4   18
  20P GAIN WILD-TYPE    4   19
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               18                 19
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   33 15
  20Q GAIN WILD-TYPE 25 16
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                48                 41 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                15                 16 
$`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        88.87        19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JX 
       49.22        36.26       121.25        29.82        66.51        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KU 
        6.94        96.59       100.18        22.98        24.62       153.63 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 
       44.84        12.85         4.11        58.55        60.89        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       43.30        28.31        28.64        23.64        39.58         5.23 
TCGA-OR-A5LF TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN 
       14.63        14.33        36.33        73.05        61.08        62.99 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG 
       61.05        28.04        36.03        18.05        23.31        15.45 

$`20Q GAIN WILD-TYPE`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB 
       44.55        68.75        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        72.39        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       49.08        11.31        24.36        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L3 TCGA-OR-A5L8 
       83.80        95.18       127.50        50.14       152.15        29.10 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LL TCGA-OR-A5LO 
       39.35        21.76        52.24        78.41        53.03        69.11 
TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59        20.25        39.48        42.51        22.32 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              4.11               4.90 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            153.63             152.15 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            36.295             33.830 
[1] "4.1 - 153.6 (36.3)" "4.9 - 152.2 (33.8)"
[1] "hr=" "1.3"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED         4       25         7       12
  20Q GAIN WILD-TYPE       5       18        11        6
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  4                  5
  STAGE II                25                 18
  STAGE III                7                 11
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    4 28  6 10
  20Q GAIN WILD-TYPE  5 20  5 10
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                4                  5
  T2               28                 20
  T3                6                  5
  T4               10                 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"
D37V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   41  7
  20Q GAIN WILD-TYPE 37  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     41    7
  20Q GAIN WILD-TYPE   37    3
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               41                 37
  1                7                  3
[1] 2 2
[1] FALSE
D37V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   29 20
  20Q GAIN WILD-TYPE 30 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     29   20
  20Q GAIN WILD-TYPE   30   11
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               29                 30
  MALE                 20                 11
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         1    41
  20Q GAIN WILD-TYPE     2                         0    35
D37V7, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   41                 35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V8, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5 19
  20Q GAIN WILD-TYPE  3 18
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5   19
  20Q GAIN WILD-TYPE    3   18
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                  3
  NOT HISPANIC OR LATINO               19                 18
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   19 12
  21Q GAIN WILD-TYPE 39 19
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                31                 58 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                12                 19 
$`21Q GAIN MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5J3 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JC 
       44.55        68.75        88.87        16.11        44.45        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        49.22        22.03 
TCGA-OR-A5JX TCGA-OR-A5K0 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KU 
       31.23        33.83        11.31        24.36        91.30       153.63 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.14        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LI TCGA-OR-A5LM TCGA-OR-A5LO TCGA-OR-A5LS 
       23.64        39.58        14.33        61.08        69.11        36.03 
TCGA-OU-A5PI 
       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        69.37        18.48        29.23         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV 
       36.26       121.25        12.59        29.82         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       72.39        18.15         6.94        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KQ 
       22.98         8.32        49.08        24.62        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       83.80        95.18       127.50       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.31        29.10        28.64         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-A5LN TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG 
       62.99        61.05        28.04        18.05        12.59        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              4.11               4.90 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            153.63             152.15 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            44.450             32.235 
[1] "4.1 - 153.6 (44.5)" "4.9 - 152.2 (32.2)"
[1] "hr=" "1.1"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED         3       15         5        7
  21Q GAIN WILD-TYPE       6       28        13       11
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  3                  6
  STAGE II                15                 28
  STAGE III                5                 13
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  21Q GAIN MUTATED    3 18  3  6
  21Q GAIN WILD-TYPE  6 30  8 14
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                3                  6
  T2               18                 30
  T3                3                  8
  T4                6                 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"
D38V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   24  6
  21Q GAIN WILD-TYPE 54  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     24    6
  21Q GAIN WILD-TYPE   54    4
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               24                 54
  1                6                  4
[1] 2 2
[1] FALSE
D38V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   21 10
  21Q GAIN WILD-TYPE 38 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     21   10
  21Q GAIN WILD-TYPE   38   21
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               21                 38
  MALE                 10                 21
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         1    27
  21Q GAIN WILD-TYPE     2                         0    49
D38V7, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   27                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V8, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    4 13
  21Q GAIN WILD-TYPE  4 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   13
  21Q GAIN WILD-TYPE    4   24
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                  4
  NOT HISPANIC OR LATINO               13                 24
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    0  3
  22Q GAIN WILD-TYPE 58 28
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 86 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 28 
$`22Q GAIN MUTATED`
TCGA-OR-A5JJ TCGA-OR-A5L2 TCGA-OR-A5LH 
       10.16        60.89        78.41 

$`22Q 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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
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        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      100.18        22.98         8.32        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.36        46.49        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       14.63        52.24        14.33        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        23.31        12.59        15.45        20.25        39.48 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             10.16               4.11 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             78.41             153.63 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            60.890             36.145 
[1] "10.2 - 78.4 (60.9)" "4.1 - 153.6 (36.1)"
[1] "hr=" "2.5"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED         0        2         0        1
  22Q GAIN WILD-TYPE       9       41        18       17
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                0                 18
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  22Q GAIN MUTATED    0  2  0  1
  22Q GAIN WILD-TYPE  9 46 11 19
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                0                 11
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  1
  22Q GAIN WILD-TYPE 76  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    1
  22Q GAIN WILD-TYPE   76    9
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                2                 76
  1                1                  9
[1] 2 2
[1] FALSE
D39V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  1
  22Q GAIN WILD-TYPE 57 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    1
  22Q GAIN WILD-TYPE   57   30
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                2                 57
  MALE                  1                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         0     3
  22Q GAIN WILD-TYPE     2                         1    73
D39V7, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    0  2
  22Q GAIN WILD-TYPE  8 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    2
  22Q GAIN WILD-TYPE    8   35
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   27 13
  XQ GAIN WILD-TYPE 31 18
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               40                49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               13                18 
$`XQ GAIN MUTATED`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J8 TCGA-OR-A5J9 
       55.13        68.75        12.00        88.87        19.04        44.45 
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        29.82 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5KO 
        6.94        96.59       100.18        22.98        24.62        46.49 
TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       83.80       153.63        12.85         4.11        58.55        60.89 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        29.10        28.64        23.64        39.58 
TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LM TCGA-OR-A5LO 
       39.35        14.63        78.41        36.33        61.08        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG 
       61.05        28.04        18.05        15.45 

$`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        69.37        46.82        49.22        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV 
       29.23         4.90        36.26        12.59         9.50        66.51 
TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
       72.39        31.23        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KT 
       49.08        11.31        24.36        91.30        88.01        95.18 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5L3 TCGA-OR-A5L6 TCGA-OR-A5LC 
      127.50        50.14        44.84       152.15        28.31         5.23 
TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN 
       21.76        52.24        14.33        73.05        53.03        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       36.03        23.31        12.59        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             4.11              4.90 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           153.63            152.15 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           39.465            33.830 
[1] "4.1 - 153.6 (39.5)" "4.9 - 152.2 (33.8)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED         4       22         8        6
  XQ GAIN WILD-TYPE       5       21        10       12
D40V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                 4                 5
  STAGE II               22                21
  STAGE III               8                10
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED    4 23  5  8
  XQ GAIN WILD-TYPE  5 25  6 12
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               4                 5
  T2              23                25
  T3               5                 6
  T4               8                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"
D40V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   37  3
  XQ GAIN WILD-TYPE 41  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     37    3
  XQ GAIN WILD-TYPE   41    7
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              37                41
  1               3                 7
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   25 15
  XQ GAIN WILD-TYPE 34 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     25   15
  XQ GAIN WILD-TYPE   34   16
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              25                34
  MALE                15                16
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1    34
  XQ GAIN WILD-TYPE     2                         0    42
D40V7, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  34                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V8, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    6 18
  XQ GAIN WILD-TYPE  2 19
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      6   18
  XQ GAIN WILD-TYPE    2   19
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                 2
  NOT HISPANIC OR LATINO              18                19
[1] 2 2
[1] FALSE

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   19 10
  1P LOSS WILD-TYPE 39 21
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               29                60 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10                21 
$`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        69.37        46.82        49.22 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       18.48        36.26        12.59        66.51        72.39        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        49.08        44.84 
TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL 
       60.89        28.31         5.23        52.24        14.33        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       61.08        62.99        36.03        23.31        39.48 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        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 
       29.82         9.50         6.94        96.59       100.18        22.98 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       24.62        11.31        24.36        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        50.14        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
        4.11        58.55       152.15        31.79        43.30        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        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        69.11        61.05        28.04 
TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       18.05        12.59        15.45        20.25        42.51        22.32 

  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 
            39.48             31.05 
[1] "5.2 - 91.5 (39.5)"  "4.1 - 153.6 (31.0)"
[1] "hr=" "1"  
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED         2       14         6        6
  1P LOSS WILD-TYPE       7       29        12       12
D41V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 2                 7
  STAGE II               14                29
  STAGE III               6                12
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    2 16  4  6
  1P LOSS WILD-TYPE  7 32  7 14
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               2                 7
  T2              16                32
  T3               4                 7
  T4               6                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"
D41V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   25  3
  1P LOSS WILD-TYPE 53  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     25    3
  1P LOSS WILD-TYPE   53    7
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              25                53
  1               3                 7
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   19 10
  1P LOSS WILD-TYPE 40 21
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19   10
  1P LOSS WILD-TYPE   40   21
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              19                40
  MALE                10                21
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         0    24
  1P LOSS WILD-TYPE     2                         1    52
D41V7, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  24                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V8, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  8
  1P LOSS WILD-TYPE  7 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    8
  1P LOSS WILD-TYPE    7   29
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               8                29
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   12  8
  1Q LOSS WILD-TYPE 46 23
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               20                69 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                8                23 
$`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        69.37        46.82        49.22 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       18.48        36.26        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5KX TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LI 
       32.68        44.84        60.89        28.31         5.23        14.33 
TCGA-OR-A5LM TCGA-OU-A5PI 
       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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        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        29.82         9.50         6.94        33.83        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      100.18        22.98         8.32        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.36        46.49        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
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        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       28.04        36.03        18.05        12.59        15.45        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  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 
            40.55             36.03 
[1] "5.2 - 91.5 (40.5)"  "4.1 - 153.6 (36.0)"
[1] "hr=" "1.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED         1        8         4        6
  1Q LOSS WILD-TYPE       8       35        14       12
D42V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                8                35
  STAGE III               4                14
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    1 10  2  6
  1Q LOSS WILD-TYPE  8 38  9 14
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               1                 8
  T2              10                38
  T3               2                 9
  T4               6                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"
D42V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   16  3
  1Q LOSS WILD-TYPE 62  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     16    3
  1Q LOSS WILD-TYPE   62    7
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              16                62
  1               3                 7
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   12  8
  1Q LOSS WILD-TYPE 47 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     12    8
  1Q LOSS WILD-TYPE   47   23
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              12                47
  MALE                 8                23
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         0    19
  1Q LOSS WILD-TYPE     2                         1    57
D42V7, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  19                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V8, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    1  6
  1Q LOSS WILD-TYPE  7 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    6
  1Q LOSS WILD-TYPE    7   31
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               6                31
[1] 2 2
[1] FALSE

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   15  2
  2P LOSS WILD-TYPE 43 29
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               17                72 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                29 
$`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        69.37        49.22        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5KX 
       36.26        12.59        66.51        72.39        31.23        44.84 
TCGA-OR-A5LG TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       52.24        62.99        36.03        23.31        39.48 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        44.45        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        29.82         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 
       96.59        32.68       100.18        22.98         8.32        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       24.62        11.31        24.36        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       83.80        95.18       153.63       127.50        50.14        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       28.31        29.10        28.64        23.64        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.35        21.76        14.63        78.41        14.33        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        69.11        61.05        28.04 
TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       18.05        12.59        15.45        20.25        42.51        22.32 

  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 
           44.840            32.235 
[1] "12.6 - 91.5 (44.8)" "4.1 - 153.6 (32.2)"
[1] "hr=" "4"  
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED         2        8         3        3
  2P LOSS WILD-TYPE       7       35        15       15
D43V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                 2                 7
  STAGE II                8                35
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    2 10  2  2
  2P LOSS WILD-TYPE  7 38  9 18
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               2                 7
  T2              10                38
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   14  2
  2P LOSS WILD-TYPE 64  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     14    2
  2P LOSS WILD-TYPE   64    8
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              14                64
  1               2                 8
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   10  7
  2P LOSS WILD-TYPE 49 24
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     10    7
  2P LOSS WILD-TYPE   49   24
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              10                49
  MALE                 7                24
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0    14
  2P LOSS WILD-TYPE     2                         1    62
D43V7, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  14                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V8, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    0  3
  2P LOSS WILD-TYPE  8 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      0    3
  2P LOSS WILD-TYPE    8   34
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                34
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   13  2
  2Q LOSS WILD-TYPE 45 29
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               15                74 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                29 
$`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        69.37        49.22        22.03 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5LN 
       36.26        12.59        66.51        72.39        31.23        62.99 
TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA 
       36.03        23.31        39.48 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        44.45        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        29.82         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 
       96.59        32.68       100.18        22.98         8.32        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       24.62        11.31        24.36        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LO 
       14.33        36.33        73.05        53.03        61.08        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       61.05        28.04        18.05        12.59        15.45        20.25 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  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 
           39.480            33.255 
[1] "12.6 - 91.5 (39.5)" "4.1 - 153.6 (33.3)"
[1] "hr=" "3.4"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED         2        8         1        3
  2Q LOSS WILD-TYPE       7       35        17       15
D44V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                 2                 7
  STAGE II                8                35
  STAGE III               1                17
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  2Q LOSS MUTATED    2  9  1  2
  2Q LOSS WILD-TYPE  7 39 10 18
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               2                 7
  T2               9                39
  T3               1                10
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   13  1
  2Q LOSS WILD-TYPE 65  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     13    1
  2Q LOSS WILD-TYPE   65    9
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              13                65
  1               1                 9
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    9  6
  2Q LOSS WILD-TYPE 50 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      9    6
  2Q LOSS WILD-TYPE   50   25
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               9                50
  MALE                 6                25
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0    12
  2Q LOSS WILD-TYPE     2                         1    64
D44V7, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  12                64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    0  1
  2Q LOSS WILD-TYPE  8 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    1
  2Q LOSS WILD-TYPE    8   36
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               1                36
[1] 2 2
[1] FALSE

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   10 10
  3P LOSS WILD-TYPE 48 21
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               20                69 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               10                21 
$`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        69.37 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K9 
       49.22        22.03         4.90        72.39        18.15        11.31 
TCGA-OR-A5KP TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM 
       91.30        28.31         5.23        14.33        53.03        61.08 
TCGA-OR-A5LS TCGA-PK-A5HB 
       36.03        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI 
       19.04        44.45        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        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 
       29.82         9.50        66.51        31.23         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       96.59        32.68       100.18        22.98         8.32        49.08 
TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.62        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        43.30        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG 
       61.05        28.04        18.05        23.31        12.59        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             4.90              4.11 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            91.30            153.63 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            29.31             39.35 
[1] "4.9 - 91.3 (29.3)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "2"  
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED         1        9         1        7
  3P LOSS WILD-TYPE       8       34        17       11
D45V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                9                34
  STAGE III               1                17
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    1  9  1  7
  3P LOSS WILD-TYPE  8 39 10 13
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               1                 8
  T2               9                39
  T3               1                10
  T4               7                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"
D45V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   16  2
  3P LOSS WILD-TYPE 62  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     16    2
  3P LOSS WILD-TYPE   62    8
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              16                62
  1               2                 8
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   11  9
  3P LOSS WILD-TYPE 48 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     11    9
  3P LOSS WILD-TYPE   48   22
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              11                48
  MALE                 9                22
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         0    16
  3P LOSS WILD-TYPE     2                         1    60
D45V7, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V8, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    1  4
  3P LOSS WILD-TYPE  7 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    4
  3P LOSS WILD-TYPE    7   33
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               4                33
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   10 10
  3Q LOSS WILD-TYPE 48 21
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               20                69 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10                21 
$`3Q LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JG TCGA-OR-A5JH 
       88.87        16.11        30.31        57.53        17.79        69.37 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JP TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5K0 
       49.22        22.03         4.90        72.39        18.15        33.83 
TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL 
       11.31        91.30         5.23        21.76        14.33        53.03 
TCGA-OR-A5LM TCGA-PK-A5HB 
       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        68.75        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JI 
       44.45        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        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        66.51        31.23         6.94        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       32.68       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       24.36        46.49        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LG 
       28.64        23.64        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        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG 
       28.04        36.03        18.05        23.31        12.59        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       20.25        39.48        22.32 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             4.90              4.11 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            91.30            153.63 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            32.07             36.33 
[1] "4.9 - 91.3 (32.1)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "1.8"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED         1       10         1        6
  3Q LOSS WILD-TYPE       8       33        17       12
D46V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II               10                33
  STAGE III               1                17
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  3Q LOSS MUTATED    1 10  1  6
  3Q LOSS WILD-TYPE  8 38 10 14
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               1                 8
  T2              10                38
  T3               1                10
  T4               6                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"
D46V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   16  2
  3Q LOSS WILD-TYPE 62  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     16    2
  3Q LOSS WILD-TYPE   62    8
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              16                62
  1               2                 8
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   12  8
  3Q LOSS WILD-TYPE 47 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     12    8
  3Q LOSS WILD-TYPE   47   23
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              12                47
  MALE                 8                23
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         1    16
  3Q LOSS WILD-TYPE     2                         0    60
D46V7, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 0
  WHITE                                  16                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V8, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  4
  3Q LOSS WILD-TYPE  6 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    4
  3Q LOSS WILD-TYPE    6   33
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               4                33
[1] 2 2
[1] FALSE

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    3  7
  4P LOSS WILD-TYPE 55 24
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                7                24 
$`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-OR-A5LI TCGA-PK-A5HA 
        4.11         5.23        14.33        39.48 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR 
       49.22        22.03        29.23         4.90        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ 
       29.82         9.50        66.51        72.39        31.23         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       33.83        96.59       100.18        22.98         8.32        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        11.31        24.36        91.30        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        50.14        44.84        12.85 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64        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-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS 
       61.08        62.99        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB 
       18.05        23.31        12.59        15.45        20.25        42.51 
TCGA-PK-A5HC 
       22.32 

  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 
           18.135            39.580 
[1] "4.1 - 46.5 (18.1)"  "4.9 - 153.6 (39.6)"
[1] "hr=" "4.9"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED         1        2         1        6
  4P LOSS WILD-TYPE       8       41        17       12
D47V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                2                41
  STAGE III               1                17
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    1  2  0  7
  4P LOSS WILD-TYPE  8 46 11 13
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               1                 8
  T2               2                46
  T3               0                11
  T4               7                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"
D47V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    9  1
  4P LOSS WILD-TYPE 69  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      9    1
  4P LOSS WILD-TYPE   69    9
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               9                69
  1               1                 9
[1] 2 2
[1] FALSE
D47V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    7  3
  4P LOSS WILD-TYPE 52 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      7    3
  4P LOSS WILD-TYPE   52   28
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               7                52
  MALE                 3                28
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       0                         0     9
  4P LOSS WILD-TYPE     2                         1    67
D47V7, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   9                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    0  4
  4P LOSS WILD-TYPE  8 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      0    4
  4P LOSS WILD-TYPE    8   33
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               4                33
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  8
  4Q LOSS WILD-TYPE 55 23
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11                78 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                8                23 
$`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-OR-A5LI TCGA-PK-A5HA 
       46.49         4.11         5.23        14.33        39.48 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        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        69.37        46.82        10.16        49.22 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       22.03        29.23         4.90        36.26       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 
        9.50        66.51        72.39        31.23         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       96.59       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5L1 
      153.63       127.50        50.14        44.84        12.85        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        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        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       23.31        12.59        15.45        20.25        42.51        22.32 

  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 
           18.120            40.485 
[1] "4.1 - 46.5 (18.1)"  "4.9 - 153.6 (40.5)"
[1] "hr=" "5.5"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED         1        2         2        6
  4Q LOSS WILD-TYPE       8       41        16       12
D48V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                2                41
  STAGE III               2                16
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    1  2  1  7
  4Q LOSS WILD-TYPE  8 46 10 13
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               1                 8
  T2               2                46
  T3               1                10
  T4               7                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"
D48V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   10  1
  4Q LOSS WILD-TYPE 68  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10    1
  4Q LOSS WILD-TYPE   68    9
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              10                68
  1               1                 9
[1] 2 2
[1] FALSE
D48V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    8  3
  4Q LOSS WILD-TYPE 51 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      8    3
  4Q LOSS WILD-TYPE   51   28
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               8                51
  MALE                 3                28
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       0                         0    10
  4Q LOSS WILD-TYPE     2                         1    66
D48V7, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1  4
  4Q LOSS WILD-TYPE  7 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    4
  4Q LOSS WILD-TYPE    7   33
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               4                33
[1] 2 2
[1] FALSE

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    3  5
  5P LOSS WILD-TYPE 55 26
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                8                81 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5                26 
$`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        44.84        52.24 
TCGA-OR-A5LI TCGA-OR-A5LL 
       14.33        53.03 

$`5P LOSS WILD-TYPE`
TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 
       68.75        15.45        12.00        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        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        69.37        46.82        10.16        49.22 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS 
       22.03        29.23         4.90        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82         9.50        66.51        72.39        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       49.08        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
        5.23        39.35        21.76        14.63        78.41        36.33 
TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       73.05        61.08        62.99        69.11        61.05        28.04 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 
       36.03        18.05        23.31        12.59        15.45        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            14.33              4.11 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            55.13            153.63 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           44.695            36.030 
[1] "14.3 - 55.1 (44.7)" "4.1 - 153.6 (36.0)"
[1] "hr=" "2.1"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         0        2         3        3
  5P LOSS WILD-TYPE       9       41        15       15
D49V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                2                41
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    0  3  3  2
  5P LOSS WILD-TYPE  9 45  8 18
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               0                 9
  T2               3                45
  T3               3                 8
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    7  1
  5P LOSS WILD-TYPE 71  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      7    1
  5P LOSS WILD-TYPE   71    9
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               7                71
  1               1                 9
[1] 2 2
[1] FALSE
D49V6, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    5  3
  5P LOSS WILD-TYPE 54 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      5    3
  5P LOSS WILD-TYPE   54   28
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               5                54
  MALE                 3                28
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     7
  5P LOSS WILD-TYPE     2                         1    69
D49V7, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    1  3
  5P LOSS WILD-TYPE  7 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      1    3
  5P LOSS WILD-TYPE    7   34
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               3                34
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    4  3
  5Q LOSS WILD-TYPE 54 28
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                82 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                28 
$`5Q LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JX TCGA-OR-A5KX TCGA-OR-A5LG 
       44.55        49.22        18.48        31.23        44.84        52.24 
TCGA-OR-A5LI 
       14.33 

$`5Q LOSS WILD-TYPE`
TCGA-OR-A5J2 TCGA-OR-A5J3 TCGA-OR-A5J4 TCGA-OR-A5J5 TCGA-OR-A5J6 TCGA-OR-A5J7 
       55.13        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        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        36.26       121.25        12.59 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JY TCGA-OR-A5JZ 
       29.82         9.50        66.51        72.39        18.15         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       49.08        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        39.58 
TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LJ 
        5.23        39.35        21.76        14.63        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        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG 
       28.04        36.03        18.05        23.31        12.59        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            14.33              4.11 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            52.24            153.63 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           44.550            36.145 
[1] "14.3 - 52.2 (44.5)" "4.1 - 153.6 (36.1)"
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         0        1         3        3
  5Q LOSS WILD-TYPE       9       42        15       15
D50V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                1                42
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    0  2  2  3
  5Q LOSS WILD-TYPE  9 46  9 17
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               0                 9
  T2               2                46
  T3               2                 9
  T4               3                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
  5Q LOSS MUTATED    6  1
  5Q LOSS WILD-TYPE 72  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      6    1
  5Q LOSS WILD-TYPE   72    9
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               6                72
  1               1                 9
[1] 2 2
[1] FALSE
D50V6, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    3  4
  5Q LOSS WILD-TYPE 56 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3    4
  5Q LOSS WILD-TYPE   56   27
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 4                27
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     7
  5Q LOSS WILD-TYPE     2                         1    69
D50V7, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   7                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    0  3
  5Q LOSS WILD-TYPE  8 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    3
  5Q LOSS WILD-TYPE    8   34
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               3                34
[1] 2 2
[1] FALSE

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   10  9
  6P LOSS WILD-TYPE 48 22
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               19                70 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                9                22 
$`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        69.37        49.22         4.90        36.26 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 TCGA-OR-A5L2 TCGA-OR-A5LC 
       12.59        66.51        18.15        32.68        60.89         5.23 
TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       21.76        14.33        53.03        36.03        18.05        23.31 
TCGA-P6-A5OG 
       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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC 
       16.11        19.04        44.45        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        29.82         9.50        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        33.83        96.59       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       49.08        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 
       44.84        12.85         4.11        58.55       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        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-PA-A5YG 
       61.08        62.99        69.11        61.05        28.04        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        39.48        42.51        22.32 

  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 
            23.31             39.53 
[1] "4.9 - 91.5 (23.3)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "1.9"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED         0       10         2        7
  6P LOSS WILD-TYPE       9       33        16       11
D51V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II               10                33
  STAGE III               2                16
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    0 11  1  7
  6P LOSS WILD-TYPE  9 37 10 13
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 9
  T2              11                37
  T3               1                10
  T4               7                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"
D51V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   16  3
  6P LOSS WILD-TYPE 62  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     16    3
  6P LOSS WILD-TYPE   62    7
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0              16                62
  1               3                 7
[1] 2 2
[1] FALSE
D51V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   13  6
  6P LOSS WILD-TYPE 46 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     13    6
  6P LOSS WILD-TYPE   46   25
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              13                46
  MALE                 6                25
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         0    16
  6P LOSS WILD-TYPE     2                         1    60
D51V7, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  16                60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V8, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    0  6
  6P LOSS WILD-TYPE  8 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      0    6
  6P LOSS WILD-TYPE    8   31
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               6                31
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   11 10
  6Q LOSS WILD-TYPE 47 21
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               21                68 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                21 
$`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        69.37        49.22 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K2 
        4.90        36.26        12.59        66.51        18.15        32.68 
TCGA-OR-A5KO TCGA-OR-A5L2 TCGA-OR-A5LC TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LS 
       46.49        60.89         5.23        14.33        53.03        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       18.05        23.31        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        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 
       29.82         9.50        72.39        31.23         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 
       96.59       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        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-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       69.11        61.05        28.04        15.45        20.25        39.48 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  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 
            23.31             39.53 
[1] "4.9 - 91.5 (23.3)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "2"  
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED         0        9         3       10
  6Q LOSS WILD-TYPE       9       34        15        8
D52V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                9                34
  STAGE III               3                15
  STAGE IV               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"
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    0 10  2 10
  6Q LOSS WILD-TYPE  9 38  9 10
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               0                 9
  T2              10                38
  T3               2                 9
  T4              10                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"
D52V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   19  3
  6Q LOSS WILD-TYPE 59  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     19    3
  6Q LOSS WILD-TYPE   59    7
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              19                59
  1               3                 7
[1] 2 2
[1] FALSE
D52V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16  6
  6Q LOSS WILD-TYPE 43 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    6
  6Q LOSS WILD-TYPE   43   25
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              16                43
  MALE                 6                25
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         0    19
  6Q LOSS WILD-TYPE     2                         1    57
D52V7, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  19                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V8, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    1  7
  6Q LOSS WILD-TYPE  7 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1    7
  6Q LOSS WILD-TYPE    7   30
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               7                30
[1] 2 2
[1] FALSE

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    2  3
  7P LOSS WILD-TYPE 56 28
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                84 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                28 
$`7P LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JP TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LT 
       57.53         4.90        39.35        14.33        18.05 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JQ TCGA-OR-A5JR 
       49.22        22.03        18.48        29.23        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        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        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       22.98         8.32        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        39.58         5.23        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        69.11        61.05        28.04        36.03        23.31 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59        15.45        20.25        39.48        42.51        22.32 

  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 
           18.050            36.295 
[1] "4.9 - 57.5 (18.1)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "2.8"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         0        1         2        1
  7P LOSS WILD-TYPE       9       42        16       17
D53V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 0                 9
  STAGE II                1                42
  STAGE III               2                16
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  7P LOSS MUTATED    0  1  1  2
  7P LOSS WILD-TYPE  9 47 10 18
D53V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               0                 9
  T2               1                47
  T3               1                10
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    4  0
  7P LOSS WILD-TYPE 74 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4    0
  7P LOSS WILD-TYPE   74   10
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               4                74
  1               0                10
[1] 2 2
[1] FALSE
D53V6, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    1  4
  7P LOSS WILD-TYPE 58 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      1    4
  7P LOSS WILD-TYPE   58   27
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               1                58
  MALE                 4                27
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       0                         0     4
  7P LOSS WILD-TYPE     2                         1    72
D53V7, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   4                72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V8, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    0  2
  7P LOSS WILD-TYPE  8 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE    8   35
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               2                35
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    1  5
  7Q LOSS WILD-TYPE 57 26
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                83 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                5                26 
$`7Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5K5 TCGA-OR-A5LD TCGA-OR-A5LI TCGA-OR-A5LT 
       57.53        69.21         8.32        39.35        14.33        18.05 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        44.45        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        69.37        46.82        10.16        49.22 
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        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        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        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.14        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG 
       23.64        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 
       69.11        61.05        28.04        36.03        23.31        12.59 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       15.45        20.25        39.48        42.51        22.32 

  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 
            28.70             36.26 
[1] "8.3 - 69.2 (28.7)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "3.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         1        0         3        1
  7Q LOSS WILD-TYPE       8       43        15       17
D54V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                0                43
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  7Q LOSS MUTATED    1  0  2  2
  7Q LOSS WILD-TYPE  8 48  9 18
D54V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               1                 8
  T2               0                48
  T3               2                 9
  T4               2                18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    5  0
  7Q LOSS WILD-TYPE 73 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      5    0
  7Q LOSS WILD-TYPE   73   10
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               5                73
  1               0                10
[1] 2 2
[1] FALSE
D54V6, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  3
  7Q LOSS WILD-TYPE 56 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    3
  7Q LOSS WILD-TYPE   56   28
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                56
  MALE                 3                28
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         0     5
  7Q LOSS WILD-TYPE     2                         1    71
D54V7, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                   5                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    0  2
  7Q LOSS WILD-TYPE  8 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    2
  7Q LOSS WILD-TYPE    8   35
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               2                35
[1] 2 2
[1] FALSE

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   10  6
  8P LOSS WILD-TYPE 48 25
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                73 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                6                25 
$`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        72.39 
TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KX TCGA-OR-A5LG TCGA-OR-A5LI 
       49.08        24.36        91.30        44.84        52.24        14.33 
TCGA-OR-A5LL TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HB 
       53.03        36.03        23.31        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        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 
       69.37        46.82        10.16        49.22        18.48        29.23 
TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU 
        4.90        36.26       121.25        12.59        29.82         9.50 
TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 
       66.51        31.23        18.15         6.94        33.83        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5K9 
       32.68       100.18        22.98         8.32        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       50.14        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH 
       39.58         5.23        39.35        21.76        14.63        78.41 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP 
       36.33        73.05        61.08        62.99        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       28.04        18.05        12.59        15.45        20.25        39.48 
TCGA-PK-A5HC 
       22.32 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            14.33              4.11 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            91.30            153.63 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            33.17             36.33 
[1] "14.3 - 91.3 (33.2)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.2"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED         1        6         3        5
  8P LOSS WILD-TYPE       8       37        15       13
D55V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                6                37
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    1  8  2  4
  8P LOSS WILD-TYPE  8 40  9 16
D55V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               1                 8
  T2               8                40
  T3               2                 9
  T4               4                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"
D55V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   12  3
  8P LOSS WILD-TYPE 66  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     12    3
  8P LOSS WILD-TYPE   66    7
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0              12                66
  1               3                 7
[1] 2 2
[1] FALSE
D55V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   11  5
  8P LOSS WILD-TYPE 48 26
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11    5
  8P LOSS WILD-TYPE   48   26
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              11                48
  MALE                 5                26
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       0                         0    13
  8P LOSS WILD-TYPE     2                         1    63
D55V7, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  13                63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    1  7
  8P LOSS WILD-TYPE  7 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    7
  8P LOSS WILD-TYPE    7   30
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               7                30
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    8  4
  8Q LOSS WILD-TYPE 50 27
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               12                77 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                27 
$`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        72.39        49.08 
TCGA-OR-A5KP TCGA-OR-A5KX TCGA-OR-A5LI TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HB 
       91.30        44.84        14.33        36.03        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        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        69.37        46.82        10.16        49.22        18.48 
TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT 
       29.23         4.90        36.26       121.25        12.59        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
        9.50        66.51        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-A5K8 
       96.59        32.68       100.18        22.98         8.32        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        24.36        46.49        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      153.63       127.50        50.14        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        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        69.11        61.05        28.04        18.05 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       12.59        15.45        20.25        39.48        22.32 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            14.33              4.11 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            91.30            153.63 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            33.17             36.33 
[1] "14.3 - 91.3 (33.2)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1"  
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED         1        4         2        4
  8Q LOSS WILD-TYPE       8       39        16       14
D56V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                4                39
  STAGE III               2                16
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  8Q LOSS MUTATED    1  6  1  3
  8Q LOSS WILD-TYPE  8 42 10 17
D56V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               1                 8
  T2               6                42
  T3               1                10
  T4               3                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"
D56V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    8  3
  8Q LOSS WILD-TYPE 70  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      8    3
  8Q LOSS WILD-TYPE   70    7
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               8                70
  1               3                 7
[1] 2 2
[1] FALSE
D56V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    9  3
  8Q LOSS WILD-TYPE 50 28
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      9    3
  8Q LOSS WILD-TYPE   50   28
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               9                50
  MALE                 3                28
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         0    10
  8Q LOSS WILD-TYPE     2                         1    66
D56V7, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V8, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    1  5
  8Q LOSS WILD-TYPE  7 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      1    5
  8Q LOSS WILD-TYPE    7   32
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   1                 7
  NOT HISPANIC OR LATINO               5                32
[1] 2 2
[1] FALSE

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   11  9
  9P LOSS WILD-TYPE 47 22
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               20                69 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                22 
$`9P LOSS MUTATED`
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JP 
       19.04        44.45        57.53        49.22        18.48         4.90 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5K0 TCGA-OR-A5K2 TCGA-OR-A5K5 
       12.59        66.51        18.15        33.83        32.68         8.32 
TCGA-OR-A5K6 TCGA-OR-A5KB TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LG 
       49.08        24.36       152.15         5.23        21.76        52.24 
TCGA-OR-A5LM TCGA-P6-A5OG 
       61.08        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        68.75        15.45        12.00        88.87 
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        69.37        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 
       36.26       121.25        29.82         9.50        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K8 TCGA-OR-A5K9 
        6.94        96.59       100.18        22.98        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
       60.89        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI 
       23.64        39.58        39.35        14.63        78.41        14.33 
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        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 
       28.04        36.03        18.05        23.31        15.45        20.25 
TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       39.48        42.51        22.32 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             4.90              4.11 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           152.15            153.63 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            28.52             39.35 
[1] "4.9 - 152.2 (28.5)" "4.1 - 153.6 (39.4)"
[1] "hr=" "1.8"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED         1        9         4        5
  9P LOSS WILD-TYPE       8       34        14       13
D57V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                9                34
  STAGE III               4                14
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    1  9  3  6
  9P LOSS WILD-TYPE  8 39  8 14
D57V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               1                 8
  T2               9                39
  T3               3                 8
  T4               6                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"
D57V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   18  1
  9P LOSS WILD-TYPE 60  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     18    1
  9P LOSS WILD-TYPE   60    9
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              18                60
  1               1                 9
[1] 2 2
[1] FALSE
D57V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   12  8
  9P LOSS WILD-TYPE 47 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12    8
  9P LOSS WILD-TYPE   47   23
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              12                47
  MALE                 8                23
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0    19
  9P LOSS WILD-TYPE     2                         1    57
D57V7, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  19                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V8, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    2  7
  9P LOSS WILD-TYPE  6 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      2    7
  9P LOSS WILD-TYPE    6   30
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                 6
  NOT HISPANIC OR LATINO               7                30
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    7  4
  9Q LOSS WILD-TYPE 51 27
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                78 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                27 
$`9Q LOSS MUTATED`
TCGA-OR-A5JC TCGA-OR-A5JK TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5K6 
       57.53        49.22        18.48        12.59        66.51        49.08 
TCGA-OR-A5KB TCGA-OR-A5L3 TCGA-OR-A5LC TCGA-OR-A5LM TCGA-P6-A5OG 
       24.36       152.15         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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JD 
       16.11        19.04        44.45        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        69.37        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        36.26       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ TCGA-OR-A5K0 
        9.50        72.39        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-A5K8 
       96.59        32.68       100.18        22.98         8.32        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       11.31        46.49        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       58.55        60.89        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       28.64        23.64        39.58        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        73.05        53.03 
TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT 
       62.99        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       23.31        15.45        20.25        39.48        42.51        22.32 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             5.23              4.11 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           152.15            153.63 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           49.080            36.145 
[1] "5.2 - 152.2 (49.1)" "4.1 - 153.6 (36.1)"
[1] "hr=" "1.1"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED         1        5         0        4
  9Q LOSS WILD-TYPE       8       38        18       14
D58V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                5                38
  STAGE III               0                18
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    1  5  0  4
  9Q LOSS WILD-TYPE  8 43 11 16
D58V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               1                 8
  T2               5                43
  T3               0                11
  T4               4                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"
D58V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   10  0
  9Q LOSS WILD-TYPE 68 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     10    0
  9Q LOSS WILD-TYPE   68   10
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              10                68
  1               0                10
[1] 2 2
[1] FALSE
D58V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    7  4
  9Q LOSS WILD-TYPE 52 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      7    4
  9Q LOSS WILD-TYPE   52   27
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               7                52
  MALE                 4                27
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         0    10
  9Q LOSS WILD-TYPE     2                         1    66
D58V7, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  10                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V8, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    0  5
  9Q LOSS WILD-TYPE  8 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      0    5
  9Q LOSS WILD-TYPE    8   32
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               5                32
[1] 2 2
[1] FALSE

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    6  6
  10P LOSS WILD-TYPE 52 25
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                12                 77 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 25 
$`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        69.37        36.26 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LM 
       12.59        66.51        18.15        60.89        28.31        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        68.75        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JF 
       19.04        44.45        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        49.22        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        29.82         9.50        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
        8.32        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L3 
       50.14        44.84        12.85         4.11        58.55       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        29.10        28.64        23.64        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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LO 
       14.33        36.33        73.05        53.03        62.99        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG 
       61.05        28.04        36.03        18.05        23.31        12.59 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       15.45        20.25        39.48        42.51        22.32 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             12.59               4.11 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             69.37             153.63 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            33.285             36.330 
[1] "12.6 - 69.4 (33.3)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.5"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED         1        7         0        4
  10P LOSS WILD-TYPE       8       36        18       14
D59V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 7                 36
  STAGE III                0                 18
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    1  7  1  3
  10P LOSS WILD-TYPE  8 41 10 17
D59V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  8
  T2                7                 41
  T3                1                 10
  T4                3                 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"
D59V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    9  3
  10P LOSS WILD-TYPE 69  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      9    3
  10P LOSS WILD-TYPE   69    7
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                9                 69
  1                3                  7
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    8  4
  10P LOSS WILD-TYPE 51 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8    4
  10P LOSS WILD-TYPE   51   27
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                8                 51
  MALE                  4                 27
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0    11
  10P LOSS WILD-TYPE     2                         1    65
D59V7, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   11                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V8, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    1  2
  10P LOSS WILD-TYPE  7 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    2
  10P LOSS WILD-TYPE    7   35
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    5  5
  10Q LOSS WILD-TYPE 53 26
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 79 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 26 
$`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        69.37        36.26        12.59 
TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5L2 TCGA-OR-A5L6 
       66.51        18.15        60.89        28.31 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        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        49.22        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        29.82         9.50        72.39 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 
       31.23         6.94        33.83        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       22.98         8.32        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM 
       78.41        14.33        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        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        12.59        15.45        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             12.59               4.11 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             69.37             153.63 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            33.285             36.330 
[1] "12.6 - 69.4 (33.3)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.5"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED         1        6         0        3
  10Q LOSS WILD-TYPE       8       37        18       15
D60V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 6                 37
  STAGE III                0                 18
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    1  6  0  3
  10Q LOSS WILD-TYPE  8 42 11 17
D60V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  8
  T2                6                 42
  T3                0                 11
  T4                3                 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"
D60V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    8  2
  10Q LOSS WILD-TYPE 70  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      8    2
  10Q LOSS WILD-TYPE   70    8
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                8                 70
  1                2                  8
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    7  3
  10Q LOSS WILD-TYPE 52 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      7    3
  10Q LOSS WILD-TYPE   52   28
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                7                 52
  MALE                  3                 28
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         0    10
  10Q LOSS WILD-TYPE     2                         1    66
D60V7, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   10                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V8, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    0  2
  10Q LOSS WILD-TYPE  8 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      0    2
  10Q LOSS WILD-TYPE    8   35
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   17  7
  11P LOSS WILD-TYPE 41 24
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                 65 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 7                 24 
$`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        69.37 
TCGA-OR-A5JI TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JW 
       46.82        49.22        22.03        36.26        66.51        72.39 
TCGA-OR-A5JY TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5L6 TCGA-OR-A5LC 
       18.15        49.08        11.31        24.36        28.31         5.23 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA TCGA-PK-A5HB 
       61.08        62.99        36.03        23.31        39.48        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ 
       19.04        44.45        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        29.82 
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        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO TCGA-OR-A5KP 
      100.18        22.98         8.32        24.62        46.49        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       31.79        43.30        29.10        28.64        23.64        39.58 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR 
       36.33        73.05        53.03        69.11        61.05        28.04 
TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       18.05        12.59        15.45        20.25        22.32 

  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 
             37.87              33.83 
[1] "5.2 - 91.5 (37.9)"  "4.1 - 153.6 (33.8)"
[1] "hr=" "1.3"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED         3       12         1        6
  11P LOSS WILD-TYPE       6       31        17       12
D61V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                12                 31
  STAGE III                1                 17
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    3 13  1  5
  11P LOSS WILD-TYPE  6 35 10 15
D61V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                3                  6
  T2               13                 35
  T3                1                 10
  T4                5                 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"
D61V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   19  3
  11P LOSS WILD-TYPE 59  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     19    3
  11P LOSS WILD-TYPE   59    7
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               19                 59
  1                3                  7
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   14 10
  11P LOSS WILD-TYPE 45 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     14   10
  11P LOSS WILD-TYPE   45   21
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               14                 45
  MALE                 10                 21
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       0                         0    19
  11P LOSS WILD-TYPE     2                         1    57
D61V7, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   19                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V8, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1  5
  11P LOSS WILD-TYPE  7 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    5
  11P LOSS WILD-TYPE    7   32
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                5                 32
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   18  5
  11Q LOSS WILD-TYPE 40 26
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                23                 66 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 26 
$`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        69.37        46.82 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW 
       49.22        22.03        36.26        12.59        66.51        72.39 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LM 
       49.08        11.31        24.36        28.31         5.23        61.08 
TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-PK-A5HA TCGA-PK-A5HB 
       62.99        36.03        23.31        39.48        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        19.04        44.45        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        29.82 
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        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO 
       32.68       100.18        22.98         8.32        24.62        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.14        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LO TCGA-OR-A5LP 
       14.33        36.33        73.05        53.03        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       28.04        18.05        12.59        15.45        20.25        22.32 

  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 
            39.480             33.255 
[1] "5.2 - 91.5 (39.5)"  "4.1 - 153.6 (33.3)"
[1] "hr=" "1.8"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED         3       13         0        5
  11Q LOSS WILD-TYPE       6       30        18       13
D62V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                13                 30
  STAGE III                0                 18
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    3 14  0  4
  11Q LOSS WILD-TYPE  6 34 11 16
D62V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                3                  6
  T2               14                 34
  T3                0                 11
  T4                4                 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"
D62V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   19  2
  11Q LOSS WILD-TYPE 59  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     19    2
  11Q LOSS WILD-TYPE   59    8
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               19                 59
  1                2                  8
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   13 10
  11Q LOSS WILD-TYPE 46 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     13   10
  11Q LOSS WILD-TYPE   46   21
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               13                 46
  MALE                 10                 21
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         0    18
  11Q LOSS WILD-TYPE     2                         1    58
D62V7, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   18                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    0  5
  11Q LOSS WILD-TYPE  8 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      0    5
  11Q LOSS WILD-TYPE    8   32
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                5                 32
[1] 2 2
[1] FALSE

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    2  3
  12P LOSS WILD-TYPE 56 28
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 84 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                 28 
$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
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        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      100.18        22.98         8.32        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.36        46.49        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       29.10        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        78.41        14.33        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HC 
       18.05        23.31        15.45        20.25        39.48        22.32 

  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 
            42.510             36.145 
[1] "12.6 - 53.0 (42.5)" "4.1 - 153.6 (36.1)"
[1] "hr=" "2.2"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         0        1         1        2
  12P LOSS WILD-TYPE       9       42        17       16
D63V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    0  1  1  2
  12P LOSS WILD-TYPE  9 47 10 18
D63V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 74 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    0
  12P LOSS WILD-TYPE   74   10
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                4                 74
  1                0                 10
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    2  3
  12P LOSS WILD-TYPE 57 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    3
  12P LOSS WILD-TYPE   57   28
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  3                 28
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         0     3
  12P LOSS WILD-TYPE     2                         1    73
D63V7, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    0  2
  12P LOSS WILD-TYPE  8 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    2
  12P LOSS WILD-TYPE    8   35
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    1  3
  12Q LOSS WILD-TYPE 57 28
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 85 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 28 
$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD 
       16.11        19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
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        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      100.18        22.98         8.32        49.08        24.62        11.31 
TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT 
       24.36        46.49        91.30        88.01        83.80        95.18 
TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ 
      153.63       127.50        50.14        44.84        12.85         4.11 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 
       58.55        60.89       152.15        31.79        43.30        28.31 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       29.10        28.64        23.64        39.58         5.23        39.35 
TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       21.76        14.63        78.41        14.33        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       18.05        23.31        15.45        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  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              36.26 
[1] "12.6 - 53.0 (35.2)" "4.1 - 153.6 (36.3)"
[1] "hr=" "3"  
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         0        1         1        2
  12Q LOSS WILD-TYPE       9       42        17       16
D64V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    0  1  1  2
  12Q LOSS WILD-TYPE  9 47 10 18
D64V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                2                 18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    4  0
  12Q LOSS WILD-TYPE 74 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      4    0
  12Q LOSS WILD-TYPE   74   10
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                4                 74
  1                0                 10
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  2
  12Q LOSS WILD-TYPE 57 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    2
  12Q LOSS WILD-TYPE   57   29
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                2                 57
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0     3
  12Q LOSS WILD-TYPE     2                         1    73
D64V7, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    0  2
  12Q LOSS WILD-TYPE  8 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE    8   35
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   21 17
  13Q LOSS WILD-TYPE 37 14
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                38                 51 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                17                 14 
$`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        69.37        46.82        49.22         4.90 
TCGA-OR-A5JQ TCGA-OR-A5JS TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 
       36.26        12.59         9.50        66.51        72.39        32.68 
TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KP TCGA-OR-A5KS TCGA-OR-A5KU 
        8.32        11.31        24.36        91.30        83.80       153.63 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LD TCGA-OR-A5LI 
        4.11        58.55        60.89        28.31        39.35        14.33 
TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG 
       73.05        53.03        62.99        36.03        23.31        12.59 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        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        68.75        12.00        88.87        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO 
       44.45        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        29.82        31.23        18.15         6.94        33.83 
TCGA-OR-A5K1 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KO 
       96.59       100.18        22.98        49.08        24.62        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KT TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       88.01        95.18       127.50        50.14        44.84        12.85 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
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-A5LM TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       36.33        61.08        69.11        61.05        28.04        18.05 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       15.45        20.25        22.32 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              4.11               5.23 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            153.63             152.15 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            37.805             33.830 
[1] "4.1 - 153.6 (37.8)" "5.2 - 152.2 (33.8)"
[1] "hr=" "1.7"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED         3       20         5        9
  13Q LOSS WILD-TYPE       6       23        13        9
D65V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                20                 23
  STAGE III                5                 13
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  13Q LOSS MUTATED    3 21  4  9
  13Q LOSS WILD-TYPE  6 27  7 11
D65V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                3                  6
  T2               21                 27
  T3                4                  7
  T4                9                 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"
D65V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   34  3
  13Q LOSS WILD-TYPE 44  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     34    3
  13Q LOSS WILD-TYPE   44    7
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               34                 44
  1                3                  7
[1] 2 2
[1] FALSE
D65V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   24 15
  13Q LOSS WILD-TYPE 35 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     24   15
  13Q LOSS WILD-TYPE   35   16
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               24                 35
  MALE                 15                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0    33
  13Q LOSS WILD-TYPE     2                         1    43
D65V7, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   33                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V8, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    2 13
  13Q LOSS WILD-TYPE  6 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      2   13
  13Q LOSS WILD-TYPE    6   24
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               13                 24
[1] 2 2
[1] FALSE

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   11  7
  14Q LOSS WILD-TYPE 47 24
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                18                 71 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 24 
$`14Q LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5JD TCGA-OR-A5JH TCGA-OR-A5JK 
       88.87        16.11        19.04        91.46        69.37        49.22 
TCGA-OR-A5JM TCGA-OR-A5JQ TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5KQ TCGA-OR-A5KZ 
       18.48        36.26        66.51        18.15        88.01         4.11 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LN TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PK-A5HA 
       28.31         5.23        62.99        18.05        12.59        39.48 

$`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        68.75        15.45        12.00        44.45 
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        29.82         9.50        72.39        31.23         6.94 
TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
       33.83        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       49.08        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5KY TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
       12.85        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LE 
       29.10        28.64        23.64        39.58        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        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        69.11        61.05        28.04        36.03 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       23.31        15.45        20.25        42.51        22.32 

  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 
            32.285             36.330 
[1] "4.1 - 91.5 (32.3)"  "4.9 - 153.6 (36.3)"
[1] "hr=" "1.2"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED         1        9         3        5
  14Q LOSS WILD-TYPE       8       34        15       13
D66V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 9                 34
  STAGE III                3                 15
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    1  9  3  5
  14Q LOSS WILD-TYPE  8 39  8 15
D66V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                1                  8
  T2                9                 39
  T3                3                  8
  T4                5                 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"
D66V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   17  1
  14Q LOSS WILD-TYPE 61  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     17    1
  14Q LOSS WILD-TYPE   61    9
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               17                 61
  1                1                  9
[1] 2 2
[1] FALSE
D66V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   11  7
  14Q LOSS WILD-TYPE 48 24
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11    7
  14Q LOSS WILD-TYPE   48   24
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               11                 48
  MALE                  7                 24
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         1    14
  14Q LOSS WILD-TYPE     2                         0    62
D66V7, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   14                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    3  5
  14Q LOSS WILD-TYPE  5 32
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    5
  14Q LOSS WILD-TYPE    5   32
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                  5
  NOT HISPANIC OR LATINO                5                 32
[1] 2 2
[1] FALSE

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   13  7
  15Q LOSS WILD-TYPE 45 24
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                20                 69 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 24 
$`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        69.37        46.82        18.48        36.26 
TCGA-OR-A5JV TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KX 
       66.51        32.68        11.31        91.30        95.18        44.84 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI 
       28.31         5.23        39.35        36.03        18.05        23.31 
TCGA-P6-A5OG TCGA-PK-A5HA 
       12.59        39.48 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE 
       19.04        44.45        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        49.22        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        29.82         9.50        72.39 
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        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
       22.98         8.32        49.08        24.62        24.36        46.49 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KY 
       88.01        83.80       153.63       127.50        50.14        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LE TCGA-OR-A5LF 
       29.10        28.64        23.64        39.58        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        36.33        73.05        53.03 
TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG 
       61.08        62.99        69.11        61.05        28.04        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HB TCGA-PK-A5HC 
       20.25        42.51        22.32 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              5.23               4.11 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             95.18             153.63 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            36.145             36.330 
[1] "5.2 - 95.2 (36.1)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "1.1"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED         3        8         5        5
  15Q LOSS WILD-TYPE       6       35        13       13
D67V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                 8                 35
  STAGE III                5                 13
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    3 10  2  6
  15Q LOSS WILD-TYPE  6 38  9 14
D67V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                3                  6
  T2               10                 38
  T3                2                  9
  T4                6                 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"
D67V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   19  2
  15Q LOSS WILD-TYPE 59  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19    2
  15Q LOSS WILD-TYPE   59    8
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               19                 59
  1                2                  8
[1] 2 2
[1] FALSE
D67V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   15  6
  15Q LOSS WILD-TYPE 44 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     15    6
  15Q LOSS WILD-TYPE   44   25
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               15                 44
  MALE                  6                 25
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         0    18
  15Q LOSS WILD-TYPE     2                         1    58
D67V7, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   18                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    1  9
  15Q LOSS WILD-TYPE  7 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1    9
  15Q LOSS WILD-TYPE    7   28
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                9                 28
[1] 2 2
[1] FALSE

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    1  5
  16P LOSS WILD-TYPE 57 26
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 6                 83 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 5                 26 
$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        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        69.37        46.82        10.16        49.22 
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        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 
        6.94        96.59        32.68       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP 
       49.08        24.62        11.31        24.36        46.49        91.30 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW 
       88.01        83.80        95.18       153.63       127.50        50.14 
TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 
       44.84        12.85         4.11        58.55        60.89       152.15 
TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
       31.79        43.30        28.31        29.10        28.64        23.64 
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-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       14.33        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 
       69.11        61.05        28.04        36.03        18.05        23.31 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       15.45        20.25        39.48        42.51        22.32 

  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             39.480 
[1] "12.6 - 39.4 (18.1)" "4.1 - 153.6 (39.5)"
[1] "hr=" "4.8"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         0        1         2        3
  16P LOSS WILD-TYPE       9       42        16       15
D68V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                2                 16
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  16P LOSS MUTATED    0  1  1  4
  16P LOSS WILD-TYPE  9 47 10 16
D68V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                4                 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"
D68V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    5  1
  16P LOSS WILD-TYPE 73  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    1
  16P LOSS WILD-TYPE   73    9
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                5                 73
  1                1                  9
[1] 2 2
[1] FALSE
D68V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  2
  16P LOSS WILD-TYPE 55 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    2
  16P LOSS WILD-TYPE   55   29
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                4                 55
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     6
  16P LOSS WILD-TYPE     2                         1    70
D68V7, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    6                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V8, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  2
  16P LOSS WILD-TYPE  7 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    2
  16P LOSS WILD-TYPE    7   35
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    1  4
  16Q LOSS WILD-TYPE 57 27
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 5                 84 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 4                 27 
$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
       31.23         6.94        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
        8.32        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.14        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH 
       23.64         5.23        21.76        14.63        52.24        78.41 
TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       14.33        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 
       69.11        61.05        28.04        36.03        18.05        23.31 
TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       12.59        15.45        20.25        39.48        42.51        22.32 

  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 
            33.830             36.295 
[1] "16.1 - 39.6 (33.8)" "4.1 - 153.6 (36.3)"
[1] "hr=" "3.4"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         0        1         2        2
  16Q LOSS WILD-TYPE       9       42        16       16
D69V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                2                 16
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  16Q LOSS MUTATED    0  1  1  3
  16Q LOSS WILD-TYPE  9 47 10 17
D69V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                3                 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"
D69V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  1
  16Q LOSS WILD-TYPE 74  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    1
  16Q LOSS WILD-TYPE   74    9
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                4                 74
  1                1                  9
[1] 2 2
[1] FALSE
D69V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    3  2
  16Q LOSS WILD-TYPE 56 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      3    2
  16Q LOSS WILD-TYPE   56   29
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         0     5
  16Q LOSS WILD-TYPE     2                         1    71
D69V7, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V8, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    1  2
  16Q LOSS WILD-TYPE  7 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1    2
  16Q LOSS WILD-TYPE    7   35
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   14 18
  17P LOSS WILD-TYPE 44 13
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                 57 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                18                 13 
$`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 
       69.37        49.22        18.48         4.90        12.59        66.51 
TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KX 
       72.39        32.68         8.32        11.31        91.30        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L2 TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC 
       12.85         4.11        60.89        28.31        39.58         5.23 
TCGA-OR-A5LE TCGA-OR-A5LI TCGA-OR-A5LM TCGA-OR-A5LS TCGA-OU-A5PI TCGA-P6-A5OG 
       21.76        14.33        61.08        36.03        23.31        12.59 
TCGA-PK-A5HA TCGA-PK-A5HB 
       39.48        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JD TCGA-OR-A5JF TCGA-OR-A5JI TCGA-OR-A5JJ 
       19.04        44.45        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        36.26       121.25        29.82         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        96.59       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ 
       22.98        49.08        24.62        24.36        46.49        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L1 
       83.80        95.18       153.63       127.50        50.14        58.55 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
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-A5LL TCGA-OR-A5LN TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LT 
       53.03        62.99        69.11        61.05        28.04        18.05 
TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       15.45        20.25        22.32 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              4.11               6.94 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             91.30             153.63 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             29.31              41.39 
[1] "4.1 - 91.3 (29.3)"  "6.9 - 153.6 (41.4)"
[1] "hr=" "3.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED         2       13         4       11
  17P LOSS WILD-TYPE       7       30        14        7
D70V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  2                  7
  STAGE II                13                 30
  STAGE III                4                 14
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    2 15  2 11
  17P LOSS WILD-TYPE  7 33  9  9
D70V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                  7
  T2               15                 33
  T3                2                  9
  T4               11                  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"
D70V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   26  4
  17P LOSS WILD-TYPE 52  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     26    4
  17P LOSS WILD-TYPE   52    6
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               26                 52
  1                4                  6
[1] 2 2
[1] FALSE
D70V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   18 14
  17P LOSS WILD-TYPE 41 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     18   14
  17P LOSS WILD-TYPE   41   17
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               18                 41
  MALE                 14                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         0    28
  17P LOSS WILD-TYPE     2                         1    48
D70V7, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   28                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    1 12
  17P LOSS WILD-TYPE  7 25
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      1   12
  17P LOSS WILD-TYPE    7   25
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO               12                 25
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   12 12
  17Q LOSS WILD-TYPE 46 19
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                24                 65 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 19 
$`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        49.22         4.90 
TCGA-OR-A5JS TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5K2 TCGA-OR-A5K9 TCGA-OR-A5KY 
       12.59        66.51        72.39        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        28.31        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        36.03        23.31        12.59        39.48        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JD TCGA-OR-A5JE TCGA-OR-A5JF 
       19.04        44.45        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 
       69.37        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 
       36.26       121.25        29.82         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        96.59       100.18        22.98         8.32 
TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ 
       49.08        24.62        24.36        46.49        91.30        88.01 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       83.80        95.18       153.63       127.50        50.14        44.84 
TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 
       58.55        60.89       152.15        31.79        43.30        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI 
       28.64        23.64        39.35        14.63        78.41        14.33 
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        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LT TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       28.04        18.05        15.45        20.25        22.32 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              4.11               6.94 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             72.39             153.63 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             29.31              41.39 
[1] "4.1 - 72.4 (29.3)"  "6.9 - 153.6 (41.4)"
[1] "hr=" "2.5"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED         1       10         3        8
  17Q LOSS WILD-TYPE       8       33        15       10
D71V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                10                 33
  STAGE III                3                 15
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    1 11  2  8
  17Q LOSS WILD-TYPE  8 37  9 12
D71V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                1                  8
  T2               11                 37
  T3                2                  9
  T4                8                 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"
D71V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   19  3
  17Q LOSS WILD-TYPE 59  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     19    3
  17Q LOSS WILD-TYPE   59    7
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               19                 59
  1                3                  7
[1] 2 2
[1] FALSE
D71V6, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10 14
  17Q LOSS WILD-TYPE 49 17
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10   14
  17Q LOSS WILD-TYPE   49   17
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               10                 49
  MALE                 14                 17
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         0    20
  17Q LOSS WILD-TYPE     2                         1    56
D71V7, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   20                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V8, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    1  9
  17Q LOSS WILD-TYPE  7 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    9
  17Q LOSS WILD-TYPE    7   28
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                9                 28
[1] 2 2
[1] FALSE

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   23 13
  18P LOSS WILD-TYPE 35 18
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                36                 53 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                13                 18 
$`18P LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       88.87        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        69.37        46.82        49.22         4.90        36.26 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
       12.59        29.82        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KT TCGA-OR-A5KY 
       32.68         8.32        46.49        91.30        95.18        12.85 
TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN 
       28.31         5.23        21.76        53.03        61.08        62.99 
TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       36.03        18.05        23.31        12.59        39.48        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        68.75        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL TCGA-OR-A5JM 
       44.45        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        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
      100.18        22.98        49.08        24.62        11.31        24.36 
TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX 
       88.01        83.80       153.63       127.50        50.14        44.84 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF 
       29.10        28.64        23.64        39.58        39.35        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LO 
       52.24        78.41        14.33        36.33        73.05        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       61.05        28.04        15.45        20.25        22.32 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              4.90               4.11 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             95.18             153.63 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            34.355             39.350 
[1] "4.9 - 95.2 (34.4)"  "4.1 - 153.6 (39.4)"
[1] "hr=" "1.1"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED         3       16         5       11
  18P LOSS WILD-TYPE       6       27        13        7
D72V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  3                  6
  STAGE II                16                 27
  STAGE III                5                 13
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    3 17  4 11
  18P LOSS WILD-TYPE  6 31  7  9
D72V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                3                  6
  T2               17                 31
  T3                4                  7
  T4               11                  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"
D72V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   31  4
  18P LOSS WILD-TYPE 47  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     31    4
  18P LOSS WILD-TYPE   47    6
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               31                 47
  1                4                  6
[1] 2 2
[1] FALSE
D72V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   22 15
  18P LOSS WILD-TYPE 37 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     22   15
  18P LOSS WILD-TYPE   37   16
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               22                 37
  MALE                 15                 16
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         1    29
  18P LOSS WILD-TYPE     2                         0    47
D72V7, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   29                 47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V8, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2 10
  18P LOSS WILD-TYPE  6 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2   10
  18P LOSS WILD-TYPE    6   27
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               10                 27
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   23 11
  18Q LOSS WILD-TYPE 35 20
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                34                 55 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                11                 20 
$`18Q LOSS MUTATED`
TCGA-OR-A5J6 TCGA-OR-A5J7 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JG 
       88.87        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 
       69.37        46.82        49.22         4.90        36.26        12.59 
TCGA-OR-A5JT TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5K2 
       29.82        66.51        72.39        31.23        18.15        32.68 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KY TCGA-OR-A5L6 TCGA-OR-A5LC TCGA-OR-A5LE 
       46.49        91.30        12.85        28.31         5.23        21.76 
TCGA-OR-A5LG TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS TCGA-OR-A5LT 
       52.24        53.03        61.08        62.99        36.03        18.05 
TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5HA TCGA-PK-A5HB 
       23.31        12.59        39.48        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        68.75        15.45        12.00        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JE TCGA-OR-A5JF TCGA-OR-A5JJ TCGA-OR-A5JL 
       44.45        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-A5K8 
       96.59       100.18        22.98         8.32        49.08        24.62 
TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       11.31        24.36        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
      127.50        50.14        44.84         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA 
      152.15        31.79        43.30        29.10        28.64        23.64 
TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LF TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ 
       39.58        39.35        14.63        78.41        14.33        36.33 
TCGA-OR-A5LK TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5H9 
       73.05        69.11        61.05        28.04        15.45        20.25 
TCGA-PK-A5HC 
       22.32 

  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 
            36.145             36.330 
[1] "4.9 - 91.5 (36.1)"  "4.1 - 153.6 (36.3)"
[1] "hr=" "1.1"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED         2       16         5       10
  18Q LOSS WILD-TYPE       7       27        13        8
D73V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  2                  7
  STAGE II                16                 27
  STAGE III                5                 13
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    2 17  4 10
  18Q LOSS WILD-TYPE  7 31  7 10
D73V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                2                  7
  T2               17                 31
  T3                4                  7
  T4               10                 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"
D73V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   29  4
  18Q LOSS WILD-TYPE 49  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     29    4
  18Q LOSS WILD-TYPE   49    6
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               29                 49
  1                4                  6
[1] 2 2
[1] FALSE
D73V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   19 16
  18Q LOSS WILD-TYPE 40 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     19   16
  18Q LOSS WILD-TYPE   40   15
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               19                 40
  MALE                 16                 15
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         1    27
  18Q LOSS WILD-TYPE     2                         0    49
D73V7, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   27                 49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V8, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    2 10
  18Q LOSS WILD-TYPE  6 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      2   10
  18Q LOSS WILD-TYPE    6   27
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    2                  6
  NOT HISPANIC OR LATINO               10                 27
[1] 2 2
[1] FALSE

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    1  4
  19P LOSS WILD-TYPE 57 27
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 84 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 27 
$`19P LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5JB TCGA-OR-A5KB TCGA-OR-A5LI TCGA-P6-A5OG 
       44.55        18.12        24.36        14.33        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        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        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        69.37        46.82        10.16        49.22 
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        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        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        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KO 
       22.98         8.32        49.08        24.62        11.31        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.14        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       23.64        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        69.11        61.05        28.04        36.03        18.05 
TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB TCGA-PK-A5HC 
       23.31        15.45        20.25        39.48        42.51        22.32 

  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 
             18.12              37.84 
[1] "12.6 - 44.5 (18.1)" "4.1 - 153.6 (37.8)"
[1] "hr=" "4.4"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         0        2         0        3
  19P LOSS WILD-TYPE       9       41        18       15
D74V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 2                 41
  STAGE III                0                 18
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    0  2  0  3
  19P LOSS WILD-TYPE  9 46 11 17
D74V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  9
  T2                2                 46
  T3                0                 11
  T4                3                 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"
D74V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    5  0
  19P LOSS WILD-TYPE 73 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      5    0
  19P LOSS WILD-TYPE   73   10
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                5                 73
  1                0                 10
[1] 2 2
[1] FALSE
D74V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3  2
  19P LOSS WILD-TYPE 56 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    2
  19P LOSS WILD-TYPE   56   29
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  2                 29
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         0     5
  19P LOSS WILD-TYPE     2                         1    71
D74V7, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    5                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V8, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    0  3
  19P LOSS WILD-TYPE  8 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    3
  19P LOSS WILD-TYPE    8   34
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                3                 34
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    1  3
  19Q LOSS WILD-TYPE 57 28
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 4                 85 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 28 
$`19Q LOSS MUTATED`
TCGA-OR-A5J1 TCGA-OR-A5KB TCGA-OR-A5LL TCGA-P6-A5OG 
       44.55        24.36        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        68.75        15.45        12.00        88.87        16.11 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD 
       19.04        44.45        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        69.37        46.82        10.16 
TCGA-OR-A5JK TCGA-OR-A5JL TCGA-OR-A5JM TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ 
       49.22        22.03        18.48        29.23         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW 
      121.25        12.59        29.82         9.50        66.51        72.39 
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        96.59        32.68 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 
      100.18        22.98         8.32        49.08        24.62        11.31 
TCGA-OR-A5KO TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU 
       46.49        91.30        88.01        83.80        95.18       153.63 
TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 
      127.50        50.14        44.84        12.85         4.11        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 
       60.89       152.15        31.79        43.30        28.31        29.10 
TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE 
       28.64        23.64        39.58         5.23        39.35        21.76 
TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK 
       14.63        52.24        78.41        14.33        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA TCGA-PK-A5HB 
       18.05        23.31        15.45        20.25        39.48        42.51 
TCGA-PK-A5HC 
       22.32 

  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 
            34.455             36.260 
[1] "12.6 - 53.0 (34.5)" "4.1 - 153.6 (36.3)"
[1] "hr=" "2.8"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         0        3         0        1
  19Q LOSS WILD-TYPE       9       40        18       17
D75V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 3                 40
  STAGE III                0                 18
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    0  3  0  1
  19Q LOSS WILD-TYPE  9 45 11 19
D75V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  9
  T2                3                 45
  T3                0                 11
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  0
  19Q LOSS WILD-TYPE 74 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    0
  19Q LOSS WILD-TYPE   74   10
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                4                 74
  1                0                 10
[1] 2 2
[1] FALSE
D75V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    3  1
  19Q LOSS WILD-TYPE 56 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      3    1
  19Q LOSS WILD-TYPE   56   30
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  1                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE     2                         1    73
D75V7, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V8, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    0  2
  19Q LOSS WILD-TYPE  8 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      0    2
  19Q LOSS WILD-TYPE    8   35
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                  8
  NOT HISPANIC OR LATINO                2                 35
[1] 2 2
[1] FALSE

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    6  3
  20P LOSS WILD-TYPE 52 28
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 80 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 28 
$`20P LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5JM TCGA-OR-A5JS TCGA-OR-A5K0 TCGA-OR-A5KP 
       16.11        30.31        18.48        12.59        33.83        91.30 
TCGA-OU-A5PI TCGA-PK-A5HB TCGA-PK-A5HC 
       23.31        42.51        22.32 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        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        69.37        46.82        10.16        49.22 
TCGA-OR-A5JL TCGA-OR-A5JO TCGA-OR-A5JP TCGA-OR-A5JQ TCGA-OR-A5JR TCGA-OR-A5JT 
       22.03        29.23         4.90        36.26       121.25        29.82 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY TCGA-OR-A5JZ 
        9.50        66.51        72.39        31.23        18.15         6.94 
TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 
       96.59        32.68       100.18        22.98         8.32        49.08 
TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS 
       24.62        11.31        24.36        46.49        88.01        83.80 
TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY 
       95.18       153.63       127.50        50.14        44.84        12.85 
TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 
        4.11        58.55        60.89       152.15        31.79        43.30 
TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC 
       28.31        29.10        28.64        23.64        39.58         5.23 
TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       39.35        21.76        14.63        52.24        78.41        14.33 
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        69.11 
TCGA-OR-A5LP TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-P6-A5OG TCGA-PA-A5YG 
       61.05        28.04        36.03        18.05        12.59        15.45 
TCGA-PK-A5H9 TCGA-PK-A5HA 
       20.25        39.48 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             12.59               4.11 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             91.30             153.63 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            23.310             39.415 
[1] "12.6 - 91.3 (23.3)" "4.1 - 153.6 (39.4)"
[1] "hr=" "1.2"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         0        3         2        3
  20P LOSS WILD-TYPE       9       40        16       15
D76V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 3                 40
  STAGE III                2                 16
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    0  4  1  3
  20P LOSS WILD-TYPE  9 44 10 17
D76V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                0                  9
  T2                4                 44
  T3                1                 10
  T4                3                 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"
D76V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    7  1
  20P LOSS WILD-TYPE 71  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      7    1
  20P LOSS WILD-TYPE   71    9
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                7                 71
  1                1                  9
[1] 2 2
[1] FALSE
D76V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    8  1
  20P LOSS WILD-TYPE 51 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      8    1
  20P LOSS WILD-TYPE   51   30
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                8                 51
  MALE                  1                 30
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       1                         0     7
  20P LOSS WILD-TYPE     1                         1    69
D76V7, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    7                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V8, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  3
  20P LOSS WILD-TYPE  7 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    3
  20P LOSS WILD-TYPE    7   34
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 34
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 57 29
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 86 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 29 
$`20Q LOSS MUTATED`
TCGA-OR-A5J7 TCGA-OR-A5JA TCGA-OR-A5KP 
       16.11        30.31        91.30 

$`20Q 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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       19.04        44.45        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        69.37        46.82        10.16        49.22 
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        36.26       121.25 
TCGA-OR-A5JS TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX 
       12.59        29.82         9.50        66.51        72.39        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        96.59        32.68       100.18 
TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB 
       22.98         8.32        49.08        24.62        11.31        24.36 
TCGA-OR-A5KO TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       46.49        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.14        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD TCGA-OR-A5LE TCGA-OR-A5LF 
       23.64        39.58         5.23        39.35        21.76        14.63 
TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI TCGA-OR-A5LJ TCGA-OR-A5LK TCGA-OR-A5LL 
       52.24        78.41        14.33        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        23.31        12.59        15.45        20.25        39.48 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             16.11               4.11 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             91.30             153.63 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
            30.310             36.295 
[1] "16.1 - 91.3 (30.3)" "4.1 - 153.6 (36.3)"
[1] "hr=" "1.9"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         0        1         1        1
  20Q LOSS WILD-TYPE       9       42        17       17
D77V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  0                  9
  STAGE II                 1                 42
  STAGE III                1                 17
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  20Q LOSS MUTATED    0  1  1  1
  20Q LOSS WILD-TYPE  9 47 10 19
D77V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                0                  9
  T2                1                 47
  T3                1                 10
  T4                1                 19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 75 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   75   10
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                3                 75
  1                0                 10
[1] 2 2
[1] FALSE
D77V6, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    3  0
  20Q LOSS WILD-TYPE 56 31
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE   56   31
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                3                 56
  MALE                  0                 31
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         0     3
  20Q LOSS WILD-TYPE     2                         1    73
D77V7, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                    3                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V8, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  1
  20Q LOSS WILD-TYPE  7 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    1
  20Q LOSS WILD-TYPE    7   36
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                1                 36
[1] 2 2
[1] FALSE

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    6  9
  21Q LOSS WILD-TYPE 52 22
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 74 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                 22 
$`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        69.37        18.48        36.26 
TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JY TCGA-OR-A5LC TCGA-OR-A5LE TCGA-OR-A5LF 
        9.50        66.51        18.15         5.23        21.76        14.63 
TCGA-OR-A5LN TCGA-P6-A5OG TCGA-PK-A5HA 
       62.99        12.59        39.48 

$`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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J9 TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JE TCGA-OR-A5JF 
       16.11        44.45        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        49.22        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        29.82        72.39        31.23 
TCGA-OR-A5JZ TCGA-OR-A5K0 TCGA-OR-A5K1 TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 
        6.94        33.83        96.59        32.68       100.18        22.98 
TCGA-OR-A5K5 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KO 
        8.32        49.08        24.62        11.31        24.36        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV 
       91.30        88.01        83.80        95.18       153.63       127.50 
TCGA-OR-A5KW TCGA-OR-A5KX TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 
       50.14        44.84        12.85         4.11        58.55        60.89 
TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 
      152.15        31.79        43.30        28.31        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LB TCGA-OR-A5LD TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LI 
       23.64        39.58        39.35        52.24        78.41        14.33 
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        69.11        61.05 
TCGA-OR-A5LR TCGA-OR-A5LS TCGA-OR-A5LT TCGA-OU-A5PI TCGA-PA-A5YG TCGA-PK-A5H9 
       28.04        36.03        18.05        23.31        15.45        20.25 
TCGA-PK-A5HB TCGA-PK-A5HC 
       42.51        22.32 

  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 
            21.760             39.465 
[1] "5.2 - 91.5 (21.8)"  "4.1 - 153.6 (39.5)"
[1] "hr=" "2.4"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED         1        6         3        5
  21Q LOSS WILD-TYPE       8       37        15       13
D78V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                  1                  8
  STAGE II                 6                 37
  STAGE III                3                 15
  STAGE IV                 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"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    1  6  3  5
  21Q LOSS WILD-TYPE  8 42  8 15
D78V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                  8
  T2                6                 42
  T3                3                  8
  T4                5                 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"
D78V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   14  1
  21Q LOSS WILD-TYPE 64  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     14    1
  21Q LOSS WILD-TYPE   64    9
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               14                 64
  1                1                  9
[1] 2 2
[1] FALSE
D78V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   11  4
  21Q LOSS WILD-TYPE 48 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     11    4
  21Q LOSS WILD-TYPE   48   27
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               11                 48
  MALE                  4                 27
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         0    13
  21Q LOSS WILD-TYPE     2                         1    63
D78V7, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  1
  WHITE                                   13                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    1  3
  21Q LOSS WILD-TYPE  7 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      1    3
  21Q LOSS WILD-TYPE    7   34
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                  7
  NOT HISPANIC OR LATINO                3                 34
[1] 2 2
[1] FALSE

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   24 23
  22Q LOSS WILD-TYPE 34  8
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                47                 42 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                23                  8 
$`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        68.75        88.87        16.11        19.04 
TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JB TCGA-OR-A5JC TCGA-OR-A5JD TCGA-OR-A5JE 
       44.45        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        69.37        46.82        49.22         4.90        36.26 
TCGA-OR-A5JR TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JW TCGA-OR-A5JX TCGA-OR-A5JY 
      121.25         9.50        66.51        72.39        31.23        18.15 
TCGA-OR-A5K2 TCGA-OR-A5K5 TCGA-OR-A5K9 TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KX 
       32.68         8.32        11.31        91.30        88.01        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L6 TCGA-OR-A5LB TCGA-OR-A5LC TCGA-OR-A5LD 
       12.85         4.11        28.31        39.58         5.23        39.35 
TCGA-OR-A5LF TCGA-OR-A5LI TCGA-OR-A5LL TCGA-OR-A5LM TCGA-OR-A5LN TCGA-OR-A5LS 
       14.63        14.33        53.03        61.08        62.99        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PK-A5H9 TCGA-PK-A5HA 
       18.05        23.31        12.59        20.25        39.48 

$`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        29.82         6.94        33.83        96.59 
TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K6 TCGA-OR-A5K8 TCGA-OR-A5KB TCGA-OR-A5KO 
      100.18        22.98        49.08        24.62        24.36        46.49 
TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5L1 
       83.80        95.18       153.63       127.50        50.14        58.55 
TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 TCGA-OR-A5L5 TCGA-OR-A5L8 TCGA-OR-A5L9 
       60.89       152.15        31.79        43.30        29.10        28.64 
TCGA-OR-A5LA TCGA-OR-A5LE TCGA-OR-A5LG TCGA-OR-A5LH TCGA-OR-A5LJ TCGA-OR-A5LK 
       23.64        21.76        52.24        78.41        36.33        73.05 
TCGA-OR-A5LO TCGA-OR-A5LP TCGA-OR-A5LR TCGA-PA-A5YG TCGA-PK-A5HB TCGA-PK-A5HC 
       69.11        61.05        28.04        15.45        42.51        22.32 

  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 
             36.26              35.08 
[1] "4.1 - 121.2 (36.3)" "6.9 - 153.6 (35.1)"
[1] "hr=" "2.8"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED         4       19        11       13
  22Q LOSS WILD-TYPE       5       24         7        5
D79V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  4                  5
  STAGE II                19                 24
  STAGE III               11                  7
  STAGE IV                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"
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    4 21  9 13
  22Q LOSS WILD-TYPE  5 27  2  7
D79V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                4                  5
  T2               21                 27
  T3                9                  2
  T4               13                  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"
D79V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   42  5
  22Q LOSS WILD-TYPE 36  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     42    5
  22Q LOSS WILD-TYPE   36    5
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               42                 36
  1                5                  5
[1] 2 2
[1] FALSE
D79V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   29 19
  22Q LOSS WILD-TYPE 30 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     29   19
  22Q LOSS WILD-TYPE   30   12
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               29                 30
  MALE                 19                 12
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    40
  22Q LOSS WILD-TYPE     1                         0    36
D79V7, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  0
  WHITE                                   40                 36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    6 14
  22Q LOSS WILD-TYPE  2 23
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   14
  22Q LOSS WILD-TYPE    2   23
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    6                  2
  NOT HISPANIC OR LATINO               14                 23
[1] 2 2
[1] FALSE

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   11  6
  XQ LOSS WILD-TYPE 47 25
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17                72 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                6                25 
$`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        72.39        18.15        33.83 
TCGA-OR-A5K6 TCGA-OR-A5K9 TCGA-OR-A5KB TCGA-OR-A5KV TCGA-OR-A5KW TCGA-OR-A5LE 
       49.08        11.31        24.36       127.50        50.14        21.76 
TCGA-OR-A5LG TCGA-OR-A5LI TCGA-OR-A5LL TCGA-PK-A5HA TCGA-PK-A5HB 
       52.24        14.33        53.03        39.48        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        68.75        15.45        12.00        88.87 
TCGA-OR-A5J7 TCGA-OR-A5J8 TCGA-OR-A5J9 TCGA-OR-A5JA TCGA-OR-A5JC TCGA-OR-A5JE 
       16.11        19.04        44.45        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        69.37        46.82        10.16        49.22 
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        36.26       121.25 
TCGA-OR-A5JT TCGA-OR-A5JU TCGA-OR-A5JV TCGA-OR-A5JX TCGA-OR-A5JZ TCGA-OR-A5K1 
       29.82         9.50        66.51        31.23         6.94        96.59 
TCGA-OR-A5K2 TCGA-OR-A5K3 TCGA-OR-A5K4 TCGA-OR-A5K5 TCGA-OR-A5K8 TCGA-OR-A5KO 
       32.68       100.18        22.98         8.32        24.62        46.49 
TCGA-OR-A5KP TCGA-OR-A5KQ TCGA-OR-A5KS TCGA-OR-A5KT TCGA-OR-A5KU TCGA-OR-A5KX 
       91.30        88.01        83.80        95.18       153.63        44.84 
TCGA-OR-A5KY TCGA-OR-A5KZ TCGA-OR-A5L1 TCGA-OR-A5L2 TCGA-OR-A5L3 TCGA-OR-A5L4 
       12.85         4.11        58.55        60.89       152.15        31.79 
TCGA-OR-A5L5 TCGA-OR-A5L6 TCGA-OR-A5L8 TCGA-OR-A5L9 TCGA-OR-A5LA TCGA-OR-A5LB 
       43.30        28.31        29.10        28.64        23.64        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        69.11        61.05        28.04        36.03 
TCGA-OR-A5LT TCGA-OU-A5PI TCGA-P6-A5OG TCGA-PA-A5YG TCGA-PK-A5H9 TCGA-PK-A5HC 
       18.05        23.31        12.59        15.45        20.25        22.32 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            11.31              4.11 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           127.50            153.63 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           39.480            36.145 
[1] "11.3 - 127.5 (39.5)" "4.1 - 153.6 (36.1)" 
[1] "hr=" "1.1"
D80V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED         1        9         3        3
  XQ LOSS WILD-TYPE       8       34        15       15
D80V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 1                 8
  STAGE II                9                34
  STAGE III               3                15
  STAGE IV                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"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    1 11  1  3
  XQ LOSS WILD-TYPE  8 37 10 17
D80V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               1                 8
  T2              11                37
  T3               1                10
  T4               3                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"
D80V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   13  3
  XQ LOSS WILD-TYPE 65  7
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     13    3
  XQ LOSS WILD-TYPE   65    7
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              13                65
  1               3                 7
[1] 2 2
[1] FALSE
D80V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   11  6
  XQ LOSS WILD-TYPE 48 25
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11    6
  XQ LOSS WILD-TYPE   48   25
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              11                48
  MALE                 6                25
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       0                         0    14
  XQ LOSS WILD-TYPE     2                         1    62
D80V7, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 1
  WHITE                                  14                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V8, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    0  7
  XQ LOSS WILD-TYPE  8 30
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      0    7
  XQ LOSS WILD-TYPE    8   30
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                 8
  NOT HISPANIC OR LATINO               7                30
[1] 2 2
[1] FALSE
