[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"        "-oTPAAD-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/PAAD-TP/10006103/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/10013780/transformed.cor.cli.txt"

nPatients in clinical file=93, in cluster file=102, common to both=86
[1] "Reduce the number of clustering variables from 80 to 72."
[1] 72 86
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                79 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                79 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               22                64 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               22                64 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                79 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                7                79 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                78 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                78 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                81 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5                81 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                78 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                78 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                83 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                83 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                83 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                83 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                74 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                74 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                77 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                77 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               25                61 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               25                61 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22                64 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               22                64 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                74 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               12                74 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21                65 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               21                65 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                83 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                83 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 82 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 82 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                 80 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                 80 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                 76 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                10                 76 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 78 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 8                 78 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 78 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 8                 78 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 80 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 80 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 78 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                 78 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                12                 74 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                12                 74 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 81 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 81 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                 75 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                 75 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                12                 74 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                12                 74 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 81 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 5                 81 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                 74 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                12                 74 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 82 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 82 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 82 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 82 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 77 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 77 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                19                 67 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                19                 67 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                22                 64 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                22                 64 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                 82 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                 82 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                82 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                82 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16                70 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               16                70 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                81 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                5                81 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                79 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                7                79 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                83 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                83 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16                70 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               16                70 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13                73 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               13                73 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11                75 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               11                75 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11                75 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               11                75 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                82 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                82 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                79 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                79 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               31                55 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               31                55 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40                46 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               40                46 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                70 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               16                70 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                79 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                79 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               36                50 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               36                50 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                63 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               23                63 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                15                 71 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                15                 71 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 71 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                15                 71 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 80 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 80 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 78 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 78 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                 78 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 8                 78 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                10                 76 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                10                 76 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                 73 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                13                 73 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 80 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 80 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                13                 73 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                13                 73 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 83 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 83 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                 54 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                32                 54 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 74 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 74 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                29                 57 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                29                 57 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                46                 40 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                46                 40 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                 75 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                 75 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 78 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                 78 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 77 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 9                 77 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 83 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 3                 83 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                 57 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                29                 57 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 66 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                20                 66 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                79 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                79 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NUMBERPACKYEARSSMOKED"                 
[17] "YEAROFTOBACCOSMOKINGONSET"             
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 86 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
          NA          295          360           NA          153          586 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FZ-5920 
           4          385          449            1          166           NA 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
          NA           NA          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
          28           20           NA            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
         361            8           19           24           21           NA 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8637 TCGA-HZ-8638 
          28           16            3            5           NA           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          23           29           NA          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
          13           33          347           NA           NA           NA 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
          NA           NA          476          851           NA           NA 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
          NA           NA           NA          488           NA           NA 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
          17          522          329          300           NA           NA 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
           8           NA           NA          181          164          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-S4-A8RP 
          35          584          110          247          416           NA 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
          NA          844           NA           NA           NA           NA 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "NUMBERPACKYEARSSMOKED"    
 [9] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
[11] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 86 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=35, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 2  6 76  2 
[1] "table(vv)"
vv
T1+T2 T3+T4 
    8    78 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 2  6 76  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 8

$Class1_nSamples
[1] 78

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
    8    78 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=17, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=13, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    4  0
  1P GAIN WILD-TYPE 46 11
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                4                57 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                11 
$`1P GAIN MUTATED`
TCGA-FB-A78T TCGA-HZ-7925 TCGA-M8-A5N4 TCGA-US-A776 
           1          361          584          844 

$`1P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
          28           20            4            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         164          127           35          110          247          416 
TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          160         1834 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 3 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
              844              1991 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            472.5             166.0 
[1] "1.0 - 844.0 (472.5)"  "3.0 - 1991.0 (166.0)"
[1] "hr="     "7.9e+07"
D1V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  1P GAIN MUTATED          0        0         2         4         0        1
  1P GAIN WILD-TYPE        2        4        12        57         2        2
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               2                12
  STAGE IIB               4                57
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of 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     7
  1P GAIN WILD-TYPE     8    71
D1V4, multiclass
       clus
vv      1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1+T2               0                 8
  T3+T4               7                71
[1] 2 2
[1] FALSE
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    2  5
  1P GAIN WILD-TYPE 19 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      2    5
  1P GAIN WILD-TYPE   19   59
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               2                19
  1               5                59
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P GAIN MUTATED    3  1  3
  1P GAIN WILD-TYPE 38  2 39
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               3                38
  M1               1                 2
  MX               3                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    3  4
  1P GAIN WILD-TYPE 41 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    4
  1P GAIN WILD-TYPE   41   38
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                41
  MALE                 4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1P GAIN MUTATED                                     6
  1P GAIN WILD-TYPE                                  68
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1P GAIN MUTATED                                       0
  1P GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1P GAIN MUTATED                                                  1
  1P GAIN WILD-TYPE                                                2
D1V8, multiclass
                                                  clus
vv                                                 1P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 1P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             68
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D1V9, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                25 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A7DR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1        TCGA-HZ-A77Q 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-IB-A7M4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"1P GAIN WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED    5  2  0  0
  1P GAIN WILD-TYPE 50 23  1  2
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               5                50
  R1               2                23
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         0     6
  1P GAIN WILD-TYPE     2                         6    68
D1V12, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   6                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"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   13  3
  1Q GAIN WILD-TYPE 37  8
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               16                45 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                3                 8 
$`1Q GAIN MUTATED`
TCGA-F2-A44H TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A4BH 
         586            1          396          361            5          194 
TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8127 TCGA-IB-A6UG 
          11         1989         1975          488          522         1968 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-US-A776 TCGA-YY-A8LH 
          35          584          844         1834 

$`1Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
         166          392          233          240           28           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           4            8          369            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          29           46           13           33          347         1951 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         476          851           17          329          300         1991 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W TCGA-PZ-A5RE 
           8          181          164          127          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D 
         416         1955          160 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 3 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1989              1991 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
              505               153 
[1] "1.0 - 1989.0 (505.0)" "3.0 - 1991.0 (153.0)"
[1] "hr=" "2.5"
D2V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  1Q GAIN MUTATED          0        0         6        14         0        2
  1Q GAIN WILD-TYPE        2        4         8        47         2        1
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               6                 8
  STAGE IIB              14                47
  STAGE III               0                 2
  STAGE IV                2                 1
[1] 6 2
[1] TRUE
[1] "dimension of 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    21
  1Q GAIN WILD-TYPE     7    57
D2V4, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1+T2               1                 7
  T3+T4              21                57
[1] 2 2
[1] FALSE
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    7 15
  1Q GAIN WILD-TYPE 14 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      7   15
  1Q GAIN WILD-TYPE   14   49
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0               7                14
  1              15                49
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   10  2 10
  1Q GAIN WILD-TYPE 31  1 32
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              10                31
  M1               2                 1
  MX              10                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"
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED    9 13
  1Q GAIN WILD-TYPE 35 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      9   13
  1Q GAIN WILD-TYPE   35   29
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               9                35
  MALE                13                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1Q GAIN MUTATED                                    20
  1Q GAIN WILD-TYPE                                  54
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1Q GAIN MUTATED                                       1
  1Q GAIN WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1Q GAIN MUTATED                                                  1
  1Q GAIN WILD-TYPE                                                2
D2V8, multiclass
                                                  clus
vv                                                 1Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 1Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             54
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D2V9, continuous
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   15  7  0  0
  1Q GAIN WILD-TYPE 40 18  1  2
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              15                40
  R1               7                18
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       0                         1    20
  1Q GAIN WILD-TYPE     2                         5    54
D2V12, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  20                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"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    4  2
  2P GAIN WILD-TYPE 46  9
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                55 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                2                 9 
$`2P GAIN MUTATED`
TCGA-FB-A545 TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-YB-A89D 
         385         1989         1975          522          300          160 

$`2P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS 
         476          851          488           17          329         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
           8         1968          181          164          127           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YY-A8LH 
        1834 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              160                 1 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1989              1991 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            453.5             164.0 
[1] "160.0 - 1989.0 (453.5)" "1.0 - 1991.0 (164.0)"  
[1] "hr=" "2.1"
D3V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  2P GAIN MUTATED          0        0         2         5         0        0
  2P GAIN WILD-TYPE        2        4        12        56         2        3
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               2                12
  STAGE IIB               5                56
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     7
  2P GAIN WILD-TYPE     8    71
D3V4, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1+T2               0                 8
  T3+T4               7                71
[1] 2 2
[1] FALSE
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  5
  2P GAIN WILD-TYPE 19 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    5
  2P GAIN WILD-TYPE   19   59
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               2                19
  1               5                59
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED    6  0  1
  2P GAIN WILD-TYPE 35  3 41
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               6                35
  M1               0                 3
  MX               1                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"
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    2  5
  2P GAIN WILD-TYPE 42 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2    5
  2P GAIN WILD-TYPE   42   37
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2P GAIN MUTATED                                     7
  2P GAIN WILD-TYPE                                  67
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2P GAIN MUTATED                                       0
  2P GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2P GAIN MUTATED                                                  0
  2P GAIN WILD-TYPE                                                3
D3V8, multiclass
                                                  clus
vv                                                 2P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 2P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             67
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D3V9, continuous
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED    3  3  0  0
  2P GAIN WILD-TYPE 52 22  1  2
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               3                52
  R1               3                22
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         0     7
  2P GAIN WILD-TYPE     2                         6    67
D3V12, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                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"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    5  2
  2Q GAIN WILD-TYPE 45  9
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                54 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                2                 9 
$`2Q GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
         385           13         1989         1975          522          300 
TCGA-YB-A89D 
         160 

$`2Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7652 
          46           11           33          347         1951          476 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
         851          488           17          329         1991            8 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
        1968          181          164          127           35          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
         110          247          416         1955          844         1834 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               13                 1 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1989              1991 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              385               165 
[1] "13.0 - 1989.0 (385.0)" "1.0 - 1991.0 (165.0)" 
[1] "hr=" "2.1"
D4V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  2Q GAIN MUTATED          0        0         2         6         0        0
  2Q GAIN WILD-TYPE        2        4        12        55         2        3
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               2                12
  STAGE IIB               6                55
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     8
  2Q GAIN WILD-TYPE     8    70
D4V4, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1+T2               0                 8
  T3+T4               8                70
[1] 2 2
[1] FALSE
D4V5, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  6
  2Q GAIN WILD-TYPE 19 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    6
  2Q GAIN WILD-TYPE   19   58
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               2                19
  1               6                58
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2Q GAIN MUTATED    6  0  2
  2Q GAIN WILD-TYPE 35  3 40
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               6                35
  M1               0                 3
  MX               2                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    2  6
  2Q GAIN WILD-TYPE 42 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      2    6
  2Q GAIN WILD-TYPE   42   36
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 6                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2Q GAIN MUTATED                                     7
  2Q GAIN WILD-TYPE                                  67
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2Q GAIN MUTATED                                       1
  2Q GAIN WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2Q GAIN MUTATED                                                  0
  2Q GAIN WILD-TYPE                                                3
D4V8, multiclass
                                                  clus
vv                                                 2Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 2Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             67
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D4V9, continuous
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED    4  3  0  0
  2Q GAIN WILD-TYPE 51 22  1  2
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               4                51
  R1               3                22
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         0     8
  2Q GAIN WILD-TYPE     2                         6    66
D4V12, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   8                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"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2  1
  3P GAIN WILD-TYPE 48 10
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                58 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                10 
$`3P GAIN MUTATED`
TCGA-FB-A5VM TCGA-HZ-7922 TCGA-IB-A6UG 
         449            4         1968 

$`3P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 
         329          300         1991            8          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         127           35          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                4                 1 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1968              1991 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            449.0             173.5 
[1] "4.0 - 1968.0 (449.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1"  
D5V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  3P GAIN MUTATED          0        1         1         3         0        0
  3P GAIN WILD-TYPE        2        3        13        58         2        3
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               1                13
  STAGE IIB               3                58
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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     4
  3P GAIN WILD-TYPE     7    74
D5V4, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1+T2               1                 7
  T3+T4               4                74
[1] 2 2
[1] FALSE
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2  3
  3P GAIN WILD-TYPE 19 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    3
  3P GAIN WILD-TYPE   19   61
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               2                19
  1               3                61
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED    4  0  1
  3P GAIN WILD-TYPE 37  3 41
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               4                37
  M1               0                 3
  MX               1                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"
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  4
  3P GAIN WILD-TYPE 43 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    4
  3P GAIN WILD-TYPE   43   38
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                43
  MALE                 4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3P GAIN MUTATED                                     5
  3P GAIN WILD-TYPE                                  69
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3P GAIN MUTATED                                       0
  3P GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3P GAIN MUTATED                                                  0
  3P GAIN WILD-TYPE                                                3
D5V8, multiclass
                                                  clus
vv                                                 3P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 3P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D5V9, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                24 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A78T        TCGA-FB-A7DR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1        TCGA-HZ-A77Q 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A7M4        TCGA-LB-A7SX 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774        TCGA-YY-A8LH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  3P GAIN MUTATED    3  2  0  0
  3P GAIN WILD-TYPE 52 23  1  2
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               3                52
  R1               2                23
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         0     5
  3P GAIN WILD-TYPE     2                         6    69
D5V12, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   5                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"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    3  1
  3Q GAIN WILD-TYPE 47 10
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                57 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                10 
$`3Q GAIN MUTATED`
TCGA-FB-A5VM TCGA-HZ-7922 TCGA-HZ-8636 TCGA-IB-A6UG 
         449            4            5         1968 

$`3Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
         300         1991            8          181          164          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
          35          584          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                4                 1 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             1968              1991 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              227               181 
[1] "4.0 - 1968.0 (227.0)" "1.0 - 1991.0 (181.0)"
[1] "hr=" "1"  
D6V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  3Q GAIN MUTATED          0        2         1         4         0        1
  3Q GAIN WILD-TYPE        2        2        13        57         2        2
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                2                 2
  STAGE IIA               1                13
  STAGE IIB               4                57
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of 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       2     6
  3Q GAIN WILD-TYPE     6    72
D6V4, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1+T2               2                 6
  T3+T4               6                72
[1] 2 2
[1] FALSE
D6V5, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    4  4
  3Q GAIN WILD-TYPE 17 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      4    4
  3Q GAIN WILD-TYPE   17   60
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               4                17
  1               4                60
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED    5  1  2
  3Q GAIN WILD-TYPE 36  2 40
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               5                36
  M1               1                 2
  MX               2                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    2  6
  3Q GAIN WILD-TYPE 42 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    6
  3Q GAIN WILD-TYPE   42   36
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 6                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3Q GAIN MUTATED                                     8
  3Q GAIN WILD-TYPE                                  66
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3Q GAIN MUTATED                                       0
  3Q GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3Q GAIN MUTATED                                                  0
  3Q GAIN WILD-TYPE                                                3
D6V8, multiclass
                                                  clus
vv                                                 3Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 3Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D6V9, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                24 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A78T        TCGA-FB-A7DR 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1        TCGA-HZ-A77Q 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A7M4        TCGA-LB-A7SX 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774        TCGA-YY-A8LH 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED    4  4  0  0
  3Q GAIN WILD-TYPE 51 21  1  2
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               4                51
  R1               4                21
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         0     7
  3Q GAIN WILD-TYPE     2                         6    67
D6V12, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                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"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    2  0
  4P GAIN WILD-TYPE 48 11
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                59 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                0                11 
$`4P GAIN MUTATED`
TCGA-HZ-7922 TCGA-YB-A89D 
           4          160 

$`4P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
         240           28           20            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1989          476          851         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         522          329          300         1991            8         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
         181          164          127           35          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
         247          416         1955          844         1834 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                 1 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
              160              1991 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               82               194 
[1] "4.0 - 160.0 (82.0)"   "1.0 - 1991.0 (194.0)"
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
D7V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  4P GAIN MUTATED          0        0         0         3         0        0
  4P GAIN WILD-TYPE        2        4        14        58         2        3
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               0                14
  STAGE IIB               3                58
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  4P GAIN MUTATED       0     3
  4P GAIN WILD-TYPE     8    75
D7V4, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1+T2               0                 8
  T3+T4               3                75
[1] 2 2
[1] FALSE
D7V5, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    0  3
  4P GAIN WILD-TYPE 21 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    3
  4P GAIN WILD-TYPE   21   61
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               0                21
  1               3                61
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    0  0  3
  4P GAIN WILD-TYPE 41  3 39
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               0                41
  M1               0                 3
  MX               3                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 42 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   42   41
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 1                41
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4P GAIN MUTATED                                     3
  4P GAIN WILD-TYPE                                  71
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4P GAIN MUTATED                                       0
  4P GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4P GAIN MUTATED                                                  0
  4P GAIN WILD-TYPE                                                3
D7V8, multiclass
                                                  clus
vv                                                 4P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 4P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D7V9, continuous
                   vv
clus                R0 R1 R2 RX
  4P GAIN MUTATED    3  0  0  0
  4P GAIN WILD-TYPE 52 25  1  2
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               3                52
  R1               0                25
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0     3
  4P GAIN WILD-TYPE     2                         6    71
D7V12, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3                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"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    2  0
  4Q GAIN WILD-TYPE 48 11
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                59 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                11 
$`4Q GAIN MUTATED`
TCGA-HZ-7922 TCGA-YB-A89D 
           4          160 

$`4Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
         240           28           20            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1989          476          851         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         522          329          300         1991            8         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
         181          164          127           35          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
         247          416         1955          844         1834 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                4                 1 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
              160              1991 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               82               194 
[1] "4.0 - 160.0 (82.0)"   "1.0 - 1991.0 (194.0)"
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
D8V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  4Q GAIN MUTATED          0        0         0         3         0        0
  4Q GAIN WILD-TYPE        2        4        14        58         2        3
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               0                14
  STAGE IIB               3                58
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  4Q GAIN MUTATED       0     3
  4Q GAIN WILD-TYPE     8    75
D8V4, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1+T2               0                 8
  T3+T4               3                75
[1] 2 2
[1] FALSE
D8V5, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  3
  4Q GAIN WILD-TYPE 21 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    3
  4Q GAIN WILD-TYPE   21   61
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0               0                21
  1               3                61
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q GAIN MUTATED    0  0  3
  4Q GAIN WILD-TYPE 41  3 39
D8V6, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0               0                41
  M1               0                 3
  MX               3                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    2  1
  4Q GAIN WILD-TYPE 42 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      2    1
  4Q GAIN WILD-TYPE   42   41
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 1                41
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4Q GAIN MUTATED                                     3
  4Q GAIN WILD-TYPE                                  71
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4Q GAIN MUTATED                                       0
  4Q GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4Q GAIN MUTATED                                                  0
  4Q GAIN WILD-TYPE                                                3
D8V8, multiclass
                                                  clus
vv                                                 4Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 4Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D8V9, continuous
                   vv
clus                R0 R1 R2 RX
  4Q GAIN MUTATED    3  0  0  0
  4Q GAIN WILD-TYPE 52 25  1  2
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               3                52
  R1               0                25
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     3
  4Q GAIN WILD-TYPE     2                         6    71
D8V12, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3                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"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    8  2
  5P GAIN WILD-TYPE 42  9
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               10                51 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 9 
$`5P GAIN MUTATED`
TCGA-FB-A5VM TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-A5SP 
         449          240            4           11         1975          300 
TCGA-IB-A6UG TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W 
        1968          127          584          110 

$`5P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
           1          166          392          233          396           28 
TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
          20            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P 
          91           23           29          194           46           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
         488           17          522          329         1991            8 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         181          164           35          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                 1 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1975              1991 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              270               166 
[1] "4.0 - 1975.0 (270.0)" "1.0 - 1991.0 (166.0)"
[1] "hr=" "1.3"
D9V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  5P GAIN MUTATED          0        1         3         8         0        0
  5P GAIN WILD-TYPE        2        3        11        53         2        3
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               3                11
  STAGE IIB               8                53
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  5P GAIN MUTATED       2    10
  5P GAIN WILD-TYPE     6    68
D9V4, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1+T2               2                 6
  T3+T4              10                68
[1] 2 2
[1] FALSE
D9V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    4  8
  5P GAIN WILD-TYPE 17 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    8
  5P GAIN WILD-TYPE   17   56
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               4                17
  1               8                56
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED    6  0  6
  5P GAIN WILD-TYPE 35  3 36
D9V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               6                35
  M1               0                 3
  MX               6                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"
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    5  7
  5P GAIN WILD-TYPE 39 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      5    7
  5P GAIN WILD-TYPE   39   35
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               5                39
  MALE                 7                35
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5P GAIN MUTATED                                    11
  5P GAIN WILD-TYPE                                  63
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5P GAIN MUTATED                                       1
  5P GAIN WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5P GAIN MUTATED                                                  0
  5P GAIN WILD-TYPE                                                3
D9V8, multiclass
                                                  clus
vv                                                 5P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 5P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             63
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D9V9, continuous
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED    6  5  0  1
  5P GAIN WILD-TYPE 49 20  1  1
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               6                49
  R1               5                20
  R2               0                 1
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         1    10
  5P GAIN WILD-TYPE     2                         5    64
D9V12, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  10                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"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    6  1
  5Q GAIN WILD-TYPE 44 10
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                7                54 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                10 
$`5Q GAIN MUTATED`
TCGA-FB-A5VM TCGA-HZ-7922 TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-A5SP TCGA-LB-A7SX 
         449            4           11         1975          300          127 
TCGA-M8-A5N4 
         584 

$`5Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS 
         851          488           17          522          329         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W 
           8         1968          181          164           35          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         247          416         1955          844          160         1834 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                4                 1 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1975              1991 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            300.0             173.5 
[1] "4.0 - 1975.0 (300.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.7"
D10V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  5Q GAIN MUTATED          0        1         2         6         0        0
  5Q GAIN WILD-TYPE        2        3        12        55         2        3
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               2                12
  STAGE IIB               6                55
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       2     7
  5Q GAIN WILD-TYPE     6    71
D10V4, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1+T2               2                 6
  T3+T4               7                71
[1] 2 2
[1] FALSE
D10V5, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    3  6
  5Q GAIN WILD-TYPE 18 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      3    6
  5Q GAIN WILD-TYPE   18   58
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               3                18
  1               6                58
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED    4  0  5
  5Q GAIN WILD-TYPE 37  3 37
D10V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               4                37
  M1               0                 3
  MX               5                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    5  4
  5Q GAIN WILD-TYPE 39 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    4
  5Q GAIN WILD-TYPE   39   38
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               5                39
  MALE                 4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5Q GAIN MUTATED                                     9
  5Q GAIN WILD-TYPE                                  65
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5Q GAIN MUTATED                                       0
  5Q GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5Q GAIN MUTATED                                                  0
  5Q GAIN WILD-TYPE                                                3
D10V8, multiclass
                                                  clus
vv                                                 5Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 5Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D10V9, continuous
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED    5  4  0  0
  5Q GAIN WILD-TYPE 50 21  1  2
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               5                50
  R1               4                21
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         1     7
  5Q GAIN WILD-TYPE     2                         5    67
D10V12, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   7                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"

Clustering(11) Variable = 7P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   17  2
  7P GAIN WILD-TYPE 33  9
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               19                42 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                2                 9 
$`7P GAIN MUTATED`
TCGA-FB-A545 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7926 TCGA-HZ-8636 TCGA-HZ-A77O 
         385          396          240            8            5           11 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-L1-A7W4 
         476         1975          522          300         1968          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-US-A776 TCGA-YB-A89D 
         127           35          584          247          844          160 
TCGA-YY-A8LH 
        1834 

$`7P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7919 
           1          166          392          233           28           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 
           4            8          369          361           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          29          194           46           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
        1951         1989          851          488           17          329 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A774 
        1991            8          181          110          416         1955 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                 1 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             1975              1991 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            300.0             131.5 
[1] "5.0 - 1975.0 (300.0)" "1.0 - 1991.0 (131.5)"
[1] "hr=" "2.2"
D11V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  7P GAIN MUTATED          0        0         6        18         0        1
  7P GAIN WILD-TYPE        2        4         8        43         2        2
D11V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               6                 8
  STAGE IIB              18                43
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of 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       1    24
  7P GAIN WILD-TYPE     7    54
D11V4, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1+T2               1                 7
  T3+T4              24                54
[1] 2 2
[1] FALSE
D11V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    7 18
  7P GAIN WILD-TYPE 14 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      7   18
  7P GAIN WILD-TYPE   14   46
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               7                14
  1              18                46
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   12  1 12
  7P GAIN WILD-TYPE 29  2 30
D11V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              12                29
  M1               1                 2
  MX              12                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"
D11V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   12 13
  7P GAIN WILD-TYPE 32 29
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     12   13
  7P GAIN WILD-TYPE   32   29
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              12                32
  MALE                13                29
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7P GAIN MUTATED                                    21
  7P GAIN WILD-TYPE                                  53
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7P GAIN MUTATED                                       3
  7P GAIN WILD-TYPE                                     5
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  7P GAIN MUTATED                                                  1
  7P GAIN WILD-TYPE                                                2
D11V8, multiclass
                                                  clus
vv                                                 7P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 7P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             53
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D11V9, continuous
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED    9 11  1  2
  7P GAIN WILD-TYPE 46 14  0  0
D11V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0               9                46
  R1              11                14
  R2               1                 0
  RX               2                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       1                         3    19
  7P GAIN WILD-TYPE     1                         3    55
D11V12, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               3                 3
  WHITE                                  19                55
[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"

Clustering(12) Variable = 7Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   14  2
  7Q GAIN WILD-TYPE 36  9
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16                45 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                2                 9 
$`7Q GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-7289 TCGA-HZ-7926 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7652 
         385          240            8            5           11          476 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        1975          522         1968          164          127           35 
TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-US-A776 TCGA-YB-A89D 
         584          247          844          160 

$`7Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
           1          166          392          233          396           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8001 
          20            4            8          369          361           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
          24           21           28           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
          23           29          194           46           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
         347         1951         1989          851          488           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-OE-A75W 
         329          300         1991            8          181          110 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-YY-A8LH 
         416         1955         1834 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                5                 1 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             1975              1991 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            243.5             166.0 
[1] "5.0 - 1975.0 (243.5)" "1.0 - 1991.0 (166.0)"
[1] "hr=" "1.8"
D12V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  7Q GAIN MUTATED          0        0         4        17         0        1
  7Q GAIN WILD-TYPE        2        4        10        44         2        2
D12V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               4                10
  STAGE IIB              17                44
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of 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       1    21
  7Q GAIN WILD-TYPE     7    57
D12V4, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1+T2               1                 7
  T3+T4              21                57
[1] 2 2
[1] FALSE
D12V5, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    5 17
  7Q GAIN WILD-TYPE 16 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      5   17
  7Q GAIN WILD-TYPE   16   47
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0               5                16
  1              17                47
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   11  1 10
  7Q GAIN WILD-TYPE 30  2 32
D12V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              11                30
  M1               1                 2
  MX              10                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"
D12V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   11 11
  7Q GAIN WILD-TYPE 33 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     11   11
  7Q GAIN WILD-TYPE   33   31
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              11                33
  MALE                11                31
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  7Q GAIN MUTATED                                    19
  7Q GAIN WILD-TYPE                                  55
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  7Q GAIN MUTATED                                       2
  7Q GAIN WILD-TYPE                                     6
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  7Q GAIN MUTATED                                                  1
  7Q GAIN WILD-TYPE                                                2
D12V8, multiclass
                                                  clus
vv                                                 7Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 7Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             55
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D12V9, continuous
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED    7 10  1  2
  7Q GAIN WILD-TYPE 48 15  0  0
D12V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0               7                48
  R1              10                15
  R2               1                 0
  RX               2                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       1                         3    16
  7Q GAIN WILD-TYPE     1                         3    58
D12V12, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               3                 3
  WHITE                                  16                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"

Clustering(13) Variable = 8P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    7  2
  8P GAIN WILD-TYPE 43  9
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                9                52 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                 9 
$`8P GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-7922 TCGA-HZ-8315 TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-A5SP 
         385            4           28           11         1975          300 
TCGA-IB-A6UG TCGA-M8-A5N4 TCGA-YB-A89D 
        1968          584          160 

$`8P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          19           24           21           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P 
          91           23           29          194           46           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
         488           17          522          329         1991            8 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE 
         181          164          127           35          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
         416         1955          844         1834 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                 1 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1975              1991 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            300.0             173.5 
[1] "4.0 - 1975.0 (300.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.3"
D13V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  8P GAIN MUTATED          0        0         4         8         0        0
  8P GAIN WILD-TYPE        2        4        10        53         2        3
D13V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               4                10
  STAGE IIB               8                53
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       1    11
  8P GAIN WILD-TYPE     7    67
D13V4, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1+T2               1                 7
  T3+T4              11                67
[1] 2 2
[1] FALSE
D13V5, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  8
  8P GAIN WILD-TYPE 17 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    8
  8P GAIN WILD-TYPE   17   56
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               4                17
  1               8                56
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED    7  0  5
  8P GAIN WILD-TYPE 34  3 37
D13V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               7                34
  M1               0                 3
  MX               5                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    6  6
  8P GAIN WILD-TYPE 38 36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      6    6
  8P GAIN WILD-TYPE   38   36
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               6                38
  MALE                 6                36
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8P GAIN MUTATED                                    12
  8P GAIN WILD-TYPE                                  62
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8P GAIN MUTATED                                       0
  8P GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8P GAIN MUTATED                                                  0
  8P GAIN WILD-TYPE                                                3
D13V8, multiclass
                                                  clus
vv                                                 8P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 8P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             62
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D13V9, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                2                24 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A7M4        TCGA-LB-A7SX 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774        TCGA-YY-A8LH 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED    5  6  0  0
  8P GAIN WILD-TYPE 50 19  1  2
D13V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               5                50
  R1               6                19
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         0    11
  8P GAIN WILD-TYPE     2                         6    63
D13V12, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  11                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"

Clustering(14) Variable = 8Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   12  2
  8Q GAIN WILD-TYPE 38  9
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               14                47 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 9 
$`8Q GAIN MUTATED`
TCGA-FB-A545 TCGA-FB-A78T TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 
         385            1            4          361           28            5 
TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-L1-A7W4 
          11         1975          522          300         1968          164 
TCGA-M8-A5N4 TCGA-YB-A89D 
         584          160 

$`8Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
         166          392          233          396          240           28 
TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
          20            8          369            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          21           16            3           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
         194           46           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
        1989          476          851          488           17          329 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W 
        1991            8          181          127           35          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
         247          416         1955          844         1834 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 3 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1975              1991 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              232               181 
[1] "1.0 - 1975.0 (232.0)" "3.0 - 1991.0 (181.0)"
[1] "hr=" "1.6"
D14V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  8Q GAIN MUTATED          0        1         4        15         0        1
  8Q GAIN WILD-TYPE        2        3        10        46         2        2
D14V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               4                10
  STAGE IIB              15                46
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  8Q GAIN MUTATED       2    19
  8Q GAIN WILD-TYPE     6    59
D14V4, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1+T2               2                 6
  T3+T4              19                59
[1] 2 2
[1] FALSE
D14V5, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    6 15
  8Q GAIN WILD-TYPE 15 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      6   15
  8Q GAIN WILD-TYPE   15   49
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               6                15
  1              15                49
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   13  1  7
  8Q GAIN WILD-TYPE 28  2 35
D14V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              13                28
  M1               1                 2
  MX               7                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"
D14V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   10 11
  8Q GAIN WILD-TYPE 34 31
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   11
  8Q GAIN WILD-TYPE   34   31
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              10                34
  MALE                11                31
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8Q GAIN MUTATED                                    20
  8Q GAIN WILD-TYPE                                  54
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8Q GAIN MUTATED                                       0
  8Q GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8Q GAIN MUTATED                                                  0
  8Q GAIN WILD-TYPE                                                3
D14V8, multiclass
                                                  clus
vv                                                 8Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 8Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             54
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D14V9, continuous
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   10  9  1  0
  8Q GAIN WILD-TYPE 45 16  0  2
D14V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              10                45
  R1               9                16
  R2               1                 0
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         0    19
  8Q GAIN WILD-TYPE     2                         6    55
D14V12, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                  19                55
[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"

Clustering(15) Variable = 9Q GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  9Q GAIN WILD-TYPE 50 11
9Q GAIN WILD-TYPE 
               61 
[1] 11
$`9Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 
        1951         1989          476          851         1975          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
          17          522          329          300         1991            8 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
        1968          181          164          127           35          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         110          247          416         1955          844          160 
TCGA-YY-A8LH 
        1834 

9Q GAIN WILD-TYPE 
                1 
9Q GAIN WILD-TYPE 
             1991 
9Q GAIN WILD-TYPE 
              181 
[1] "1.0 - 1991.0 (181.0)"
D15V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  9Q GAIN MUTATED          0        0         1         2         0        0
  9Q GAIN WILD-TYPE        2        4        13        59         2        3
D15V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               1                13
  STAGE IIB               2                59
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     3
  9Q GAIN WILD-TYPE     8    75
D15V4, multiclass
       clus
vv      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1+T2               0                 8
  T3+T4               3                75
[1] 2 2
[1] FALSE
D15V5, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1  2
  9Q GAIN WILD-TYPE 20 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    2
  9Q GAIN WILD-TYPE   20   62
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0               1                20
  1               2                62
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q GAIN MUTATED    2  0  1
  9Q GAIN WILD-TYPE 39  3 41
D15V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               2                39
  M1               0                 3
  MX               1                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"
D15V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED    1  2
  9Q GAIN WILD-TYPE 43 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1    2
  9Q GAIN WILD-TYPE   43   40
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               1                43
  MALE                 2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9Q GAIN MUTATED                                     3
  9Q GAIN WILD-TYPE                                  71
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9Q GAIN MUTATED                                       0
  9Q GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  9Q GAIN MUTATED                                                  0
  9Q GAIN WILD-TYPE                                                3
D15V8, multiclass
                                                  clus
vv                                                 9Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 9Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D15V9, continuous
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED    2  1  0  0
  9Q GAIN WILD-TYPE 53 24  1  2
D15V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               2                53
  R1               1                24
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         0     3
  9Q GAIN WILD-TYPE     2                         6    71
D15V12, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3                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"

Clustering(16) Variable = 10P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    3  0
  10P GAIN WILD-TYPE 47 11
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 58 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                 11 
$`10P GAIN MUTATED`
TCGA-IB-A5SP TCGA-LB-A7SX TCGA-LB-A8F3 
         300          127           35 

$`10P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 
        1951         1989          476          851         1975          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          522          329         1991            8         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         181          164          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                35                  1 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
               300               1991 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             127.0              187.5 
[1] "35.0 - 300.0 (127.0)" "1.0 - 1991.0 (187.5)"
[1] "hr="     "9500000"
D16V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  10P GAIN MUTATED          0        0         2         2         0        0
  10P GAIN WILD-TYPE        2        4        12        59         2        3
D16V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                2                 12
  STAGE IIB                2                 59
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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     4
  10P GAIN WILD-TYPE     8    74
D16V4, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                4                 74
[1] 2 2
[1] FALSE
D16V5, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  2
  10P GAIN WILD-TYPE 19 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    2
  10P GAIN WILD-TYPE   19   62
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                2                 19
  1                2                 62
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10P GAIN MUTATED    2  0  2
  10P GAIN WILD-TYPE 39  3 40
D16V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                2                 39
  M1                0                  3
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    2  2
  10P GAIN WILD-TYPE 42 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      2    2
  10P GAIN WILD-TYPE   42   40
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                2                 42
  MALE                  2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10P GAIN MUTATED                                     4
  10P GAIN WILD-TYPE                                  70
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10P GAIN MUTATED                                       0
  10P GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10P GAIN MUTATED                                                  0
  10P GAIN WILD-TYPE                                                3
D16V8, multiclass
                                                  clus
vv                                                 10P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 10P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D16V9, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 25 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UG         TCGA-IB-A7M4 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"10P GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  10P GAIN MUTATED    2  2  0  0
  10P GAIN WILD-TYPE 53 23  1  2
D16V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                2                 53
  R1                2                 23
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         3     1
  10P GAIN WILD-TYPE     2                         3    73
D16V12, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                3                  3
  WHITE                                    1                 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"

Clustering(17) Variable = 10Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  10Q GAIN MUTATED    3  1
  10Q GAIN WILD-TYPE 47 10
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 4                 57 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 10 
$`10Q GAIN MUTATED`
TCGA-IB-7886 TCGA-IB-A5SP TCGA-LB-A7SX TCGA-LB-A8F3 
        1975          300          127           35 

$`10Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476          851          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         522          329         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         164          584          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                35                  1 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              1975               1991 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             213.5              181.0 
[1] "35.0 - 1975.0 (213.5)" "1.0 - 1991.0 (181.0)" 
[1] "hr=" "1.3"
D17V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  10Q GAIN MUTATED          0        0         2         3         0        1
  10Q GAIN WILD-TYPE        2        4        12        58         2        2
D17V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                2                 12
  STAGE IIB                3                 58
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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     6
  10Q GAIN WILD-TYPE     8    72
D17V4, multiclass
       clus
vv      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                6                 72
[1] 2 2
[1] FALSE
D17V5, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  4
  10Q GAIN WILD-TYPE 19 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    4
  10Q GAIN WILD-TYPE   19   60
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0                2                 19
  1                4                 60
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q GAIN MUTATED    3  1  2
  10Q GAIN WILD-TYPE 38  2 40
D17V6, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                3                 38
  M1                1                  2
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  4
  10Q GAIN WILD-TYPE 42 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    4
  10Q GAIN WILD-TYPE   42   38
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                 42
  MALE                  4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10Q GAIN MUTATED                                     6
  10Q GAIN WILD-TYPE                                  68
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10Q GAIN MUTATED                                       0
  10Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10Q GAIN MUTATED                                                  0
  10Q GAIN WILD-TYPE                                                3
D17V8, multiclass
                                                  clus
vv                                                 10Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 10Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              68
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D17V9, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7887         TCGA-IB-7891 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-OE-A75W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  10Q GAIN MUTATED    3  3  0  0
  10Q GAIN WILD-TYPE 52 22  1  2
D17V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                3                 52
  R1                3                 22
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         3     3
  10Q GAIN WILD-TYPE     2                         3    71
D17V12, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                3                  3
  WHITE                                    3                 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"

Clustering(18) Variable = 11P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    6  1
  11P GAIN WILD-TYPE 44 10
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 7                 54 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 1                 10 
$`11P GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-A4BH TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-M8-A5N4 
         385          194          522          300         1968          584 
TCGA-US-A776 
         844 

$`11P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK 
           3            5           91           23           29           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
         476          851         1975          488           17          329 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
        1991            8          181          164          127           35 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         110          247          416         1955          160         1834 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
               194                  1 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1968               1991 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             522.0              156.5 
[1] "194.0 - 1968.0 (522.0)" "1.0 - 1991.0 (156.5)"  
[1] "hr=" "1.7"
D18V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  11P GAIN MUTATED          0        0         4         6         0        0
  11P GAIN WILD-TYPE        2        4        10        55         2        3
D18V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                4                 10
  STAGE IIB                6                 55
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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    10
  11P GAIN WILD-TYPE     8    68
D18V4, multiclass
       clus
vv      11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4               10                 68
[1] 2 2
[1] FALSE
D18V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    4  6
  11P GAIN WILD-TYPE 17 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4    6
  11P GAIN WILD-TYPE   17   58
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                4                 17
  1                6                 58
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11P GAIN MUTATED    7  0  3
  11P GAIN WILD-TYPE 34  3 39
D18V6, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                7                 34
  M1                0                  3
  MX                3                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    3  7
  11P GAIN WILD-TYPE 41 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      3    7
  11P GAIN WILD-TYPE   41   35
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11P GAIN MUTATED                                     9
  11P GAIN WILD-TYPE                                  65
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11P GAIN MUTATED                                       0
  11P GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11P GAIN MUTATED                                                  1
  11P GAIN WILD-TYPE                                                2
D18V8, multiclass
                                                  clus
vv                                                 11P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 11P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D18V9, continuous
[1] "Remove cluster labels:" "11P GAIN MUTATED"      
clus
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-A5SS 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-LB-A7SX         TCGA-OE-A75W 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" "11P GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED    3  6  0  0
  11P GAIN WILD-TYPE 52 19  1  2
D18V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                3                 52
  R1                6                 19
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         0     9
  11P GAIN WILD-TYPE     2                         6    65
D18V12, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    9                 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"

Clustering(19) Variable = 11Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    3  2
  11Q GAIN WILD-TYPE 47  9
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 5                 56 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                  9 
$`11Q GAIN MUTATED`
TCGA-FB-A545 TCGA-IB-7886 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-M8-A5N4 
         385         1975          300         1968          584 

$`11Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
        1989          476          851          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
         329         1991            8          181          164          127 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
          35          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               300                  1 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1975               1991 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
               584                162 
[1] "300.0 - 1975.0 (584.0)" "1.0 - 1991.0 (162.0)"  
[1] "hr=" "1.2"
D19V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  11Q GAIN MUTATED          0        0         3         5         0        0
  11Q GAIN WILD-TYPE        2        4        11        56         2        3
D19V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                3                 11
  STAGE IIB                5                 56
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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     8
  11Q GAIN WILD-TYPE     8    70
D19V4, multiclass
       clus
vv      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                8                 70
[1] 2 2
[1] FALSE
D19V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  5
  11Q GAIN WILD-TYPE 18 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    5
  11Q GAIN WILD-TYPE   18   59
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                3                 18
  1                5                 59
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11Q GAIN MUTATED    6  0  2
  11Q GAIN WILD-TYPE 35  3 40
D19V6, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                6                 35
  M1                0                  3
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    3  5
  11Q GAIN WILD-TYPE 41 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      3    5
  11Q GAIN WILD-TYPE   41   37
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11Q GAIN MUTATED                                     8
  11Q GAIN WILD-TYPE                                  66
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11Q GAIN MUTATED                                       0
  11Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11Q GAIN MUTATED                                                  0
  11Q GAIN WILD-TYPE                                                3
D19V8, multiclass
                                                  clus
vv                                                 11Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 11Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D19V9, continuous
[1] "Remove cluster labels:" "11Q GAIN MUTATED"      
clus
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7887         TCGA-IB-7891 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-LB-A7SX         TCGA-OE-A75W 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" "11Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  11Q GAIN MUTATED    3  4  0  0
  11Q GAIN WILD-TYPE 52 21  1  2
D19V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                3                 52
  R1                4                 21
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0     7
  11Q GAIN WILD-TYPE     2                         6    67
D19V12, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 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"

Clustering(20) Variable = 12P GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    3  1
  12P GAIN WILD-TYPE 47 10
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                 57 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                 10 
$`12P GAIN MUTATED`
TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-A77O TCGA-IB-A6UG 
         240            4           11         1968 

$`12P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
         300         1991            8          181          164          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
          35          584          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                  1 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1968               1991 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             125.5              181.0 
[1] "4.0 - 1968.0 (125.5)" "1.0 - 1991.0 (181.0)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  12P GAIN MUTATED          0        1         0         7         0        0
  12P GAIN WILD-TYPE        2        3        14        54         2        3
D20V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 1                  3
  STAGE IIA                0                 14
  STAGE IIB                7                 54
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       2     6
  12P GAIN WILD-TYPE     6    72
D20V4, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1+T2                2                  6
  T3+T4                6                 72
[1] 2 2
[1] FALSE
D20V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    1  7
  12P GAIN WILD-TYPE 20 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    7
  12P GAIN WILD-TYPE   20   57
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                1                 20
  1                7                 57
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P GAIN MUTATED    3  0  5
  12P GAIN WILD-TYPE 38  3 37
D20V6, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                3                 38
  M1                0                  3
  MX                5                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    2  6
  12P GAIN WILD-TYPE 42 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      2    6
  12P GAIN WILD-TYPE   42   36
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                2                 42
  MALE                  6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12P GAIN MUTATED                                     7
  12P GAIN WILD-TYPE                                  67
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12P GAIN MUTATED                                       1
  12P GAIN WILD-TYPE                                     7
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12P GAIN MUTATED                                                  0
  12P GAIN WILD-TYPE                                                3
D20V8, multiclass
                                                  clus
vv                                                 12P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 12P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              67
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D20V9, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                 25 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A7M4         TCGA-LB-A7SX 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"12P GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED    4  3  0  1
  12P GAIN WILD-TYPE 51 22  1  1
D20V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                4                 51
  R1                3                 22
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       0                         0     7
  12P GAIN WILD-TYPE     2                         6    67
D20V12, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 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"

Clustering(21) Variable = 12Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2  1
  12Q GAIN WILD-TYPE 48 10
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 58 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                 10 
$`12Q GAIN MUTATED`
TCGA-HZ-7289 TCGA-HZ-7922 TCGA-IB-A6UG 
         240            4         1968 

$`12Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 
         329          300         1991            8          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         127           35          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                  1 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1968               1991 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             240.0              173.5 
[1] "4.0 - 1968.0 (240.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  12Q GAIN MUTATED          0        0         0         6         0        0
  12Q GAIN WILD-TYPE        2        4        14        55         2        3
D21V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                0                 14
  STAGE IIB                6                 55
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     6
  12Q GAIN WILD-TYPE     8    72
D21V4, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                6                 72
[1] 2 2
[1] FALSE
D21V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    0  6
  12Q GAIN WILD-TYPE 21 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      0    6
  12Q GAIN WILD-TYPE   21   58
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                0                 21
  1                6                 58
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED    2  0  4
  12Q GAIN WILD-TYPE 39  3 38
D21V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                2                 39
  M1                0                  3
  MX                4                 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"
D21V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    1  5
  12Q GAIN WILD-TYPE 43 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    5
  12Q GAIN WILD-TYPE   43   37
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                1                 43
  MALE                  5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12Q GAIN MUTATED                                     5
  12Q GAIN WILD-TYPE                                  69
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12Q GAIN MUTATED                                       1
  12Q GAIN WILD-TYPE                                     7
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12Q GAIN MUTATED                                                  0
  12Q GAIN WILD-TYPE                                                3
D21V8, multiclass
                                                  clus
vv                                                 12Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 12Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D21V9, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                 25 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A7M4         TCGA-LB-A7SX 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"12Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED    2  3  0  1
  12Q GAIN WILD-TYPE 53 22  1  1
D21V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                2                 53
  R1                3                 22
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         0     6
  12Q GAIN WILD-TYPE     2                         6    68
D21V12, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    6                 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"

Clustering(22) Variable = 13Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    5  1
  13Q GAIN WILD-TYPE 45 10
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 6                 55 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 10 
$`13Q GAIN MUTATED`
TCGA-H6-A45N TCGA-HZ-7922 TCGA-HZ-A77O TCGA-HZ-A77P TCGA-IB-A5SO TCGA-YB-A89D 
         233            4           11           13          329          160 

$`13Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          392          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS 
        1975          488           17          522          300         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
           8         1968          181          164          127           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YY-A8LH 
        1834 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 4                  1 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               329               1991 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              86.5              194.0 
[1] "4.0 - 329.0 (86.5)"   "1.0 - 1991.0 (194.0)"
[1] "hr=" "5.4"
D22V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  13Q GAIN MUTATED          0        0         0         8         0        0
  13Q GAIN WILD-TYPE        2        4        14        53         2        3
D22V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                0                 14
  STAGE IIB                8                 53
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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     7
  13Q GAIN WILD-TYPE     7    71
D22V4, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1+T2                1                  7
  T3+T4                7                 71
[1] 2 2
[1] FALSE
D22V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    0  8
  13Q GAIN WILD-TYPE 21 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      0    8
  13Q GAIN WILD-TYPE   21   56
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                0                 21
  1                8                 56
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q GAIN MUTATED    2  0  6
  13Q GAIN WILD-TYPE 39  3 36
D22V6, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                2                 39
  M1                0                  3
  MX                6                 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"
D22V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    4  4
  13Q GAIN WILD-TYPE 40 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4    4
  13Q GAIN WILD-TYPE   40   38
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                4                 40
  MALE                  4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  13Q GAIN MUTATED                                     6
  13Q GAIN WILD-TYPE                                  68
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  13Q GAIN MUTATED                                       2
  13Q GAIN WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  13Q GAIN MUTATED                                                  0
  13Q GAIN WILD-TYPE                                                3
D22V8, multiclass
                                                  clus
vv                                                 13Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 13Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              68
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D22V9, continuous
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 25 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-IB-7644 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7887         TCGA-IB-7891 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-LB-A7SX 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"13Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED    7  0  0  0
  13Q GAIN WILD-TYPE 48 25  1  2
D22V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                7                 48
  R1                0                 25
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         0     7
  13Q GAIN WILD-TYPE     2                         6    67
D22V12, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    7                 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"

Clustering(23) Variable = 14Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED    8  2
  14Q GAIN WILD-TYPE 42  9
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                10                 51 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 2                  9 
$`14Q GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-IB-7886 TCGA-IB-8127 
         385            4            5          194         1975          522 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-M8-A5N4 TCGA-YB-A89D 
        1968          181          584          160 

$`14Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
          91           23           29           46           11           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
         488           17          329          300         1991            8 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         164          127           35          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
        1955          844         1834 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 4                  1 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              1975               1991 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             289.5              164.0 
[1] "4.0 - 1975.0 (289.5)" "1.0 - 1991.0 (164.0)"
[1] "hr=" "1.4"
D23V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  14Q GAIN MUTATED          0        0         1        10         0        1
  14Q GAIN WILD-TYPE        2        4        13        51         2        2
D23V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                1                 13
  STAGE IIB               10                 51
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       0    12
  14Q GAIN WILD-TYPE     8    66
D23V4, multiclass
       clus
vv      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4               12                 66
[1] 2 2
[1] FALSE
D23V5, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    2 10
  14Q GAIN WILD-TYPE 19 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   10
  14Q GAIN WILD-TYPE   19   54
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0                2                 19
  1               10                 54
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q GAIN MUTATED    5  1  6
  14Q GAIN WILD-TYPE 36  2 36
D23V6, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                5                 36
  M1                1                  2
  MX                6                 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"
D23V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5  7
  14Q GAIN WILD-TYPE 39 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    7
  14Q GAIN WILD-TYPE   39   35
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                5                 39
  MALE                  7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  14Q GAIN MUTATED                                    12
  14Q GAIN WILD-TYPE                                  62
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  14Q GAIN MUTATED                                       0
  14Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  14Q GAIN MUTATED                                                  0
  14Q GAIN WILD-TYPE                                                3
D23V8, multiclass
                                                  clus
vv                                                 14Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 14Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              62
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D23V9, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q GAIN MUTATED    5  6  0  0
  14Q GAIN WILD-TYPE 50 19  1  2
D23V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                5                 50
  R1                6                 19
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0    11
  14Q GAIN WILD-TYPE     2                         6    63
D23V12, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   11                 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"

Clustering(24) Variable = 15Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    1  1
  15Q GAIN WILD-TYPE 49 10
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 59 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 10 
$`15Q GAIN MUTATED`
TCGA-HZ-7922 TCGA-IB-7886 
           4         1975 

$`15Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
         240           28           20            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
        1989          476          851          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                  1 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1975               1991 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             989.5              181.0 
[1] "4.0 - 1975.0 (989.5)" "1.0 - 1991.0 (181.0)"
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
D24V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  15Q GAIN MUTATED          0        0         0         5         0        0
  15Q GAIN WILD-TYPE        2        4        14        56         2        3
D24V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                0                 14
  STAGE IIB                5                 56
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  15Q GAIN MUTATED       0     5
  15Q GAIN WILD-TYPE     8    73
D24V4, multiclass
       clus
vv      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                5                 73
[1] 2 2
[1] FALSE
D24V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    0  5
  15Q GAIN WILD-TYPE 21 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    5
  15Q GAIN WILD-TYPE   21   59
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                0                 21
  1                5                 59
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED    2  0  3
  15Q GAIN WILD-TYPE 39  3 39
D24V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                2                 39
  M1                0                  3
  MX                3                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  2
  15Q GAIN WILD-TYPE 41 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   41   40
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  15Q GAIN MUTATED                                     5
  15Q GAIN WILD-TYPE                                  69
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  15Q GAIN MUTATED                                       0
  15Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  15Q GAIN MUTATED                                                  0
  15Q GAIN WILD-TYPE                                                3
D24V8, multiclass
                                                  clus
vv                                                 15Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 15Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D24V9, continuous
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7887         TCGA-IB-7891 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-LB-A7SX 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-US-A774         TCGA-YY-A8LH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN MUTATED    3  2  0  0
  15Q GAIN WILD-TYPE 52 23  1  2
D24V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                3                 52
  R1                2                 23
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0     5
  15Q GAIN WILD-TYPE     2                         6    69
D24V12, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    5                 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"

Clustering(25) Variable = 16P GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    9  1
  16P GAIN WILD-TYPE 41 10
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                10                 51 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 10 
$`16P GAIN MUTATED`
TCGA-HZ-7289 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
         240            5           11         1975          522          300 
TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-YB-A89D 
         181          127          584          160 

$`16P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           3           91           23           29          194           46 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
         851          488           17          329         1991            8 
TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
        1968          164           35          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
        1955          844         1834 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                  1 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1975               1991 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             210.5              166.0 
[1] "5.0 - 1975.0 (210.5)" "1.0 - 1991.0 (166.0)"
[1] "hr=" "2"  
D25V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  16P GAIN MUTATED          0        1         2         7         0        1
  16P GAIN WILD-TYPE        2        3        12        54         2        2
D25V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 1                  3
  STAGE IIA                2                 12
  STAGE IIB                7                 54
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       2     9
  16P GAIN WILD-TYPE     6    69
D25V4, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1+T2                2                  6
  T3+T4                9                 69
[1] 2 2
[1] FALSE
D25V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  7
  16P GAIN WILD-TYPE 17 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    7
  16P GAIN WILD-TYPE   17   57
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                4                 17
  1                7                 57
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED    5  1  5
  16P GAIN WILD-TYPE 36  2 37
D25V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                5                 36
  M1                1                  2
  MX                5                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    4  7
  16P GAIN WILD-TYPE 40 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      4    7
  16P GAIN WILD-TYPE   40   35
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                4                 40
  MALE                  7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16P GAIN MUTATED                                    10
  16P GAIN WILD-TYPE                                  64
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16P GAIN MUTATED                                       1
  16P GAIN WILD-TYPE                                     7
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  16P GAIN MUTATED                                                  0
  16P GAIN WILD-TYPE                                                3
D25V8, multiclass
                                                  clus
vv                                                 16P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 16P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              64
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D25V9, continuous
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED    4  6  0  1
  16P GAIN WILD-TYPE 51 19  1  1
D25V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                4                 51
  R1                6                 19
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         1     8
  16P GAIN WILD-TYPE     2                         5    66
D25V12, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    8                 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"

Clustering(26) Variable = 16Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   10  1
  16Q GAIN WILD-TYPE 40 10
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                11                 50 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 10 
$`16Q GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-8127 
         385            5           46           11         1975          522 
TCGA-IB-A5SP TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-YB-A89D 
         300          181          127          584          160 

$`16Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P 
           3           91           23           29          194           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         488           17          329         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         164           35          110          247          416         1955 
TCGA-US-A776 TCGA-YY-A8LH 
         844         1834 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                  1 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              1975               1991 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               181                180 
[1] "5.0 - 1975.0 (181.0)" "1.0 - 1991.0 (180.0)"
[1] "hr=" "2.1"
D26V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  16Q GAIN MUTATED          0        1         2         8         0        1
  16Q GAIN WILD-TYPE        2        3        12        53         2        2
D26V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 1                  3
  STAGE IIA                2                 12
  STAGE IIB                8                 53
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       2    10
  16Q GAIN WILD-TYPE     6    68
D26V4, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1+T2                2                  6
  T3+T4               10                 68
[1] 2 2
[1] FALSE
D26V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  8
  16Q GAIN WILD-TYPE 17 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    8
  16Q GAIN WILD-TYPE   17   56
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                4                 17
  1                8                 56
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16Q GAIN MUTATED    6  1  5
  16Q GAIN WILD-TYPE 35  2 37
D26V6, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                6                 35
  M1                1                  2
  MX                5                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    5  7
  16Q GAIN WILD-TYPE 39 35
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5    7
  16Q GAIN WILD-TYPE   39   35
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                5                 39
  MALE                  7                 35
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16Q GAIN MUTATED                                    11
  16Q GAIN WILD-TYPE                                  63
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16Q GAIN MUTATED                                       1
  16Q GAIN WILD-TYPE                                     7
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  16Q GAIN MUTATED                                                  0
  16Q GAIN WILD-TYPE                                                3
D26V8, multiclass
                                                  clus
vv                                                 16Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 16Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              63
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D26V9, continuous
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED    4  7  0  0
  16Q GAIN WILD-TYPE 51 18  1  2
D26V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                4                 51
  R1                7                 18
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         1     9
  16Q GAIN WILD-TYPE     2                         5    65
D26V12, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    9                 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"

Clustering(27) Variable = 17Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    4  0
  17Q GAIN WILD-TYPE 46 11
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 4                 57 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 0                 11 
$`17Q GAIN MUTATED`
TCGA-FB-A545 TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-M8-A5N4 
         385          181           35          584 

$`17Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1989          476          851         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         522          329          300         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         164          127          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                35                  1 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               584               1991 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               283                166 
[1] "35.0 - 584.0 (283.0)" "1.0 - 1991.0 (166.0)"
[1] "hr="     "7.5e+07"
D27V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  17Q GAIN MUTATED          0        0         2         3         0        0
  17Q GAIN WILD-TYPE        2        4        12        58         2        3
D27V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                2                 12
  STAGE IIB                3                 58
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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     5
  17Q GAIN WILD-TYPE     8    73
D27V4, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                5                 73
[1] 2 2
[1] FALSE
D27V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2  3
  17Q GAIN WILD-TYPE 19 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    3
  17Q GAIN WILD-TYPE   19   61
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                2                 19
  1                3                 61
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED    3  0  2
  17Q GAIN WILD-TYPE 38  3 40
D27V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                3                 38
  M1                0                  3
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    3  2
  17Q GAIN WILD-TYPE 41 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      3    2
  17Q GAIN WILD-TYPE   41   40
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17Q GAIN MUTATED                                     5
  17Q GAIN WILD-TYPE                                  69
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17Q GAIN MUTATED                                       0
  17Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  17Q GAIN MUTATED                                                  0
  17Q GAIN WILD-TYPE                                                3
D27V8, multiclass
                                                  clus
vv                                                 17Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 17Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D27V9, continuous
[1] "Remove cluster labels:" "17Q GAIN MUTATED"      
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 1                 25 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UG         TCGA-LB-A7SX 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"17Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED    2  2  0  0
  17Q GAIN WILD-TYPE 53 23  1  2
D27V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                2                 53
  R1                2                 23
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         1     3
  17Q GAIN WILD-TYPE     2                         5    71
D27V12, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    3                 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"

Clustering(28) Variable = 18P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   10  0
  18P GAIN WILD-TYPE 40 11
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                10                 51 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                 11 
$`18P GAIN MUTATED`
TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A77O 
         396          240           20          361            5           11 
TCGA-IB-8127 TCGA-IB-A7M4 TCGA-PZ-A5RE TCGA-US-A776 
         522          181          247          844 

$`18P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7918 
         449            1          166          392          233           28 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           4            8          369            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          29          194           46           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 
        1951         1989          476          851         1975          488 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          329          300         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY 
         164          127           35          584          110          416 
TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          160         1834 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 5                  1 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
               844               1991 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             243.5              164.0 
[1] "5.0 - 844.0 (243.5)"  "1.0 - 1991.0 (164.0)"
[1] "hr="     "9.2e+07"
D28V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  18P GAIN MUTATED          0        0         3         8         0        1
  18P GAIN WILD-TYPE        2        4        11        53         2        2
D28V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                3                 11
  STAGE IIB                8                 53
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       1    11
  18P GAIN WILD-TYPE     7    67
D28V4, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1+T2                1                  7
  T3+T4               11                 67
[1] 2 2
[1] FALSE
D28V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  8
  18P GAIN WILD-TYPE 17 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    8
  18P GAIN WILD-TYPE   17   56
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                4                 17
  1                8                 56
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P GAIN MUTATED    3  1  8
  18P GAIN WILD-TYPE 38  2 34
D28V6, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                3                 38
  M1                1                  2
  MX                8                 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"
D28V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    4  8
  18P GAIN WILD-TYPE 40 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4    8
  18P GAIN WILD-TYPE   40   34
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                4                 40
  MALE                  8                 34
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18P GAIN MUTATED                                     9
  18P GAIN WILD-TYPE                                  65
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18P GAIN MUTATED                                       2
  18P GAIN WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18P GAIN MUTATED                                                  1
  18P GAIN WILD-TYPE                                                2
D28V8, multiclass
                                                  clus
vv                                                 18P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 18P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D28V9, continuous
                    vv
clus                 R0 R1 R2 RX
  18P GAIN MUTATED    7  3  0  1
  18P GAIN WILD-TYPE 48 22  1  1
D28V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                7                 48
  R1                3                 22
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       0                         0    12
  18P GAIN WILD-TYPE     2                         6    62
D28V12, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   12                 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"

Clustering(29) Variable = 18Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    2  1
  18Q GAIN WILD-TYPE 48 10
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 58 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 10 
$`18Q GAIN MUTATED`
TCGA-IB-7886 TCGA-IB-A7M4 TCGA-US-A776 
        1975          181          844 

$`18Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476          851          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         522          329          300         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          160         1834 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               181                  1 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              1975               1991 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
               844                165 
[1] "181.0 - 1975.0 (844.0)" "1.0 - 1991.0 (165.0)"  
[1] "hr=" "1.4"
D29V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  18Q GAIN MUTATED          0        0         2         2         0        0
  18Q GAIN WILD-TYPE        2        4        12        59         2        3
D29V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                2                 12
  STAGE IIB                2                 59
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  18Q GAIN MUTATED       0     4
  18Q GAIN WILD-TYPE     8    74
D29V4, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                4                 74
[1] 2 2
[1] FALSE
D29V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    2  2
  18Q GAIN WILD-TYPE 19 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      2    2
  18Q GAIN WILD-TYPE   19   62
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                2                 19
  1                2                 62
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    2  0  2
  18Q GAIN WILD-TYPE 39  3 40
D29V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                2                 39
  M1                0                  3
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    0  4
  18Q GAIN WILD-TYPE 44 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      0    4
  18Q GAIN WILD-TYPE   44   38
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                0                 44
  MALE                  4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18Q GAIN MUTATED                                     3
  18Q GAIN WILD-TYPE                                  71
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18Q GAIN MUTATED                                       0
  18Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18Q GAIN MUTATED                                                  1
  18Q GAIN WILD-TYPE                                                2
D29V8, multiclass
                                                  clus
vv                                                 18Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 18Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D29V9, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7887         TCGA-IB-7891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-LB-A7SX         TCGA-OE-A75W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN MUTATED    3  1  0  0
  18Q GAIN WILD-TYPE 52 24  1  2
D29V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                3                 52
  R1                1                 24
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       0                         0     4
  18Q GAIN WILD-TYPE     2                         6    70
D29V12, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    4                 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"

Clustering(30) Variable = 19P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    3  1
  19P GAIN WILD-TYPE 47 10
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 57 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 10 
$`19P GAIN MUTATED`
TCGA-FB-A545 TCGA-IB-7886 TCGA-IB-8127 TCGA-YB-A89D 
         385         1975          522          160 

$`19P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
        1989          476          851          488           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 
         300         1991            8         1968          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         127           35          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
        1955          844         1834 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
               160                  1 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1975               1991 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             453.5              166.0 
[1] "160.0 - 1975.0 (453.5)" "1.0 - 1991.0 (166.0)"  
[1] "hr=" "1.6"
D30V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  19P GAIN MUTATED          0        0         0         4         0        0
  19P GAIN WILD-TYPE        2        4        14        57         2        3
D30V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                0                 14
  STAGE IIB                4                 57
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     4
  19P GAIN WILD-TYPE     8    74
D30V4, multiclass
       clus
vv      19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                4                 74
[1] 2 2
[1] FALSE
D30V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    0  4
  19P GAIN WILD-TYPE 21 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      0    4
  19P GAIN WILD-TYPE   21   60
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                0                 21
  1                4                 60
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED    3  0  1
  19P GAIN WILD-TYPE 38  3 41
D30V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                3                 38
  M1                0                  3
  MX                1                 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"
D30V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    1  3
  19P GAIN WILD-TYPE 43 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1    3
  19P GAIN WILD-TYPE   43   39
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                1                 43
  MALE                  3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19P GAIN MUTATED                                     4
  19P GAIN WILD-TYPE                                  70
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19P GAIN MUTATED                                       0
  19P GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19P GAIN MUTATED                                                  0
  19P GAIN WILD-TYPE                                                3
D30V8, multiclass
                                                  clus
vv                                                 19P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 19P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D30V9, continuous
[1] "Remove cluster labels:" "19P GAIN MUTATED"      
clus
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7887         TCGA-IB-7891 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-A5SS         TCGA-IB-A6UG 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-LB-A7SX         TCGA-OE-A75W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED    1  2  0  0
  19P GAIN WILD-TYPE 54 23  1  2
D30V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                1                 54
  R1                2                 23
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         0     4
  19P GAIN WILD-TYPE     2                         6    70
D30V12, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    4                 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"

Clustering(31) Variable = 19Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    7  2
  19Q GAIN WILD-TYPE 43  9
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 9                 52 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                  9 
$`19Q GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-7922 TCGA-HZ-8001 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8127 
         385            4           19         1975          488          522 
TCGA-IB-A6UG TCGA-LB-A7SX TCGA-YB-A89D 
        1968          127          160 

$`19Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
         851           17          329          300         1991            8 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         181          164           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YY-A8LH 
         416         1955          844         1834 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 4                  1 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1975               1991 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             385.0              173.5 
[1] "4.0 - 1975.0 (385.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.4"
D31V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  19Q GAIN MUTATED          0        0         0         8         1        0
  19Q GAIN WILD-TYPE        2        4        14        53         1        3
D31V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                0                 14
  STAGE IIB                8                 53
  STAGE III                1                  1
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     9
  19Q GAIN WILD-TYPE     8    69
D31V4, multiclass
       clus
vv      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                9                 69
[1] 2 2
[1] FALSE
D31V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    1  8
  19Q GAIN WILD-TYPE 20 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1    8
  19Q GAIN WILD-TYPE   20   56
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                1                 20
  1                8                 56
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED    5  0  4
  19Q GAIN WILD-TYPE 36  3 38
D31V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                5                 36
  M1                0                  3
  MX                4                 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"
D31V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    3  6
  19Q GAIN WILD-TYPE 41 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    6
  19Q GAIN WILD-TYPE   41   36
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  6                 36
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19Q GAIN MUTATED                                     9
  19Q GAIN WILD-TYPE                                  65
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19Q GAIN MUTATED                                       0
  19Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19Q GAIN MUTATED                                                  0
  19Q GAIN WILD-TYPE                                                3
D31V8, multiclass
                                                  clus
vv                                                 19Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 19Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D31V9, continuous
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED    4  4  0  0
  19Q GAIN WILD-TYPE 51 21  1  2
D31V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                4                 51
  R1                4                 21
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         1     8
  19Q GAIN WILD-TYPE     2                         5    66
D31V12, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    8                 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"

Clustering(32) Variable = 20P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   12  1
  20P GAIN WILD-TYPE 38 10
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                13                 48 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                 10 
$`20P GAIN MUTATED`
TCGA-FB-A545 TCGA-FB-A5VM TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-A77O TCGA-HZ-A77Q 
         385          449          240            4           11           33 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-LB-A8F3 TCGA-US-A776 TCGA-YB-A89D 
        1975          522          300           35          844          160 
TCGA-YY-A8LH 
        1834 

$`20P GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A78T 
         295          360          153          586            4            1 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
         166          392          233          396           28           20 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-IB-7644 
          23           29          194           46           13          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476          851          488           17 
TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 
         329         1991            8         1968          181          164 
TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         127          584          110          247          416         1955 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 4                  1 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              1975               1991 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               300                165 
[1] "4.0 - 1975.0 (300.0)" "1.0 - 1991.0 (165.0)"
[1] "hr=" "2.7"
D32V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  20P GAIN MUTATED          0        2         3        14         0        0
  20P GAIN WILD-TYPE        2        2        11        47         2        3
D32V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 2                  2
  STAGE IIA                3                 11
  STAGE IIB               14                 47
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       3    16
  20P GAIN WILD-TYPE     5    62
D32V4, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1+T2                3                  5
  T3+T4               16                 62
[1] 2 2
[1] FALSE
D32V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    5 14
  20P GAIN WILD-TYPE 16 50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5   14
  20P GAIN WILD-TYPE   16   50
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                5                 16
  1               14                 50
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED    7  0 12
  20P GAIN WILD-TYPE 34  3 30
D32V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                7                 34
  M1                0                  3
  MX               12                 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"
D32V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    7 12
  20P GAIN WILD-TYPE 37 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      7   12
  20P GAIN WILD-TYPE   37   30
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                7                 37
  MALE                 12                 30
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20P GAIN MUTATED                                    15
  20P GAIN WILD-TYPE                                  59
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20P GAIN MUTATED                                       3
  20P GAIN WILD-TYPE                                     5
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20P GAIN MUTATED                                                  1
  20P GAIN WILD-TYPE                                                2
D32V8, multiclass
                                                  clus
vv                                                 20P GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 20P GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              59
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D32V9, continuous
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   11  6  0  1
  20P GAIN WILD-TYPE 44 19  1  1
D32V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               11                 44
  R1                6                 19
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         1    17
  20P GAIN WILD-TYPE     2                         5    57
D32V12, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   17                 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"

Clustering(33) Variable = 20Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   15  1
  20Q GAIN WILD-TYPE 35 10
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                16                 45 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                 10 
$`20Q GAIN MUTATED`
TCGA-FB-A545 TCGA-FB-A5VM TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-A77O 
         385          449          240           28            4           11 
TCGA-HZ-A77Q TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7M4 TCGA-L1-A7W4 
          33         1975          522          300          181          164 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-YB-A89D TCGA-YY-A8LH 
          35          584          160         1834 

$`20Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A78T 
         295          360          153          586            4            1 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7923 
         166          392          233          396           20            8 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
         369          361            8           19           24           21 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
          28           16            3            5           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-IB-7644 TCGA-IB-7649 
          29          194           46           13          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
        1989          476          851          488           17          329 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W TCGA-PZ-A5RE 
        1991            8         1968          127          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         416         1955          844 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 4                  1 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1975               1991 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             210.5              166.0 
[1] "4.0 - 1975.0 (210.5)" "1.0 - 1991.0 (166.0)"
[1] "hr=" "2.8"
D33V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  20Q GAIN MUTATED          0        2         3        17         0        0
  20Q GAIN WILD-TYPE        2        2        11        44         2        3
D33V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 2                  2
  STAGE IIA                3                 11
  STAGE IIB               17                 44
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       3    19
  20Q GAIN WILD-TYPE     5    59
D33V4, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1+T2                3                  5
  T3+T4               19                 59
[1] 2 2
[1] FALSE
D33V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    5 17
  20Q GAIN WILD-TYPE 16 47
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5   17
  20Q GAIN WILD-TYPE   16   47
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                5                 16
  1               17                 47
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED   10  0 12
  20Q GAIN WILD-TYPE 31  3 30
D33V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               10                 31
  M1                0                  3
  MX               12                 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"
D33V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    9 13
  20Q GAIN WILD-TYPE 35 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9   13
  20Q GAIN WILD-TYPE   35   29
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                9                 35
  MALE                 13                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20Q GAIN MUTATED                                    19
  20Q GAIN WILD-TYPE                                  55
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20Q GAIN MUTATED                                       3
  20Q GAIN WILD-TYPE                                     5
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20Q GAIN MUTATED                                                  0
  20Q GAIN WILD-TYPE                                                3
D33V8, multiclass
                                                  clus
vv                                                 20Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 20Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              55
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D33V9, continuous
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED   12  7  1  1
  20Q GAIN WILD-TYPE 43 18  0  1
D33V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               12                 43
  R1                7                 18
  R2                1                  0
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         1    19
  20Q GAIN WILD-TYPE     2                         5    55
D33V12, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   19                 55
[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"

Clustering(34) Variable = 22Q GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    3  0
  22Q GAIN WILD-TYPE 47 11
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 58 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                 11 
$`22Q GAIN MUTATED`
TCGA-FB-A545 TCGA-HZ-7922 TCGA-LB-A7SX 
         385            4          127 

$`22Q GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         164           35          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                  1 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
               385               1991 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             127.0              187.5 
[1] "4.0 - 385.0 (127.0)"  "1.0 - 1991.0 (187.5)"
[1] "hr="     "2.6e+07"
D34V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  22Q GAIN MUTATED          0        0         1         3         0        0
  22Q GAIN WILD-TYPE        2        4        13        58         2        3
D34V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                1                 13
  STAGE IIB                3                 58
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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     4
  22Q GAIN WILD-TYPE     8    74
D34V4, multiclass
       clus
vv      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1+T2                0                  8
  T3+T4                4                 74
[1] 2 2
[1] FALSE
D34V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    1  3
  22Q GAIN WILD-TYPE 20 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    3
  22Q GAIN WILD-TYPE   20   61
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                1                 20
  1                3                 61
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q GAIN MUTATED    2  0  2
  22Q GAIN WILD-TYPE 39  3 40
D34V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                2                 39
  M1                0                  3
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  1
  22Q GAIN WILD-TYPE 41 41
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    1
  22Q GAIN WILD-TYPE   41   41
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 41
  MALE                  1                 41
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  22Q GAIN MUTATED                                     4
  22Q GAIN WILD-TYPE                                  70
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  22Q GAIN MUTATED                                       0
  22Q GAIN WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  22Q GAIN MUTATED                                                  0
  22Q GAIN WILD-TYPE                                                3
D34V8, multiclass
                                                  clus
vv                                                 22Q GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 22Q GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D34V9, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 25 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UG         TCGA-IB-A7M4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-YY-A8LH 
"22Q GAIN WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  22Q GAIN MUTATED    2  1  0  0
  22Q GAIN WILD-TYPE 53 24  1  2
D34V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                2                 53
  R1                1                 24
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         1     3
  22Q GAIN WILD-TYPE     2                         5    71
D34V12, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    3                 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"

Clustering(35) Variable = XQ GAIN MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    2  0
  XQ GAIN WILD-TYPE 48 11
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                59 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                0                11 
$`XQ GAIN MUTATED`
TCGA-FB-A78T TCGA-HZ-8001 
           1           19 

$`XQ GAIN WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
           8           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                 3 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19              1991 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               10               194 
[1] "1.0 - 19.0 (10.0)"    "3.0 - 1991.0 (194.0)"
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
D35V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  XQ GAIN MUTATED          0        0         0         3         1        0
  XQ GAIN WILD-TYPE        2        4        14        58         1        3
D35V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               0                14
  STAGE IIB               3                58
  STAGE III               1                 1
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     4
  XQ GAIN WILD-TYPE     8    74
D35V4, multiclass
       clus
vv      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1+T2               0                 8
  T3+T4               4                74
[1] 2 2
[1] FALSE
D35V5, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    1  3
  XQ GAIN WILD-TYPE 20 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    3
  XQ GAIN WILD-TYPE   20   61
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0               1                20
  1               3                61
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED    1  0  3
  XQ GAIN WILD-TYPE 40  3 39
D35V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               1                40
  M1               0                 3
  MX               3                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED    2  2
  XQ GAIN WILD-TYPE 42 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      2    2
  XQ GAIN WILD-TYPE   42   40
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               2                42
  MALE                 2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XQ GAIN MUTATED                                     4
  XQ GAIN WILD-TYPE                                  70
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XQ GAIN MUTATED                                       0
  XQ GAIN WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XQ GAIN MUTATED                                                  0
  XQ GAIN WILD-TYPE                                                3
D35V8, multiclass
                                                  clus
vv                                                 XQ GAIN MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 XQ GAIN WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D35V9, continuous
[1] "Remove cluster labels:" "XQ GAIN MUTATED"       
clus
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                1                25 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A7DR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1        TCGA-HZ-A77Q 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-IB-A7M4 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-YY-A8LH 
"XQ GAIN WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED    4  0  0  0
  XQ GAIN WILD-TYPE 51 25  1  2
D35V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               4                51
  R1               0                25
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         0     4
  XQ GAIN WILD-TYPE     2                         6    70
D35V12, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"

Clustering(36) Variable = 1P LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    8  4
  1P LOSS WILD-TYPE 42  7
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12                49 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                 7 
$`1P LOSS MUTATED`
TCGA-FB-A7DR TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
         166           11         1989         1975          522          300 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-YY-A8LH 
        1991         1968          181           35          110         1834 

$`1P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7652 
          46           13           33          347         1951          476 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-L1-A7W4 
         851          488           17          329            8          164 
TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         127          584          247          416         1955          844 
TCGA-YB-A89D 
         160 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               11                 1 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             1991              1955 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              411               160 
[1] "11.0 - 1991.0 (411.0)" "1.0 - 1955.0 (160.0)" 
[1] "hr="     "7.9e+08"
D36V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  1P LOSS MUTATED          0        0         4        12         0        0
  1P LOSS WILD-TYPE        2        4        10        49         2        3
D36V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               4                10
  STAGE IIB              12                49
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  1P LOSS MUTATED       1    15
  1P LOSS WILD-TYPE     7    63
D36V4, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1+T2               1                 7
  T3+T4              15                63
[1] 2 2
[1] FALSE
D36V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    3 12
  1P LOSS WILD-TYPE 18 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   12
  1P LOSS WILD-TYPE   18   52
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               3                18
  1              12                52
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED   10  0  6
  1P LOSS WILD-TYPE 31  3 36
D36V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0              10                31
  M1               0                 3
  MX               6                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"
D36V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    6 10
  1P LOSS WILD-TYPE 38 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6   10
  1P LOSS WILD-TYPE   38   32
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               6                38
  MALE                10                32
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1P LOSS MUTATED                                    15
  1P LOSS WILD-TYPE                                  59
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1P LOSS MUTATED                                       0
  1P LOSS WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1P LOSS MUTATED                                                  1
  1P LOSS WILD-TYPE                                                2
D36V8, multiclass
                                                  clus
vv                                                 1P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 1P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             59
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D36V9, continuous
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   11  5  0  0
  1P LOSS WILD-TYPE 44 20  1  2
D36V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              11                44
  R1               5                20
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       1                         2    13
  1P LOSS WILD-TYPE     1                         4    61
D36V12, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  13                61
[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"

Clustering(37) Variable = 1Q LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    2  0
  1Q LOSS WILD-TYPE 48 11
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                59 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                0                11 
$`1Q LOSS MUTATED`
TCGA-IB-A5SP TCGA-IB-A7M4 
         300          181 

$`1Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 
        1951         1989          476          851         1975          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          522          329         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              181                 1 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              300              1991 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            240.5             166.0 
[1] "181.0 - 300.0 (240.5)" "1.0 - 1991.0 (166.0)" 
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
D37V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  1Q LOSS MUTATED          0        0         1         4         0        0
  1Q LOSS WILD-TYPE        2        4        13        57         2        3
D37V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               1                13
  STAGE IIB               4                57
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     5
  1Q LOSS WILD-TYPE     8    73
D37V4, multiclass
       clus
vv      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1+T2               0                 8
  T3+T4               5                73
[1] 2 2
[1] FALSE
D37V5, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    1  4
  1Q LOSS WILD-TYPE 20 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    4
  1Q LOSS WILD-TYPE   20   60
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0               1                20
  1               4                60
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  1Q LOSS MUTATED    3  0  2
  1Q LOSS WILD-TYPE 38  3 40
D37V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               3                38
  M1               0                 3
  MX               2                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    1  4
  1Q LOSS WILD-TYPE 43 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    4
  1Q LOSS WILD-TYPE   43   38
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               1                43
  MALE                 4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  1Q LOSS MUTATED                                     5
  1Q LOSS WILD-TYPE                                  69
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  1Q LOSS MUTATED                                       0
  1Q LOSS WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  1Q LOSS MUTATED                                                  0
  1Q LOSS WILD-TYPE                                                3
D37V8, multiclass
                                                  clus
vv                                                 1Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 1Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D37V9, continuous
[1] "Remove cluster labels:" "1Q LOSS MUTATED"       
clus
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                1                25 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UG 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-YY-A8LH 
"1Q LOSS WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  1Q LOSS MUTATED    3  2  0  0
  1Q LOSS WILD-TYPE 52 23  1  2
D37V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               3                52
  R1               2                23
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         1     4
  1Q LOSS WILD-TYPE     2                         5    70
D37V12, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   4                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"

Clustering(38) Variable = 2P LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    4  0
  2P LOSS WILD-TYPE 46 11
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                4                57 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                11 
$`2P LOSS MUTATED`
TCGA-H6-8124 TCGA-HZ-7289 TCGA-IB-7652 TCGA-US-A776 
         392          240          476          844 

$`2P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
         449            1          166          233          396           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 
         300         1991            8         1968          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         127           35          584          110          247          416 
TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          160         1834 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              240                 1 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              844              1991 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
              434               164 
[1] "240.0 - 844.0 (434.0)" "1.0 - 1991.0 (164.0)" 
[1] "hr="     "8.1e+07"
D38V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  2P LOSS MUTATED          0        0         2         5         0        0
  2P LOSS WILD-TYPE        2        4        12        56         2        3
D38V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               2                12
  STAGE IIB               5                56
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  2P LOSS MUTATED       0     7
  2P LOSS WILD-TYPE     8    71
D38V4, multiclass
       clus
vv      2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1+T2               0                 8
  T3+T4               7                71
[1] 2 2
[1] FALSE
D38V5, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    2  5
  2P LOSS WILD-TYPE 19 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    5
  2P LOSS WILD-TYPE   19   59
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0               2                19
  1               5                59
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2P LOSS MUTATED    4  0  3
  2P LOSS WILD-TYPE 37  3 39
D38V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               4                37
  M1               0                 3
  MX               3                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    3  4
  2P LOSS WILD-TYPE 41 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3    4
  2P LOSS WILD-TYPE   41   38
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               3                41
  MALE                 4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2P LOSS MUTATED                                     5
  2P LOSS WILD-TYPE                                  69
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2P LOSS MUTATED                                       1
  2P LOSS WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2P LOSS MUTATED                                                  1
  2P LOSS WILD-TYPE                                                2
D38V8, multiclass
                                                  clus
vv                                                 2P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 2P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D38V9, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                25 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-H6-A45N        TCGA-H8-A6C1        TCGA-HZ-A77Q 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-IB-A7M4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-YY-A8LH 
"2P LOSS WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  2P LOSS MUTATED    3  3  0  1
  2P LOSS WILD-TYPE 52 22  1  1
D38V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               3                52
  R1               3                22
  R2               0                 1
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       1                         1     5
  2P LOSS WILD-TYPE     1                         5    69
D38V12, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   5                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"

Clustering(39) Variable = 2Q LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    2  0
  2Q LOSS WILD-TYPE 48 11
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                59 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                11 
$`2Q LOSS MUTATED`
TCGA-H6-8124 TCGA-US-A776 
         392          844 

$`2Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1989          476          851         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         522          329          300         1991            8         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
         181          164          127           35          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         247          416         1955          160         1834 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              392                 1 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              844              1991 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
              618               166 
[1] "392.0 - 844.0 (618.0)" "1.0 - 1991.0 (166.0)" 
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
D39V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  2Q LOSS MUTATED          0        0         1         2         0        0
  2Q LOSS WILD-TYPE        2        4        13        59         2        3
D39V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               1                13
  STAGE IIB               2                59
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  2Q LOSS MUTATED       0     3
  2Q LOSS WILD-TYPE     8    75
D39V4, multiclass
       clus
vv      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1+T2               0                 8
  T3+T4               3                75
[1] 2 2
[1] FALSE
D39V5, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    1  2
  2Q LOSS WILD-TYPE 20 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    2
  2Q LOSS WILD-TYPE   20   62
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0               1                20
  1               2                62
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED    2  0  1
  2Q LOSS WILD-TYPE 39  3 41
D39V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               2                39
  M1               0                 3
  MX               1                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"
D39V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    1  2
  2Q LOSS WILD-TYPE 43 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    2
  2Q LOSS WILD-TYPE   43   40
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               1                43
  MALE                 2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  2Q LOSS MUTATED                                     2
  2Q LOSS WILD-TYPE                                  72
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  2Q LOSS MUTATED                                       0
  2Q LOSS WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  2Q LOSS MUTATED                                                  1
  2Q LOSS WILD-TYPE                                                2
D39V8, multiclass
                                                  clus
vv                                                 2Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 2Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             72
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D39V9, continuous
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                25 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-H6-A45N        TCGA-H8-A6C1        TCGA-HZ-A77Q 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651        TCGA-IB-7885 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891        TCGA-IB-8126 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-IB-8127        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-IB-A7M4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-LB-A7SX        TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-YY-A8LH 
"2Q LOSS WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  2Q LOSS MUTATED    2  1  0  0
  2Q LOSS WILD-TYPE 53 24  1  2
D39V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               2                53
  R1               1                24
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     3
  2Q LOSS WILD-TYPE     2                         6    71
D39V12, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   3                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"

Clustering(40) Variable = 3P LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   10  1
  3P LOSS WILD-TYPE 40 10
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               11                50 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                10 
$`3P LOSS MUTATED`
TCGA-F2-A44H TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7886 
         586           28          361           46           11         1975 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-YY-A8LH 
         522          300          127           35         1834 

$`3P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 
          20            4            8          369            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-HZ-A77Q 
          91           23           29          194           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 
         347         1951         1989          476          851          488 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
          17          329         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         164          584          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D 
         844          160 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               11                 1 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1975              1991 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            300.0             173.5 
[1] "11.0 - 1975.0 (300.0)" "1.0 - 1991.0 (173.5)" 
[1] "hr=" "2.2"
D40V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  3P LOSS MUTATED          0        1         3        12         0        0
  3P LOSS WILD-TYPE        2        3        11        49         2        3
D40V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               3                11
  STAGE IIB              12                49
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  3P LOSS MUTATED       2    14
  3P LOSS WILD-TYPE     6    64
D40V4, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1+T2               2                 6
  T3+T4              14                64
[1] 2 2
[1] FALSE
D40V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    4 12
  3P LOSS WILD-TYPE 17 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      4   12
  3P LOSS WILD-TYPE   17   52
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0               4                17
  1              12                52
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED    8  0  8
  3P LOSS WILD-TYPE 33  3 34
D40V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               8                33
  M1               0                 3
  MX               8                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"
D40V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    6 10
  3P LOSS WILD-TYPE 38 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      6   10
  3P LOSS WILD-TYPE   38   32
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               6                38
  MALE                10                32
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3P LOSS MUTATED                                    15
  3P LOSS WILD-TYPE                                  59
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3P LOSS MUTATED                                       1
  3P LOSS WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3P LOSS MUTATED                                                  0
  3P LOSS WILD-TYPE                                                3
D40V8, multiclass
                                                  clus
vv                                                 3P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 3P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             59
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D40V9, continuous
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED    8  8  0  0
  3P LOSS WILD-TYPE 47 17  1  2
D40V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               8                47
  R1               8                17
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       0                         2    13
  3P LOSS WILD-TYPE     2                         4    61
D40V12, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  13                61
[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"

Clustering(41) Variable = 3Q LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    9  1
  3Q LOSS WILD-TYPE 41 10
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10                51 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                10 
$`3Q LOSS MUTATED`
TCGA-F2-A44H TCGA-HZ-7925 TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7886 TCGA-IB-8127 
         586          361           46           11         1975          522 
TCGA-IB-A5SP TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-YY-A8LH 
         300          127           35         1834 

$`3Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
          28           20            4            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P 
           5           91           23           29          194           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         488           17          329         1991            8         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         181          164          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
        1955          844          160 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               11                 1 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1975              1991 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            330.5             166.0 
[1] "11.0 - 1975.0 (330.5)" "1.0 - 1991.0 (166.0)" 
[1] "hr=" "2.2"
D41V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  3Q LOSS MUTATED          0        0         3        10         0        0
  3Q LOSS WILD-TYPE        2        4        11        51         2        3
D41V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               3                11
  STAGE IIB              10                51
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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    12
  3Q LOSS WILD-TYPE     7    66
D41V4, multiclass
       clus
vv      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1+T2               1                 7
  T3+T4              12                66
[1] 2 2
[1] FALSE
D41V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3 10
  3Q LOSS WILD-TYPE 18 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3   10
  3Q LOSS WILD-TYPE   18   54
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               3                18
  1              10                54
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    6  0  7
  3Q LOSS WILD-TYPE 35  3 35
D41V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               6                35
  M1               0                 3
  MX               7                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"
D41V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    5  8
  3Q LOSS WILD-TYPE 39 34
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    8
  3Q LOSS WILD-TYPE   39   34
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               5                39
  MALE                 8                34
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  3Q LOSS MUTATED                                    12
  3Q LOSS WILD-TYPE                                  62
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  3Q LOSS MUTATED                                       1
  3Q LOSS WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  3Q LOSS MUTATED                                                  0
  3Q LOSS WILD-TYPE                                                3
D41V8, multiclass
                                                  clus
vv                                                 3Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 3Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             62
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D41V9, continuous
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED    7  6  0  0
  3Q LOSS WILD-TYPE 48 19  1  2
D41V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               7                48
  R1               6                19
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       0                         3    10
  3Q LOSS WILD-TYPE     2                         3    64
D41V12, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               3                 3
  WHITE                                  10                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"

Clustering(42) Variable = 4P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    7  1
  4P LOSS WILD-TYPE 43 10
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                53 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                10 
$`4P LOSS MUTATED`
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-7918 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-IB-7886 
         449          166           28          361            5         1975 
TCGA-IB-A5SP TCGA-IB-A7M4 
         300          181 

$`4P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 
           1          392          233          396          240           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           4            8          369            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
          29          194           46           11           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 
         347         1951         1989          476          851          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          522          329         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                 1 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1975              1991 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            240.5             164.0 
[1] "5.0 - 1975.0 (240.5)" "1.0 - 1991.0 (164.0)"
[1] "hr=" "1.8"
D42V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  4P LOSS MUTATED          0        1         2         7         0        1
  4P LOSS WILD-TYPE        2        3        12        54         2        2
D42V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               2                12
  STAGE IIB               7                54
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of 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    10
  4P LOSS WILD-TYPE     7    68
D42V4, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1+T2               1                 7
  T3+T4              10                68
[1] 2 2
[1] FALSE
D42V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3  7
  4P LOSS WILD-TYPE 18 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    7
  4P LOSS WILD-TYPE   18   57
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               3                18
  1               7                57
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED    7  1  3
  4P LOSS WILD-TYPE 34  2 39
D42V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               7                34
  M1               1                 2
  MX               3                39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    2  9
  4P LOSS WILD-TYPE 42 33
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2    9
  4P LOSS WILD-TYPE   42   33
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               2                42
  MALE                 9                33
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4P LOSS MUTATED                                    10
  4P LOSS WILD-TYPE                                  64
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4P LOSS MUTATED                                       0
  4P LOSS WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4P LOSS MUTATED                                                  1
  4P LOSS WILD-TYPE                                                2
D42V8, multiclass
                                                  clus
vv                                                 4P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 4P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             64
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D42V9, continuous
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED    6  5  0  0
  4P LOSS WILD-TYPE 49 20  1  2
D42V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               6                49
  R1               5                20
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       1                         1     9
  4P LOSS WILD-TYPE     1                         5    65
D42V12, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   9                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"

Clustering(43) Variable = 4Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    7  1
  4Q LOSS WILD-TYPE 43 10
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                8                53 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                10 
$`4Q LOSS MUTATED`
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-IB-7886 
         449          166          361            5          194         1975 
TCGA-IB-A5SP TCGA-IB-A7M4 
         300          181 

$`4Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
           1          392          233          396          240           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 
          20            4            8          369            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
          24           21           28           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
          23           29           46           11           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 
         347         1951         1989          476          851          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          522          329         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                 1 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1975              1991 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
              247               160 
[1] "5.0 - 1975.0 (247.0)" "1.0 - 1991.0 (160.0)"
[1] "hr=" "1.9"
D43V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  4Q LOSS MUTATED          0        1         2         7         0        1
  4Q LOSS WILD-TYPE        2        3        12        54         2        2
D43V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               2                12
  STAGE IIB               7                54
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of 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    10
  4Q LOSS WILD-TYPE     7    68
D43V4, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1+T2               1                 7
  T3+T4              10                68
[1] 2 2
[1] FALSE
D43V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    3  7
  4Q LOSS WILD-TYPE 18 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      3    7
  4Q LOSS WILD-TYPE   18   57
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0               3                18
  1               7                57
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED    5  1  5
  4Q LOSS WILD-TYPE 36  2 37
D43V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               5                36
  M1               1                 2
  MX               5                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    1 10
  4Q LOSS WILD-TYPE 43 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1   10
  4Q LOSS WILD-TYPE   43   32
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               1                43
  MALE                10                32
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  4Q LOSS MUTATED                                    10
  4Q LOSS WILD-TYPE                                  64
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  4Q LOSS MUTATED                                       0
  4Q LOSS WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  4Q LOSS MUTATED                                                  1
  4Q LOSS WILD-TYPE                                                2
D43V8, multiclass
                                                  clus
vv                                                 4Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 4Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             64
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D43V9, continuous
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED    6  5  0  0
  4Q LOSS WILD-TYPE 49 20  1  2
D43V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0               6                49
  R1               5                20
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       1                         1     9
  4Q LOSS WILD-TYPE     1                         5    65
D43V12, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   9                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"

Clustering(44) Variable = 5P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    3  0
  5P LOSS WILD-TYPE 47 11
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                58 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                0                11 
$`5P LOSS MUTATED`
TCGA-FB-A545 TCGA-IB-8127 TCGA-IB-A7M4 
         385          522          181 

$`5P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1989          476          851         1975          488           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-L1-A7W4 
         329          300         1991            8         1968          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         127           35          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              181                 1 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              522              1991 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
              385               165 
[1] "181.0 - 522.0 (385.0)" "1.0 - 1991.0 (165.0)" 
[1] "hr="     "7.5e+07"
D44V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  5P LOSS MUTATED          0        0         0         4         0        0
  5P LOSS WILD-TYPE        2        4        14        57         2        3
D44V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               0                14
  STAGE IIB               4                57
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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     4
  5P LOSS WILD-TYPE     8    74
D44V4, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1+T2               0                 8
  T3+T4               4                74
[1] 2 2
[1] FALSE
D44V5, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    0  4
  5P LOSS WILD-TYPE 21 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      0    4
  5P LOSS WILD-TYPE   21   60
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0               0                21
  1               4                60
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5P LOSS MUTATED    2  0  2
  5P LOSS WILD-TYPE 39  3 40
D44V6, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               2                39
  M1               0                 3
  MX               2                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    2  2
  5P LOSS WILD-TYPE 42 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    2
  5P LOSS WILD-TYPE   42   40
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                42
  MALE                 2                40
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5P LOSS MUTATED                                     4
  5P LOSS WILD-TYPE                                  70
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5P LOSS MUTATED                                       0
  5P LOSS WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5P LOSS MUTATED                                                  0
  5P LOSS WILD-TYPE                                                3
D44V8, multiclass
                                                  clus
vv                                                 5P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 5P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D44V9, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                24 
       TCGA-F2-6880        TCGA-FB-A4P5        TCGA-FB-A5VM        TCGA-FB-A78T 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FB-A7DR        TCGA-H6-8124        TCGA-H6-A45N        TCGA-H8-A6C1 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-HZ-A77Q        TCGA-IB-7644        TCGA-IB-7649        TCGA-IB-7651 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IB-7885        TCGA-IB-7886        TCGA-IB-7887        TCGA-IB-7891 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-IB-8126        TCGA-IB-A5SS        TCGA-IB-A6UG        TCGA-LB-A7SX 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-OE-A75W        TCGA-S4-A8RP        TCGA-US-A774        TCGA-YY-A8LH 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
                   vv
clus                R0 R1 R2 RX
  5P LOSS MUTATED    2  1  0  0
  5P LOSS WILD-TYPE 53 24  1  2
D44V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0               2                53
  R1               1                24
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         0     4
  5P LOSS WILD-TYPE     2                         6    70
D44V12, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   4                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"

Clustering(45) Variable = 5Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    4  1
  5Q LOSS WILD-TYPE 46 10
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                5                56 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                10 
$`5Q LOSS MUTATED`
TCGA-FB-A545 TCGA-HZ-7289 TCGA-IB-8127 TCGA-IB-A6UG TCGA-IB-A7M4 
         385          240          522         1968          181 

$`5Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
           1          166          392          233          396           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
         476          851         1975          488           17          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
         300         1991            8          164          127           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              181                 1 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1968              1991 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
              385               162 
[1] "181.0 - 1968.0 (385.0)" "1.0 - 1991.0 (162.0)"  
[1] "hr=" "1.3"
D45V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  5Q LOSS MUTATED          0        0         0         7         0        0
  5Q LOSS WILD-TYPE        2        4        14        54         2        3
D45V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               0                14
  STAGE IIB               7                54
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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     7
  5Q LOSS WILD-TYPE     8    71
D45V4, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1+T2               0                 8
  T3+T4               7                71
[1] 2 2
[1] FALSE
D45V5, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    0  7
  5Q LOSS WILD-TYPE 21 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    7
  5Q LOSS WILD-TYPE   21   57
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0               0                21
  1               7                57
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED    3  0  4
  5Q LOSS WILD-TYPE 38  3 38
D45V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               3                38
  M1               0                 3
  MX               4                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"
D45V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED    2  5
  5Q LOSS WILD-TYPE 42 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      2    5
  5Q LOSS WILD-TYPE   42   37
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               2                42
  MALE                 5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  5Q LOSS MUTATED                                     6
  5Q LOSS WILD-TYPE                                  68
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  5Q LOSS MUTATED                                       1
  5Q LOSS WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  5Q LOSS MUTATED                                                  0
  5Q LOSS WILD-TYPE                                                3
D45V8, multiclass
                                                  clus
vv                                                 5Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 5Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             68
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D45V9, continuous
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED    2  3  0  1
  5Q LOSS WILD-TYPE 53 22  1  1
D45V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               2                53
  R1               3                22
  R2               0                 1
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         0     7
  5Q LOSS WILD-TYPE     2                         6    67
D45V12, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               0                 6
  WHITE                                   7                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"

Clustering(46) Variable = 6P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   18  3
  6P LOSS WILD-TYPE 32  8
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               21                40 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3                 8 
$`6P LOSS MUTATED`
TCGA-F2-A44H TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8001 
         586          392          240           20          361           19 
TCGA-HZ-8315 TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7886 
          28           46           11           13           33         1975 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX TCGA-PZ-A5RE 
         522          300         1991         1968          127          247 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

$`6P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7922 
           1          166          233          396           28            4 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 
           8          369            8           24           21           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 
         347         1951         1989          476          851          488 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 
          17          329            8          181          164           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A774 
         584          110          416         1955 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11                 1 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             1991              1989 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              247               165 
[1] "11.0 - 1991.0 (247.0)" "1.0 - 1989.0 (165.0)" 
[1] "hr=" "4.3"
D46V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  6P LOSS MUTATED          0        1         5        24         1        0
  6P LOSS WILD-TYPE        2        3         9        37         1        3
D46V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               5                 9
  STAGE IIB              24                37
  STAGE III               1                 1
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  6P LOSS MUTATED       2    29
  6P LOSS WILD-TYPE     6    49
D46V4, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1+T2               2                 6
  T3+T4              29                49
[1] 2 2
[1] FALSE
D46V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    7 24
  6P LOSS WILD-TYPE 14 40
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      7   24
  6P LOSS WILD-TYPE   14   40
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               7                14
  1              24                40
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6P LOSS MUTATED   15  0 16
  6P LOSS WILD-TYPE 26  3 26
D46V6, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0              15                26
  M1               0                 3
  MX              16                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   12 19
  6P LOSS WILD-TYPE 32 23
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     12   19
  6P LOSS WILD-TYPE   32   23
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              12                32
  MALE                19                23
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6P LOSS MUTATED                                    25
  6P LOSS WILD-TYPE                                  49
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6P LOSS MUTATED                                       4
  6P LOSS WILD-TYPE                                     4
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  6P LOSS MUTATED                                                  1
  6P LOSS WILD-TYPE                                                2
D46V8, multiclass
                                                  clus
vv                                                 6P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 6P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             49
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D46V9, continuous
                   vv
clus                R0 R1 R2 RX
  6P LOSS MUTATED   19 10  0  1
  6P LOSS WILD-TYPE 36 15  1  1
D46V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              19                36
  R1              10                15
  R2               0                 1
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       0                         2    28
  6P LOSS WILD-TYPE     2                         4    46
D46V12, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  28                46
[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"

Clustering(47) Variable = 6Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   23  4
  6Q LOSS WILD-TYPE 27  7
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               27                34 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                 7 
$`6Q LOSS MUTATED`
TCGA-F2-A44H TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 
         586          385          392          240           20            4 
TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-HZ-A77P 
         361           19           28            5           11           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
          33          347          851         1975          522          300 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
        1991         1968          127          584          110          247 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

$`6Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T 
         295          360          153            4          449            1 
TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7923 TCGA-HZ-7924 
         166          233          396           28            8          369 
TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
           8           24           21           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-IB-7649 TCGA-IB-7651 
          23           29          194           46         1951         1989 
TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A7M4 
         476          488           17          329            8          181 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-US-A774 
         164           35          416         1955 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                4                 1 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1991              1989 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            300.0             158.5 
[1] "4.0 - 1991.0 (300.0)" "1.0 - 1989.0 (158.5)"
[1] "hr=" "3.1"
D47V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  6Q LOSS MUTATED          0        1         8        28         1        2
  6Q LOSS WILD-TYPE        2        3         6        33         1        1
D47V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               8                 6
  STAGE IIB              28                33
  STAGE III               1                 1
  STAGE IV                2                 1
[1] 6 2
[1] TRUE
[1] "dimension of 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       2    38
  6Q LOSS WILD-TYPE     6    40
D47V4, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1+T2               2                 6
  T3+T4              38                40
[1] 2 2
[1] FALSE
D47V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   11 29
  6Q LOSS WILD-TYPE 10 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11   29
  6Q LOSS WILD-TYPE   10   35
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              11                10
  1              29                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED   21  2 17
  6Q LOSS WILD-TYPE 20  1 25
D47V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0              21                20
  M1               2                 1
  MX              17                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   20 20
  6Q LOSS WILD-TYPE 24 22
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     20   20
  6Q LOSS WILD-TYPE   24   22
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              20                24
  MALE                20                22
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  6Q LOSS MUTATED                                    35
  6Q LOSS WILD-TYPE                                  39
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  6Q LOSS MUTATED                                       3
  6Q LOSS WILD-TYPE                                     5
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  6Q LOSS MUTATED                                                  1
  6Q LOSS WILD-TYPE                                                2
D47V8, multiclass
                                                  clus
vv                                                 6Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           35
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 6Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             39
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D47V9, continuous
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED   24 13  0  1
  6Q LOSS WILD-TYPE 31 12  1  1
D47V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              24                31
  R1              13                12
  R2               0                 1
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       0                         2    36
  6Q LOSS WILD-TYPE     2                         4    38
D47V12, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  36                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"

Clustering(48) Variable = 8P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   10  0
  8P LOSS WILD-TYPE 40 11
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                51 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                0                11 
$`8P LOSS MUTATED`
TCGA-FB-A7DR TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-IB-A7M4 
         166          240           20          361            5          181 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-US-A776 
         164           35          110          844 

$`8P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
         449            1          392          233          396           28 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           4            8          369            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
          29          194           46           11           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
         347         1951         1989          476          851         1975 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         488           17          522          329          300         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY 
           8         1968          127          584          247          416 
TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          160         1834 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                5                 1 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              844              1991 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              165               233 
[1] "5.0 - 844.0 (165.0)"  "1.0 - 1991.0 (233.0)"
[1] "hr="     "8.3e+07"
D48V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  8P LOSS MUTATED          0        1         4        10         0        1
  8P LOSS WILD-TYPE        2        3        10        51         2        2
D48V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                1                 3
  STAGE IIA               4                10
  STAGE IIB              10                51
  STAGE III               0                 2
  STAGE IV                1                 2
[1] 6 2
[1] TRUE
[1] "dimension of 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    15
  8P LOSS WILD-TYPE     7    63
D48V4, multiclass
       clus
vv      8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1+T2               1                 7
  T3+T4              15                63
[1] 2 2
[1] FALSE
D48V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    5 10
  8P LOSS WILD-TYPE 16 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      5   10
  8P LOSS WILD-TYPE   16   54
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               5                16
  1              10                54
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED    7  1  8
  8P LOSS WILD-TYPE 34  2 34
D48V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               7                34
  M1               1                 2
  MX               8                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"
D48V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    6 10
  8P LOSS WILD-TYPE 38 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      6   10
  8P LOSS WILD-TYPE   38   32
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               6                38
  MALE                10                32
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8P LOSS MUTATED                                    12
  8P LOSS WILD-TYPE                                  62
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8P LOSS MUTATED                                       1
  8P LOSS WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8P LOSS MUTATED                                                  2
  8P LOSS WILD-TYPE                                                1
D48V8, multiclass
                                                  clus
vv                                                 8P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
                                                  clus
vv                                                 8P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             62
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
[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"
D48V9, continuous
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   10  4  1  1
  8P LOSS WILD-TYPE 45 21  0  1
D48V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              10                45
  R1               4                21
  R2               1                 0
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       1                         1    13
  8P LOSS WILD-TYPE     1                         5    61
D48V12, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                  13                61
[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"

Clustering(49) Variable = 8Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    5  0
  8Q LOSS WILD-TYPE 45 11
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                56 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                11 
$`8Q LOSS MUTATED`
TCGA-FB-A7DR TCGA-HZ-7289 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-US-A776 
         166          240           35          110          844 

$`8Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
         449            1          392          233          396           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         164          127          584          247          416         1955 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               35                 1 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
              844              1991 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            166.0             187.5 
[1] "35.0 - 844.0 (166.0)" "1.0 - 1991.0 (187.5)"
[1] "hr="     "2.7e+07"
D49V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  8Q LOSS MUTATED          0        0         4         3         0        0
  8Q LOSS WILD-TYPE        2        4        10        58         2        3
D49V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               4                10
  STAGE IIB               3                58
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  8Q LOSS MUTATED       0     7
  8Q LOSS WILD-TYPE     8    71
D49V4, multiclass
       clus
vv      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1+T2               0                 8
  T3+T4               7                71
[1] 2 2
[1] FALSE
D49V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    3  3
  8Q LOSS WILD-TYPE 18 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    3
  8Q LOSS WILD-TYPE   18   61
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               3                18
  1               3                61
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED    2  0  5
  8Q LOSS WILD-TYPE 39  3 37
D49V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               2                39
  M1               0                 3
  MX               5                37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  5
  8Q LOSS WILD-TYPE 42 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    5
  8Q LOSS WILD-TYPE   42   37
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                42
  MALE                 5                37
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  8Q LOSS MUTATED                                     4
  8Q LOSS WILD-TYPE                                  70
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  8Q LOSS MUTATED                                       1
  8Q LOSS WILD-TYPE                                     7
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  8Q LOSS MUTATED                                                  2
  8Q LOSS WILD-TYPE                                                1
D49V8, multiclass
                                                  clus
vv                                                 8Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               2
                                                  clus
vv                                                 8Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 1
[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"
D49V9, continuous
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED    5  1  0  1
  8Q LOSS WILD-TYPE 50 24  1  1
D49V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               5                50
  R1               1                24
  R2               0                 1
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       1                         1     5
  8Q LOSS WILD-TYPE     1                         5    69
D49V12, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   5                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"

Clustering(50) Variable = 9P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   22  3
  9P LOSS WILD-TYPE 28  8
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               25                36 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                 8 
$`9P LOSS MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A545 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         153          586          385          392          396          240 
TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A77O 
          28            4          361           23          194           11 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
        1951          476          851         1975          522          300 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-YY-A8LH 
        1834 

$`9P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR 
         295          360            4          449            1          166 
TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 
         233           20            8          369            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          91           29           46           13           33          347 
TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
        1989          488           17          329         1991            8 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
        1968          181          416         1955          844          160 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                4                 1 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             1975              1991 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            300.0              68.5 
[1] "4.0 - 1975.0 (300.0)" "1.0 - 1991.0 (68.5)" 
[1] "hr=" "1.4"
D50V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  9P LOSS MUTATED          0        0         7        29         0        0
  9P LOSS WILD-TYPE        2        4         7        32         2        3
D50V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               7                 7
  STAGE IIB              29                32
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  9P LOSS MUTATED       2    34
  9P LOSS WILD-TYPE     6    44
D50V4, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1+T2               2                 6
  T3+T4              34                44
[1] 2 2
[1] FALSE
D50V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    7 29
  9P LOSS WILD-TYPE 14 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7   29
  9P LOSS WILD-TYPE   14   35
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0               7                14
  1              29                35
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   20  0 16
  9P LOSS WILD-TYPE 21  3 26
D50V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              20                21
  M1               0                 3
  MX              16                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   21 15
  9P LOSS WILD-TYPE 23 27
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     21   15
  9P LOSS WILD-TYPE   23   27
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              21                23
  MALE                15                27
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9P LOSS MUTATED                                    33
  9P LOSS WILD-TYPE                                  41
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9P LOSS MUTATED                                       2
  9P LOSS WILD-TYPE                                     6
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  9P LOSS MUTATED                                                  0
  9P LOSS WILD-TYPE                                                3
D50V8, multiclass
                                                  clus
vv                                                 9P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           33
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 9P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             41
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D50V9, continuous
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED   19 13  1  1
  9P LOSS WILD-TYPE 36 12  0  1
D50V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              19                36
  R1              13                12
  R2               1                 0
  RX               1                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       1                         3    29
  9P LOSS WILD-TYPE     1                         3    45
D50V12, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               3                 3
  WHITE                                  29                45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = 9Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   16  2
  9Q LOSS WILD-TYPE 34  9
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               18                43 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                2                 9 
$`9Q LOSS MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7922 
         153          586          392          396           28            4 
TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-8127 
          23          194           46           11         1951          522 
TCGA-IB-A5SP TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-YY-A8LH 
         300          127           35          584          247         1834 

$`9Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
         295          360            4          385          449            1 
TCGA-FB-A7DR TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 
         166          233          240           20            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A77P 
          16            3            5           91           29           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
          33          347         1989          476          851         1975 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         488           17          329         1991            8         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         181          164          110          416         1955          844 
TCGA-YB-A89D 
         160 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                4                 1 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             1951              1991 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            220.5             166.0 
[1] "4.0 - 1951.0 (220.5)" "1.0 - 1991.0 (166.0)"
[1] "hr=" "1.2"
D51V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  9Q LOSS MUTATED          0        0         6        17         0        0
  9Q LOSS WILD-TYPE        2        4         8        44         2        3
D51V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               6                 8
  STAGE IIB              17                44
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of 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       2    21
  9Q LOSS WILD-TYPE     6    57
D51V4, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1+T2               2                 6
  T3+T4              21                57
[1] 2 2
[1] FALSE
D51V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    6 17
  9Q LOSS WILD-TYPE 15 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6   17
  9Q LOSS WILD-TYPE   15   47
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0               6                15
  1              17                47
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED   10  0 13
  9Q LOSS WILD-TYPE 31  3 29
D51V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0              10                31
  M1               0                 3
  MX              13                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"
D51V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   13 10
  9Q LOSS WILD-TYPE 31 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     13   10
  9Q LOSS WILD-TYPE   31   32
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              13                31
  MALE                10                32
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  9Q LOSS MUTATED                                    21
  9Q LOSS WILD-TYPE                                  53
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  9Q LOSS MUTATED                                       2
  9Q LOSS WILD-TYPE                                     6
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  9Q LOSS MUTATED                                                  0
  9Q LOSS WILD-TYPE                                                3
D51V8, multiclass
                                                  clus
vv                                                 9Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                           21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               0
                                                  clus
vv                                                 9Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             53
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 3
[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"
D51V9, continuous
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED   12 10  0  0
  9Q LOSS WILD-TYPE 43 15  1  2
D51V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              12                43
  R1              10                15
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         2    18
  9Q LOSS WILD-TYPE     2                         4    56
D51V12, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 2
  BLACK OR AFRICAN AMERICAN               2                 4
  WHITE                                  18                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"

Clustering(52) Variable = 10P LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    6  2
  10P LOSS WILD-TYPE 44  9
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 8                 53 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  9 
$`10P LOSS MUTATED`
TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7885 
         385          392          240           11           33          851 
TCGA-IB-7886 TCGA-IB-A6UG 
        1975         1968 

$`10P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
           1          166          233          396           28           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P 
          91           23           29          194           46           13 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 
         347         1951         1989          476          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 
         522          329          300         1991            8          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                11                  1 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              1975               1991 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             388.5              164.0 
[1] "11.0 - 1975.0 (388.5)" "1.0 - 1991.0 (164.0)" 
[1] "hr=" "1.4"
D52V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  10P LOSS MUTATED          0        2         1        11         0        1
  10P LOSS WILD-TYPE        2        2        13        50         2        2
D52V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 2                  2
  STAGE IIA                1                 13
  STAGE IIB               11                 50
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       3    12
  10P LOSS WILD-TYPE     5    66
D52V4, multiclass
       clus
vv      10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1+T2                3                  5
  T3+T4               12                 66
[1] 2 2
[1] FALSE
D52V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3 12
  10P LOSS WILD-TYPE 18 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   12
  10P LOSS WILD-TYPE   18   52
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                3                 18
  1               12                 52
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED    9  1  5
  10P LOSS WILD-TYPE 32  2 37
D52V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                9                 32
  M1                1                  2
  MX                5                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    6  9
  10P LOSS WILD-TYPE 38 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      6    9
  10P LOSS WILD-TYPE   38   33
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                6                 38
  MALE                  9                 33
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10P LOSS MUTATED                                    13
  10P LOSS WILD-TYPE                                  61
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10P LOSS MUTATED                                       2
  10P LOSS WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10P LOSS MUTATED                                                  0
  10P LOSS WILD-TYPE                                                3
D52V8, multiclass
                                                  clus
vv                                                 10P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 10P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              61
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D52V9, continuous
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED    9  4  0  1
  10P LOSS WILD-TYPE 46 21  1  1
D52V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                9                 46
  R1                4                 21
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         0    14
  10P LOSS WILD-TYPE     2                         6    60
D52V12, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   14                 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"

Clustering(53) Variable = 10Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    8  1
  10Q LOSS WILD-TYPE 42 10
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 9                 52 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                 10 
$`10Q LOSS MUTATED`
TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77Q 
         385          392          240           28           11           33 
TCGA-IB-7885 TCGA-IB-A6UG TCGA-US-A776 
         851         1968          844 

$`10Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7922 
           1          166          233          396           20            4 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-IB-7644 
          23           29          194           46           13          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 
         522          329          300         1991            8          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          160         1834 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                11                  1 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              1968               1991 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               385                165 
[1] "11.0 - 1968.0 (385.0)" "1.0 - 1991.0 (165.0)" 
[1] "hr=" "1.7"
D53V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  10Q LOSS MUTATED          0        1         2        12         0        0
  10Q LOSS WILD-TYPE        2        3        12        49         2        3
D53V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 1                  3
  STAGE IIA                2                 12
  STAGE IIB               12                 49
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       2    13
  10Q LOSS WILD-TYPE     6    65
D53V4, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1+T2                2                  6
  T3+T4               13                 65
[1] 2 2
[1] FALSE
D53V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    3 12
  10Q LOSS WILD-TYPE 18 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   12
  10Q LOSS WILD-TYPE   18   52
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                3                 18
  1               12                 52
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED    9  0  6
  10Q LOSS WILD-TYPE 32  3 36
D53V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                9                 32
  M1                0                  3
  MX                6                 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"
D53V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    6  9
  10Q LOSS WILD-TYPE 38 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      6    9
  10Q LOSS WILD-TYPE   38   33
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                6                 38
  MALE                  9                 33
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  10Q LOSS MUTATED                                    12
  10Q LOSS WILD-TYPE                                  62
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  10Q LOSS MUTATED                                       2
  10Q LOSS WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  10Q LOSS MUTATED                                                  1
  10Q LOSS WILD-TYPE                                                2
D53V8, multiclass
                                                  clus
vv                                                 10Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 10Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              62
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D53V9, continuous
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED    9  4  0  1
  10Q LOSS WILD-TYPE 46 21  1  1
D53V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                9                 46
  R1                4                 21
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         0    14
  10Q LOSS WILD-TYPE     2                         6    60
D53V12, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                   14                 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"

Clustering(54) Variable = 11P LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    4  1
  11P LOSS WILD-TYPE 46 10
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 56 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 10 
$`11P LOSS MUTATED`
TCGA-F2-A44H TCGA-HZ-7918 TCGA-IB-7652 TCGA-IB-7886 TCGA-LB-A7SX 
         586           28          476         1975          127 

$`11P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
         851          488           17          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 
        1991            8         1968          181          164           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                28                  1 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1975               1991 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             476.0              173.5 
[1] "28.0 - 1975.0 (476.0)" "1.0 - 1991.0 (173.5)" 
[1] "hr=" "1.6"
D54V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  11P LOSS MUTATED          0        0         1         5         0        0
  11P LOSS WILD-TYPE        2        4        13        56         2        3
D54V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                1                 13
  STAGE IIB                5                 56
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     6
  11P LOSS WILD-TYPE     8    72
D54V4, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4                6                 72
[1] 2 2
[1] FALSE
D54V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    1  5
  11P LOSS WILD-TYPE 20 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    5
  11P LOSS WILD-TYPE   20   59
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                1                 20
  1                5                 59
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED    5  0  1
  11P LOSS WILD-TYPE 36  3 41
D54V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                5                 36
  M1                0                  3
  MX                1                 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"
D54V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    3  3
  11P LOSS WILD-TYPE 41 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    3
  11P LOSS WILD-TYPE   41   39
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                3                 41
  MALE                  3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11P LOSS MUTATED                                     6
  11P LOSS WILD-TYPE                                  68
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11P LOSS MUTATED                                       0
  11P LOSS WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11P LOSS MUTATED                                                  0
  11P LOSS WILD-TYPE                                                3
D54V8, multiclass
                                                  clus
vv                                                 11P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 11P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              68
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D54V9, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7887         TCGA-IB-7891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-OE-A75W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED    3  3  0  0
  11P LOSS WILD-TYPE 52 22  1  2
D54V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                3                 52
  R1                3                 22
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         1     4
  11P LOSS WILD-TYPE     1                         5    70
D54V12, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    4                 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"

Clustering(55) Variable = 11Q LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    7  0
  11Q LOSS WILD-TYPE 43 11
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 54 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                 11 
$`11Q LOSS MUTATED`
TCGA-F2-A44H TCGA-FB-A78T TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A77P TCGA-LB-A7SX 
         586            1          240           28           13          127 
TCGA-US-A776 
         844 

$`11Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7922 
         166          392          233          396           20            4 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q 
          23           29          194           46           11           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
         347         1951         1989          476          851         1975 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         488           17          522          329          300         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 
           8         1968          181          164           35          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         110          247          416         1955          160         1834 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  3 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
               844               1991 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             127.0              187.5 
[1] "1.0 - 844.0 (127.0)"  "3.0 - 1991.0 (187.5)"
[1] "hr="     "7.7e+07"
D55V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  11Q LOSS MUTATED          0        0         2         6         0        0
  11Q LOSS WILD-TYPE        2        4        12        55         2        3
D55V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                2                 12
  STAGE IIB                6                 55
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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       0     8
  11Q LOSS WILD-TYPE     8    70
D55V4, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4                8                 70
[1] 2 2
[1] FALSE
D55V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    2  6
  11Q LOSS WILD-TYPE 19 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    6
  11Q LOSS WILD-TYPE   19   58
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                2                 19
  1                6                 58
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED    4  0  4
  11Q LOSS WILD-TYPE 37  3 38
D55V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                4                 37
  M1                0                  3
  MX                4                 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"
D55V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3  5
  11Q LOSS WILD-TYPE 41 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    5
  11Q LOSS WILD-TYPE   41   37
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                3                 41
  MALE                  5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  11Q LOSS MUTATED                                     5
  11Q LOSS WILD-TYPE                                  69
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  11Q LOSS MUTATED                                       2
  11Q LOSS WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  11Q LOSS MUTATED                                                  1
  11Q LOSS WILD-TYPE                                                2
D55V8, multiclass
                                                  clus
vv                                                 11Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 11Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D55V9, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-H6-8124         TCGA-H6-A45N 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-IB-7644 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7885 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-7886         TCGA-IB-7887         TCGA-IB-7891 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-OE-A75W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED    5  2  0  1
  11Q LOSS WILD-TYPE 50 23  1  1
D55V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                5                 50
  R1                2                 23
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       0                         1     7
  11Q LOSS WILD-TYPE     2                         5    67
D55V12, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    7                 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"

Clustering(56) Variable = 12P LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    5  1
  12P LOSS WILD-TYPE 45 10
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                 55 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 10 
$`12P LOSS MUTATED`
TCGA-FB-A7DR TCGA-HZ-7919 TCGA-HZ-8636 TCGA-IB-7886 TCGA-IB-A5SP TCGA-LB-A7SX 
         166           20            5         1975          300          127 

$`12P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS 
         851          488           17          522          329         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 
           8         1968          181          164           35          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         110          247          416         1955          844          160 
TCGA-YY-A8LH 
        1834 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                  1 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1975               1991 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             146.5              194.0 
[1] "5.0 - 1975.0 (146.5)" "1.0 - 1991.0 (194.0)"
[1] "hr=" "1.4"
D56V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  12P LOSS MUTATED          0        0         3         4         0        1
  12P LOSS WILD-TYPE        2        4        11        57         2        2
D56V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                3                 11
  STAGE IIB                4                 57
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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     8
  12P LOSS WILD-TYPE     8    70
D56V4, multiclass
       clus
vv      12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4                8                 70
[1] 2 2
[1] FALSE
D56V5, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3  4
  12P LOSS WILD-TYPE 18 60
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    4
  12P LOSS WILD-TYPE   18   60
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                3                 18
  1                4                 60
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12P LOSS MUTATED    6  1  1
  12P LOSS WILD-TYPE 35  2 41
D56V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                6                 35
  M1                1                  2
  MX                1                 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"
D56V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED    3  5
  12P LOSS WILD-TYPE 41 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    5
  12P LOSS WILD-TYPE   41   37
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                3                 41
  MALE                  5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12P LOSS MUTATED                                     7
  12P LOSS WILD-TYPE                                  67
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12P LOSS MUTATED                                       0
  12P LOSS WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12P LOSS MUTATED                                                  1
  12P LOSS WILD-TYPE                                                2
D56V8, multiclass
                                                  clus
vv                                                 12P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 12P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              67
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D56V9, continuous
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED    3  5  0  0
  12P LOSS WILD-TYPE 52 20  1  2
D56V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0                3                 52
  R1                5                 20
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       1                         2     5
  12P LOSS WILD-TYPE     1                         4    69
D56V12, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                    5                 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"

Clustering(57) Variable = 12Q LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    5  1
  12Q LOSS WILD-TYPE 45 10
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 6                 55 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 10 
$`12Q LOSS MUTATED`
TCGA-FB-A7DR TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7886 TCGA-LB-A7SX 
         166            5           11          476         1975          127 

$`12Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           3           91           23           29          194           46 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 
          13           33          347         1951         1989          851 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         488           17          522          329          300         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 
           8         1968          181          164           35          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         110          247          416         1955          844          160 
TCGA-YY-A8LH 
        1834 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 5                  1 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              1975               1991 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             146.5              194.0 
[1] "5.0 - 1975.0 (146.5)" "1.0 - 1991.0 (194.0)"
[1] "hr=" "1.5"
D57V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  12Q LOSS MUTATED          0        1         2         6         0        1
  12Q LOSS WILD-TYPE        2        3        12        55         2        2
D57V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 1                  3
  STAGE IIA                2                 12
  STAGE IIB                6                 55
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       2     8
  12Q LOSS WILD-TYPE     6    70
D57V4, multiclass
       clus
vv      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1+T2                2                  6
  T3+T4                8                 70
[1] 2 2
[1] FALSE
D57V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    3  6
  12Q LOSS WILD-TYPE 18 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    6
  12Q LOSS WILD-TYPE   18   58
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                3                 18
  1                6                 58
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  12Q LOSS MUTATED    7  1  2
  12Q LOSS WILD-TYPE 34  2 40
D57V6, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                7                 34
  M1                1                  2
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    5  5
  12Q LOSS WILD-TYPE 39 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      5    5
  12Q LOSS WILD-TYPE   39   37
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                5                 39
  MALE                  5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  12Q LOSS MUTATED                                     9
  12Q LOSS WILD-TYPE                                  65
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  12Q LOSS MUTATED                                       0
  12Q LOSS WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  12Q LOSS MUTATED                                                  1
  12Q LOSS WILD-TYPE                                                2
D57V8, multiclass
                                                  clus
vv                                                 12Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 12Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D57V9, continuous
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS MUTATED    5  5  0  0
  12Q LOSS WILD-TYPE 50 20  1  2
D57V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                5                 50
  R1                5                 20
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       2                         2     5
  12Q LOSS WILD-TYPE     0                         4    69
D57V12, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    2                  0
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                    5                 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"

Clustering(58) Variable = 13Q LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    9  2
  13Q LOSS WILD-TYPE 41  9
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                11                 50 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                  9 
$`13Q LOSS MUTATED`
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-IB-7885 TCGA-IB-7886 
         240           28            5           46          851         1975 
TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
         522         1991          181          164          127 

$`13Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P 
          91           23           29          194           11           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 
          33          347         1951         1989          476          488 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG TCGA-LB-A8F3 
          17          329          300            8         1968           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                  1 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1991               1989 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               181                180 
[1] "5.0 - 1991.0 (181.0)" "1.0 - 1989.0 (180.0)"
[1] "hr=" "5.3"
D58V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  13Q LOSS MUTATED          0        0         0        12         0        1
  13Q LOSS WILD-TYPE        2        4        14        49         2        2
D58V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                0                 14
  STAGE IIB               12                 49
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       0    13
  13Q LOSS WILD-TYPE     8    65
D58V4, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4               13                 65
[1] 2 2
[1] FALSE
D58V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    1 12
  13Q LOSS WILD-TYPE 20 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1   12
  13Q LOSS WILD-TYPE   20   52
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0                1                 20
  1               12                 52
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED    8  1  4
  13Q LOSS WILD-TYPE 33  2 38
D58V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                8                 33
  M1                1                  2
  MX                4                 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"
D58V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    5  8
  13Q LOSS WILD-TYPE 39 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      5    8
  13Q LOSS WILD-TYPE   39   34
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                5                 39
  MALE                  8                 34
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  13Q LOSS MUTATED                                    11
  13Q LOSS WILD-TYPE                                  63
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  13Q LOSS MUTATED                                       2
  13Q LOSS WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  13Q LOSS MUTATED                                                  0
  13Q LOSS WILD-TYPE                                                3
D58V8, multiclass
                                                  clus
vv                                                 13Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 13Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              63
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D58V9, continuous
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED    5  6  1  1
  13Q LOSS WILD-TYPE 50 19  0  1
D58V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                5                 50
  R1                6                 19
  R2                1                  0
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         2    11
  13Q LOSS WILD-TYPE     2                         4    63
D58V12, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   11                 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"

Clustering(59) Variable = 14Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    4  0
  14Q LOSS WILD-TYPE 46 11
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 4                 57 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 0                 11 
$`14Q LOSS MUTATED`
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-LB-A7SX TCGA-LB-A8F3 
         449          166          127           35 

$`14Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
           1          392          233          396          240           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         164          584          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                35                  1 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               449               1991 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             146.5              194.0 
[1] "35.0 - 449.0 (146.5)" "1.0 - 1991.0 (194.0)"
[1] "hr="     "2.6e+07"
D59V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  14Q LOSS MUTATED          0        1         2         3         0        0
  14Q LOSS WILD-TYPE        2        3        12        58         2        3
D59V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 1                  3
  STAGE IIA                2                 12
  STAGE IIB                3                 58
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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     5
  14Q LOSS WILD-TYPE     7    73
D59V4, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1+T2                1                  7
  T3+T4                5                 73
[1] 2 2
[1] FALSE
D59V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    2  3
  14Q LOSS WILD-TYPE 19 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      2    3
  14Q LOSS WILD-TYPE   19   61
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0                2                 19
  1                3                 61
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED    3  0  3
  14Q LOSS WILD-TYPE 38  3 39
D59V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                3                 38
  M1                0                  3
  MX                3                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    3  3
  14Q LOSS WILD-TYPE 41 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3    3
  14Q LOSS WILD-TYPE   41   39
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                3                 41
  MALE                  3                 39
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  14Q LOSS MUTATED                                     5
  14Q LOSS WILD-TYPE                                  69
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  14Q LOSS MUTATED                                       0
  14Q LOSS WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  14Q LOSS MUTATED                                                  1
  14Q LOSS WILD-TYPE                                                2
D59V8, multiclass
                                                  clus
vv                                                 14Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             5
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 14Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              69
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D59V9, continuous
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED    3  3  0  0
  14Q LOSS WILD-TYPE 52 22  1  2
D59V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0                3                 52
  R1                3                 22
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       1                         2     3
  14Q LOSS WILD-TYPE     1                         4    71
D59V12, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                    3                 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"

Clustering(60) Variable = 15Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    9  1
  15Q LOSS WILD-TYPE 41 10
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                 51 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 10 
$`15Q LOSS MUTATED`
TCGA-FB-A545 TCGA-FB-A7DR TCGA-HZ-A4BK TCGA-IB-7644 TCGA-IB-8127 TCGA-IB-A5SP 
         385          166           46          347          522          300 
TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-US-A776 
         181          127          584          844 

$`15Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
           1          392          233          396          240           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O 
           5           91           23           29          194           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          13           33         1951         1989          476          851 
TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
        1975          488           17          329         1991            8 
TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
        1968          164           35          110          247          416 
TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          160         1834 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                46                  1 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
               844               1991 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             323.5              160.0 
[1] "46.0 - 844.0 (323.5)" "1.0 - 1991.0 (160.0)"
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  15Q LOSS MUTATED          0        1         5         6         0        1
  15Q LOSS WILD-TYPE        2        3         9        55         2        2
D60V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 1                  3
  STAGE IIA                5                  9
  STAGE IIB                6                 55
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       1    12
  15Q LOSS WILD-TYPE     7    66
D60V4, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1+T2                1                  7
  T3+T4               12                 66
[1] 2 2
[1] FALSE
D60V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    5  7
  15Q LOSS WILD-TYPE 16 57
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5    7
  15Q LOSS WILD-TYPE   16   57
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                5                 16
  1                7                 57
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED    8  1  4
  15Q LOSS WILD-TYPE 33  2 38
D60V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                8                 33
  M1                1                  2
  MX                4                 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"
D60V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    4  9
  15Q LOSS WILD-TYPE 40 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      4    9
  15Q LOSS WILD-TYPE   40   33
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                4                 40
  MALE                  9                 33
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  15Q LOSS MUTATED                                     9
  15Q LOSS WILD-TYPE                                  65
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  15Q LOSS MUTATED                                       1
  15Q LOSS WILD-TYPE                                     7
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  15Q LOSS MUTATED                                                  2
  15Q LOSS WILD-TYPE                                                1
D60V8, multiclass
                                                  clus
vv                                                 15Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                2
                                                  clus
vv                                                 15Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  1
[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"
D60V9, continuous
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED    6  6  0  0
  15Q LOSS WILD-TYPE 49 19  1  2
D60V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                6                 49
  R1                6                 19
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       1                         1     9
  15Q LOSS WILD-TYPE     1                         5    65
D60V12, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    9                 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"

Clustering(61) Variable = 16P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    2  0
  16P LOSS WILD-TYPE 48 11
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 59 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 0                 11 
$`16P LOSS MUTATED`
TCGA-FB-A545 TCGA-HZ-A4BK 
         385           46 

$`16P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                46                  1 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
               385               1991 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             215.5              181.0 
[1] "46.0 - 385.0 (215.5)" "1.0 - 1991.0 (181.0)"
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
D61V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  16P LOSS MUTATED          0        0         0         3         0        0
  16P LOSS WILD-TYPE        2        4        14        58         2        3
D61V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                0                 14
  STAGE IIB                3                 58
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  16P LOSS MUTATED       0     3
  16P LOSS WILD-TYPE     8    75
D61V4, multiclass
       clus
vv      16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4                3                 75
[1] 2 2
[1] FALSE
D61V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    0  3
  16P LOSS WILD-TYPE 21 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    3
  16P LOSS WILD-TYPE   21   61
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                0                 21
  1                3                 61
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED    1  0  2
  16P LOSS WILD-TYPE 40  3 40
D61V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                1                 40
  M1                0                  3
  MX                2                 40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  2
  16P LOSS WILD-TYPE 43 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    2
  16P LOSS WILD-TYPE   43   40
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 43
  MALE                  2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  16P LOSS MUTATED                                     2
  16P LOSS WILD-TYPE                                  72
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  16P LOSS MUTATED                                       1
  16P LOSS WILD-TYPE                                     7
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  16P LOSS MUTATED                                                  0
  16P LOSS WILD-TYPE                                                3
D61V8, multiclass
                                                  clus
vv                                                 16P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 16P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              72
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D61V9, continuous
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED    1  1  0  0
  16P LOSS WILD-TYPE 54 24  1  2
D61V10, multiclass
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 81 
        TCGA-F2-6879         TCGA-F2-6880         TCGA-F2-7273 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F2-7276         TCGA-F2-A44G         TCGA-F2-A44H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FB-A4P5         TCGA-FB-A5VM         TCGA-FB-A78T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FB-A7DR         TCGA-FZ-5920         TCGA-FZ-5922 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FZ-5923         TCGA-H6-8124         TCGA-H8-A6C1 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-7289         TCGA-HZ-7918         TCGA-HZ-7919 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-7920         TCGA-HZ-7922         TCGA-HZ-7923 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-7924         TCGA-HZ-7925         TCGA-HZ-7926 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-8001         TCGA-HZ-8002         TCGA-HZ-8003 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-8005         TCGA-HZ-8315         TCGA-HZ-8317 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-8519         TCGA-HZ-8636         TCGA-HZ-8637 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-8638         TCGA-HZ-A49G         TCGA-HZ-A49H 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-A49I         TCGA-HZ-A4BH         TCGA-HZ-A77O 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HZ-A77P         TCGA-HZ-A77Q         TCGA-IB-7644 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7645         TCGA-IB-7646         TCGA-IB-7647 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7652 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7888         TCGA-IB-7889         TCGA-IB-7890 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-7893         TCGA-IB-7897 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-A5SP         TCGA-IB-A5SQ         TCGA-IB-A5SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IB-A5ST         TCGA-IB-A6UG         TCGA-IB-A7M4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-L1-A7W4         TCGA-LB-A7SX         TCGA-LB-A8F3 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-M8-A5N4         TCGA-OE-A75W         TCGA-Q3-A5QY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-US-A776 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-US-A779         TCGA-US-A77E         TCGA-US-A77G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-US-A77J         TCGA-YB-A89D         TCGA-YY-A8LH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D61V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     3
  16P LOSS WILD-TYPE     2                         6    71
D61V12, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    3                 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"

Clustering(62) Variable = 17P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   20  4
  17P LOSS WILD-TYPE 30  7
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                24                 37 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 4                  7 
$`17P LOSS MUTATED`
TCGA-F2-A44G TCGA-FB-A545 TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 
         153          385            1          396          240           20 
TCGA-HZ-7922 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
           4           28            5          194           46           11 
TCGA-IB-7644 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS 
         347          476         1975          522          300         1991 
TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-YY-A8LH 
         181          127          584          110          247         1834 

$`17P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR 
         295          360          586            4          449          166 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
         392          233           28            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 
           8           19           24           21           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7649 
          91           23           29           13           33         1951 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST 
        1989          851          488           17          329            8 
TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
        1968          164           35          416         1955          844 
TCGA-YB-A89D 
         160 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  3 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              1991               1989 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               217                164 
[1] "1.0 - 1991.0 (217.0)" "3.0 - 1989.0 (164.0)"
[1] "hr=" "1.9"
D62V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  17P LOSS MUTATED          0        0         6        24         0        2
  17P LOSS WILD-TYPE        2        4         8        37         2        1
D62V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                6                  8
  STAGE IIB               24                 37
  STAGE III                0                  2
  STAGE IV                 2                  1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  17P LOSS MUTATED       1    31
  17P LOSS WILD-TYPE     7    47
D62V4, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1+T2                1                  7
  T3+T4               31                 47
[1] 2 2
[1] FALSE
D62V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    7 25
  17P LOSS WILD-TYPE 14 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      7   25
  17P LOSS WILD-TYPE   14   39
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                7                 14
  1               25                 39
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   15  2 15
  17P LOSS WILD-TYPE 26  1 27
D62V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               15                 26
  M1                2                  1
  MX               15                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   17 15
  17P LOSS WILD-TYPE 27 27
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     17   15
  17P LOSS WILD-TYPE   27   27
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               17                 27
  MALE                 15                 27
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17P LOSS MUTATED                                    28
  17P LOSS WILD-TYPE                                  46
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17P LOSS MUTATED                                       3
  17P LOSS WILD-TYPE                                     5
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  17P LOSS MUTATED                                                  0
  17P LOSS WILD-TYPE                                                3
D62V8, multiclass
                                                  clus
vv                                                 17P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            28
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 17P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              46
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D62V9, continuous
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   14 15  0  1
  17P LOSS WILD-TYPE 41 10  1  1
D62V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               14                 41
  R1               15                 10
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         2    28
  17P LOSS WILD-TYPE     1                         4    46
D62V12, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   28                 46
[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"

Clustering(63) Variable = 17Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    8  1
  17Q LOSS WILD-TYPE 42 10
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 9                 52 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                 10 
$`17Q LOSS MUTATED`
TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-IB-7652 
         240            4            5          194           46          476 
TCGA-IB-7886 TCGA-IB-A5SP TCGA-YY-A8LH 
        1975          300         1834 

$`17Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
          91           23           29           11           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
         347         1951         1989          851          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         522          329         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         416         1955          844          160 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 4                  1 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              1975               1991 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
               240                165 
[1] "4.0 - 1975.0 (240.0)" "1.0 - 1991.0 (165.0)"
[1] "hr=" "1.9"
D63V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  17Q LOSS MUTATED          0        0         2         9         0        1
  17Q LOSS WILD-TYPE        2        4        12        52         2        2
D63V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                2                 12
  STAGE IIB                9                 52
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  17Q LOSS MUTATED       0    12
  17Q LOSS WILD-TYPE     8    66
D63V4, multiclass
       clus
vv      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4               12                 66
[1] 2 2
[1] FALSE
D63V5, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    3  9
  17Q LOSS WILD-TYPE 18 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      3    9
  17Q LOSS WILD-TYPE   18   55
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0                3                 18
  1                9                 55
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED    6  1  5
  17Q LOSS WILD-TYPE 35  2 37
D63V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                6                 35
  M1                1                  2
  MX                5                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED    4  8
  17Q LOSS WILD-TYPE 40 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4    8
  17Q LOSS WILD-TYPE   40   34
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                4                 40
  MALE                  8                 34
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  17Q LOSS MUTATED                                     9
  17Q LOSS WILD-TYPE                                  65
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  17Q LOSS MUTATED                                       2
  17Q LOSS WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  17Q LOSS MUTATED                                                  0
  17Q LOSS WILD-TYPE                                                3
D63V8, multiclass
                                                  clus
vv                                                 17Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 17Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D63V9, continuous
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7887         TCGA-IB-7891 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IB-8126         TCGA-IB-8127         TCGA-IB-A5SS 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-IB-A6UG         TCGA-IB-A7M4         TCGA-LB-A7SX 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS MUTATED    5  6  0  1
  17Q LOSS WILD-TYPE 50 19  1  1
D63V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                5                 50
  R1                6                 19
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       1                         1    10
  17Q LOSS WILD-TYPE     1                         5    64
D63V12, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   10                 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"

Clustering(64) Variable = 18P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   18  5
  18P LOSS WILD-TYPE 32  6
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                23                 38 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 5                  6 
$`18P LOSS MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N 
         153          586          449            1          166          233 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK 
           8           19           28           23          194           46 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8126 
          13           33          347          851         1975           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-M8-A5N4 TCGA-OE-A75W 
         329          300         1991          584          110 

$`18P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-FB-A545 TCGA-H6-8124 TCGA-H8-A6C1 
         295          360            4          385          392          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
         361           24           21           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A77O TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          91           29           11         1951         1989          476 
TCGA-IB-7891 TCGA-IB-8127 TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 
         488          522            8         1968          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         127           35          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  3 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              1991               1989 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             166.0              210.5 
[1] "1.0 - 1991.0 (166.0)" "3.0 - 1989.0 (210.5)"
[1] "hr=" "1"  
D64V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  18P LOSS MUTATED          0        3         6        17         2        1
  18P LOSS WILD-TYPE        2        1         8        44         0        2
D64V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 3                  1
  STAGE IIA                6                  8
  STAGE IIB               17                 44
  STAGE III                2                  0
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       4    25
  18P LOSS WILD-TYPE     4    53
D64V4, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1+T2                4                  4
  T3+T4               25                 53
[1] 2 2
[1] FALSE
D64V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    9 19
  18P LOSS WILD-TYPE 12 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      9   19
  18P LOSS WILD-TYPE   12   45
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                9                 12
  1               19                 45
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED   17  1 11
  18P LOSS WILD-TYPE 24  2 31
D64V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0               17                 24
  M1                1                  2
  MX               11                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   15 14
  18P LOSS WILD-TYPE 29 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     15   14
  18P LOSS WILD-TYPE   29   28
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               15                 29
  MALE                 14                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18P LOSS MUTATED                                    24
  18P LOSS WILD-TYPE                                  50
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18P LOSS MUTATED                                       4
  18P LOSS WILD-TYPE                                     4
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18P LOSS MUTATED                                                  1
  18P LOSS WILD-TYPE                                                2
D64V8, multiclass
                                                  clus
vv                                                 18P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 18P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              50
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D64V9, continuous
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   16 11  0  1
  18P LOSS WILD-TYPE 39 14  1  1
D64V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               16                 39
  R1               11                 14
  R2                0                  1
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       1                         1    25
  18P LOSS WILD-TYPE     1                         5    49
D64V12, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   25                 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"

Clustering(65) Variable = 18Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   29  6
  18Q LOSS WILD-TYPE 21  5
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                35                 26 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 6                  5 
$`18Q LOSS MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-8124 
         153          586          385          449          166          392 
TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
         233          396           20          361            8           19 
TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          28            5           23          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
          13           33          347         1951          476          851 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG 
          17          522          329          300         1991         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127          584          110          247 

$`18Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-FB-A78T TCGA-HZ-7289 TCGA-HZ-7918 
         295          360            4            1          240           28 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 
           4            8          369           24           21           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-IB-7651 TCGA-IB-7886 TCGA-IB-7891 
           3           91           29         1989         1975          488 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
           8          181           35          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 5                  1 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              1991               1989 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             233.0              125.5 
[1] "5.0 - 1991.0 (233.0)" "1.0 - 1989.0 (125.5)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  18Q LOSS MUTATED          0        3         7        31         2        3
  18Q LOSS WILD-TYPE        2        1         7        30         0        0
D65V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 3                  1
  STAGE IIA                7                  7
  STAGE IIB               31                 30
  STAGE III                2                  0
  STAGE IV                 3                  0
[1] 6 2
[1] TRUE
[1] "dimension of 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       5    41
  18Q LOSS WILD-TYPE     3    37
D65V4, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1+T2                5                  3
  T3+T4               41                 37
[1] 2 2
[1] FALSE
D65V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   11 34
  18Q LOSS WILD-TYPE 10 30
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     11   34
  18Q LOSS WILD-TYPE   10   30
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               11                 10
  1               34                 30
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED   24  3 19
  18Q LOSS WILD-TYPE 17  0 23
D65V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               24                 17
  M1                3                  0
  MX               19                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   25 21
  18Q LOSS WILD-TYPE 19 21
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     25   21
  18Q LOSS WILD-TYPE   19   21
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               25                 19
  MALE                 21                 21
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  18Q LOSS MUTATED                                    39
  18Q LOSS WILD-TYPE                                  35
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  18Q LOSS MUTATED                                       5
  18Q LOSS WILD-TYPE                                     3
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  18Q LOSS MUTATED                                                  1
  18Q LOSS WILD-TYPE                                                2
D65V8, multiclass
                                                  clus
vv                                                 18Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            39
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 18Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              35
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D65V9, continuous
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED   23 18  1  1
  18Q LOSS WILD-TYPE 32  7  0  1
D65V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0               23                 32
  R1               18                  7
  R2                1                  0
  RX                1                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       2                         2    39
  18Q LOSS WILD-TYPE     0                         4    35
D65V12, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    2                  0
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                   39                 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"

Clustering(66) Variable = 19P LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    7  1
  19P LOSS WILD-TYPE 43 10
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 8                 53 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 10 
$`19P LOSS MUTATED`
TCGA-H6-8124 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-IB-7885 TCGA-IB-A6UG TCGA-L1-A7W4 
         392            4            5          851         1968          164 
TCGA-LB-A7SX TCGA-US-A776 
         127          844 

$`19P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        1975          488           17          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
        1991            8          181           35          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         247          416         1955          160         1834 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                  1 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1968               1991 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
               278                181 
[1] "4.0 - 1968.0 (278.0)" "1.0 - 1991.0 (181.0)"
[1] "hr=" "1.5"
D66V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  19P LOSS MUTATED          0        0         1         9         0        1
  19P LOSS WILD-TYPE        2        4        13        52         2        2
D66V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                1                 13
  STAGE IIB                9                 52
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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    11
  19P LOSS WILD-TYPE     8    67
D66V4, multiclass
       clus
vv      19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4               11                 67
[1] 2 2
[1] FALSE
D66V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  9
  19P LOSS WILD-TYPE 19 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    9
  19P LOSS WILD-TYPE   19   55
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                2                 19
  1                9                 55
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19P LOSS MUTATED    5  1  5
  19P LOSS WILD-TYPE 36  2 37
D66V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                5                 36
  M1                1                  2
  MX                5                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    6  5
  19P LOSS WILD-TYPE 38 37
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      6    5
  19P LOSS WILD-TYPE   38   37
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                6                 38
  MALE                  5                 37
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19P LOSS MUTATED                                    10
  19P LOSS WILD-TYPE                                  64
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19P LOSS MUTATED                                       0
  19P LOSS WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19P LOSS MUTATED                                                  1
  19P LOSS WILD-TYPE                                                2
D66V8, multiclass
                                                  clus
vv                                                 19P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 19P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              64
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D66V9, continuous
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED    5  5  1  0
  19P LOSS WILD-TYPE 50 20  0  2
D66V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                5                 50
  R1                5                 20
  R2                1                  0
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         1    10
  19P LOSS WILD-TYPE     2                         5    64
D66V12, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   10                 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"

Clustering(67) Variable = 19Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    5  0
  19Q LOSS WILD-TYPE 45 11
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                 56 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 0                 11 
$`19Q LOSS MUTATED`
TCGA-H6-8124 TCGA-HZ-8636 TCGA-IB-7885 TCGA-L1-A7W4 TCGA-US-A776 
         392            5          851          164          844 

$`19Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           3           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         476         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-LB-A7SX 
         300         1991            8         1968          181          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
          35          584          110          247          416         1955 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 5                  1 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
               851               1991 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             392.0              173.5 
[1] "5.0 - 851.0 (392.0)"  "1.0 - 1991.0 (173.5)"
[1] "hr="   "8e+07"
D67V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  19Q LOSS MUTATED          0        0         1         6         0        1
  19Q LOSS WILD-TYPE        2        4        13        55         2        2
D67V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                1                 13
  STAGE IIB                6                 55
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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     8
  19Q LOSS WILD-TYPE     8    70
D67V4, multiclass
       clus
vv      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4                8                 70
[1] 2 2
[1] FALSE
D67V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  6
  19Q LOSS WILD-TYPE 19 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    6
  19Q LOSS WILD-TYPE   19   58
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                2                 19
  1                6                 58
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  19Q LOSS MUTATED    4  1  3
  19Q LOSS WILD-TYPE 37  2 39
D67V6, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                4                 37
  M1                1                  2
  MX                3                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    4  4
  19Q LOSS WILD-TYPE 40 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      4    4
  19Q LOSS WILD-TYPE   40   38
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                4                 40
  MALE                  4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  19Q LOSS MUTATED                                     7
  19Q LOSS WILD-TYPE                                  67
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  19Q LOSS MUTATED                                       0
  19Q LOSS WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  19Q LOSS MUTATED                                                  1
  19Q LOSS WILD-TYPE                                                2
D67V8, multiclass
                                                  clus
vv                                                 19Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 19Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              67
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D67V9, continuous
[1] "Remove cluster labels:" "19Q LOSS MUTATED"      
clus
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 24 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-A45N 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-H8-A6C1         TCGA-HZ-A77Q         TCGA-IB-7644 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IB-7649         TCGA-IB-7651         TCGA-IB-7886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IB-7887         TCGA-IB-7891         TCGA-IB-8126 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IB-8127         TCGA-IB-A5SS         TCGA-IB-A6UG 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-IB-A7M4         TCGA-LB-A7SX         TCGA-OE-A75W 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-S4-A8RP         TCGA-US-A774         TCGA-YY-A8LH 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  19Q LOSS MUTATED    4  3  1  0
  19Q LOSS WILD-TYPE 51 22  0  2
D67V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                4                 51
  R1                3                 22
  R2                1                  0
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         0     8
  19Q LOSS WILD-TYPE     2                         6    66
D67V12, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                0                  6
  WHITE                                    8                 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"

Clustering(68) Variable = 20P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    6  0
  20P LOSS WILD-TYPE 44 11
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 6                 55 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 0                 11 
$`20P LOSS MUTATED`
TCGA-FB-A78T TCGA-HZ-A49G TCGA-HZ-A4BK TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-M8-A5N4 
           1           23           46          181          127          584 

$`20P LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O 
           3            5           91           29          194           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A8F3 
         300         1991            8         1968          164           35 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         110          247          416         1955          844          160 
TCGA-YY-A8LH 
        1834 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  3 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               584               1991 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              86.5              233.0 
[1] "1.0 - 584.0 (86.5)"   "3.0 - 1991.0 (233.0)"
[1] "hr="     "2.7e+07"
D68V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  20P LOSS MUTATED          0        0         1         8         0        0
  20P LOSS WILD-TYPE        2        4        13        53         2        3
D68V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                1                 13
  STAGE IIB                8                 53
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1+T2 T3+T4
  20P LOSS MUTATED       1     8
  20P LOSS WILD-TYPE     7    70
D68V4, multiclass
       clus
vv      20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1+T2                1                  7
  T3+T4                8                 70
[1] 2 2
[1] FALSE
D68V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    1  8
  20P LOSS WILD-TYPE 20 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    8
  20P LOSS WILD-TYPE   20   56
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                1                 20
  1                8                 56
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20P LOSS MUTATED    4  0  5
  20P LOSS WILD-TYPE 37  3 37
D68V6, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                4                 37
  M1                0                  3
  MX                5                 37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    5  4
  20P LOSS WILD-TYPE 39 38
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      5    4
  20P LOSS WILD-TYPE   39   38
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                5                 39
  MALE                  4                 38
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20P LOSS MUTATED                                     8
  20P LOSS WILD-TYPE                                  66
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                     7
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20P LOSS MUTATED                                                  0
  20P LOSS WILD-TYPE                                                3
D68V8, multiclass
                                                  clus
vv                                                 20P LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 20P LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D68V9, continuous
                    vv
clus                 R0 R1 R2 RX
  20P LOSS MUTATED    3  6  0  0
  20P LOSS WILD-TYPE 52 19  1  2
D68V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                3                 52
  R1                6                 19
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         2     6
  20P LOSS WILD-TYPE     2                         4    68
D68V12, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                2                  4
  WHITE                                    6                 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"

Clustering(69) Variable = 20Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    2  0
  20Q LOSS WILD-TYPE 48 11
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                 59 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 0                 11 
$`20Q LOSS MUTATED`
TCGA-LB-A7SX TCGA-US-A776 
         127          844 

$`20Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 
        1951         1989          476          851         1975          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
          17          522          329          300         1991            8 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
        1968          181          164           35          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         247          416         1955          160         1834 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
               127                  1 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
               844               1991 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             485.5              181.0 
[1] "127.0 - 844.0 (485.5)" "1.0 - 1991.0 (181.0)" 
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
D69V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  20Q LOSS MUTATED          0        0         1         2         0        0
  20Q LOSS WILD-TYPE        2        4        13        59         2        3
D69V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                1                 13
  STAGE IIB                2                 59
  STAGE III                0                  2
  STAGE IV                 0                  3
[1] 6 2
[1] TRUE
[1] "dimension of 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     3
  20Q LOSS WILD-TYPE     8    75
D69V4, multiclass
       clus
vv      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1+T2                0                  8
  T3+T4                3                 75
[1] 2 2
[1] FALSE
D69V5, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 20 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   20   62
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                1                 20
  1                2                 62
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  20Q LOSS MUTATED    0  0  3
  20Q LOSS WILD-TYPE 41  3 39
D69V6, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  M0                0                 41
  M1                0                  3
  MX                3                 39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    1  2
  20Q LOSS WILD-TYPE 43 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    2
  20Q LOSS WILD-TYPE   43   40
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                1                 43
  MALE                  2                 40
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  20Q LOSS MUTATED                                     2
  20Q LOSS WILD-TYPE                                  72
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                     8
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  20Q LOSS MUTATED                                                  1
  20Q LOSS WILD-TYPE                                                2
D69V8, multiclass
                                                  clus
vv                                                 20Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 20Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              72
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D69V9, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 25 
        TCGA-F2-6880         TCGA-FB-A4P5         TCGA-FB-A5VM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-FB-A78T         TCGA-FB-A7DR         TCGA-H6-8124 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-H6-A45N         TCGA-H8-A6C1         TCGA-HZ-A77Q 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-7644         TCGA-IB-7649         TCGA-IB-7651 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-7885         TCGA-IB-7886         TCGA-IB-7887 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-7891         TCGA-IB-8126         TCGA-IB-8127 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IB-A5SS         TCGA-IB-A6UG         TCGA-IB-A7M4 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-OE-A75W         TCGA-S4-A8RP         TCGA-US-A774 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-YY-A8LH 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 R0 R1 R2 RX
  20Q LOSS MUTATED    1  2  0  0
  20Q LOSS WILD-TYPE 54 23  1  2
D69V10, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  R0                1                 54
  R1                2                 23
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1     2
  20Q LOSS WILD-TYPE     2                         5    72
D69V12, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                    2                 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"

Clustering(70) Variable = 21Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   17  6
  21Q LOSS WILD-TYPE 33  5
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                23                 38 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                  5 
$`21Q LOSS MUTATED`
TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
         385            1          392          396           28           20 
TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q 
           4            5          194           46           11           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-A5SP 
         347         1951         1989          851         1975          300 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-OE-A75W TCGA-YB-A89D TCGA-YY-A8LH 
        1991         1968          110          160         1834 

$`21Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A7DR TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
         166          233          240            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-IB-7652 
           3           91           23           29           13          476 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A7M4 
         488           17          522          329            8          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY 
         164          127           35          584          247          416 
TCGA-US-A774 TCGA-US-A776 
        1955          844 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                  3 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1991               1955 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               300                165 
[1] "1.0 - 1991.0 (300.0)" "3.0 - 1955.0 (165.0)"
[1] "hr=" "3.5"
D70V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  21Q LOSS MUTATED          0        0         3        24         0        2
  21Q LOSS WILD-TYPE        2        4        11        37         2        1
D70V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                3                 11
  STAGE IIB               24                 37
  STAGE III                0                  2
  STAGE IV                 2                  1
[1] 6 2
[1] TRUE
[1] "dimension of 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    28
  21Q LOSS WILD-TYPE     7    50
D70V4, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1+T2                1                  7
  T3+T4               28                 50
[1] 2 2
[1] FALSE
D70V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    4 25
  21Q LOSS WILD-TYPE 17 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   25
  21Q LOSS WILD-TYPE   17   39
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0                4                 17
  1               25                 39
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED   16  2 11
  21Q LOSS WILD-TYPE 25  1 31
D70V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0               16                 25
  M1                2                  1
  MX               11                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   16 13
  21Q LOSS WILD-TYPE 28 29
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     16   13
  21Q LOSS WILD-TYPE   28   29
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               16                 28
  MALE                 13                 29
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  21Q LOSS MUTATED                                    26
  21Q LOSS WILD-TYPE                                  48
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  21Q LOSS MUTATED                                       3
  21Q LOSS WILD-TYPE                                     5
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  21Q LOSS MUTATED                                                  0
  21Q LOSS WILD-TYPE                                                3
D70V8, multiclass
                                                  clus
vv                                                 21Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            26
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                0
                                                  clus
vv                                                 21Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              48
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  3
[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"
D70V9, continuous
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   16 12  0  0
  21Q LOSS WILD-TYPE 39 13  1  2
D70V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               16                 39
  R1               12                 13
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         1    27
  21Q LOSS WILD-TYPE     2                         5    47
D70V12, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    0                  2
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   27                 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"

Clustering(71) Variable = 22Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   15  1
  22Q LOSS WILD-TYPE 35 10
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                16                 45 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 10 
$`22Q LOSS MUTATED`
TCGA-F2-A44H TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK 
         586            1          166            5          194           46 
TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7M4 
          11           33         1975          522          300          181 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-YB-A89D TCGA-YY-A8LH 
         110          247          160         1834 

$`22Q LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
         392          233          396          240           28           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
          24           21           28           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          23           29           13          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS 
         476          851          488           17          329         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
           8         1968          164          127           35          584 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         416         1955          844 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  3 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              1975               1991 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             173.5              233.0 
[1] "1.0 - 1975.0 (173.5)" "3.0 - 1991.0 (233.0)"
[1] "hr=" "2.4"
D71V2, continuous
                    vv
clus                 STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  22Q LOSS MUTATED          0        0         4        15         0        1
  22Q LOSS WILD-TYPE        2        4        10        46         2        2
D71V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE IA                 0                  2
  STAGE IB                 0                  4
  STAGE IIA                4                 10
  STAGE IIB               15                 46
  STAGE III                0                  2
  STAGE IV                 1                  2
[1] 6 2
[1] TRUE
[1] "dimension of 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       1    19
  22Q LOSS WILD-TYPE     7    59
D71V4, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1+T2                1                  7
  T3+T4               19                 59
[1] 2 2
[1] FALSE
D71V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4 15
  22Q LOSS WILD-TYPE 17 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4   15
  22Q LOSS WILD-TYPE   17   49
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0                4                 17
  1               15                 49
[1] 2 2
[1] FALSE
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED   10  1  9
  22Q LOSS WILD-TYPE 31  2 33
D71V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0               10                 31
  M1                1                  2
  MX                9                 33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    6 14
  22Q LOSS WILD-TYPE 38 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6   14
  22Q LOSS WILD-TYPE   38   28
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                6                 38
  MALE                 14                 28
[1] 2 2
[1] FALSE
                    vv
clus                 PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  22Q LOSS MUTATED                                    16
  22Q LOSS WILD-TYPE                                  58
                    vv
clus                 PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  22Q LOSS MUTATED                                       2
  22Q LOSS WILD-TYPE                                     6
                    vv
clus                 PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  22Q LOSS MUTATED                                                  1
  22Q LOSS WILD-TYPE                                                2
D71V8, multiclass
                                                  clus
vv                                                 22Q LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            16
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                           2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                1
                                                  clus
vv                                                 22Q LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                              58
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                             6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                  2
[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"
D71V9, continuous
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   12  7  0  0
  22Q LOSS WILD-TYPE 43 18  1  2
D71V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               12                 43
  R1                7                 18
  R2                0                  1
  RX                0                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         1    18
  22Q LOSS WILD-TYPE     1                         5    56
D71V12, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  1
  BLACK OR AFRICAN AMERICAN                1                  5
  WHITE                                   18                 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"

Clustering(72) Variable = XQ LOSS MUTATION ANALYSIS
D72V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    6  1
  XQ LOSS WILD-TYPE 44 10
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                7                54 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                1                10 
$`XQ LOSS MUTATED`
TCGA-H6-8124 TCGA-HZ-7918 TCGA-IB-7652 TCGA-IB-A6UG TCGA-LB-A7SX TCGA-OE-A75W 
         392           28          476         1968          127          110 
TCGA-US-A776 
         844 

$`XQ LOSS WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          233          396          240 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 
         300         1991            8          181          164           35 
TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         584          247          416         1955          160         1834 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               28                 1 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             1968              1991 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            392.0             173.5 
[1] "28.0 - 1968.0 (392.0)" "1.0 - 1991.0 (173.5)" 
[1] "hr=" "1.4"
D72V2, continuous
                   vv
clus                STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III STAGE IV
  XQ LOSS MUTATED          0        0         2         5         0        0
  XQ LOSS WILD-TYPE        2        4        12        56         2        3
D72V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE IA                0                 2
  STAGE IB                0                 4
  STAGE IIA               2                12
  STAGE IIB               5                56
  STAGE III               0                 2
  STAGE IV                0                 3
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1+T2 T3+T4
  XQ LOSS MUTATED       0     7
  XQ LOSS WILD-TYPE     8    71
D72V4, multiclass
       clus
vv      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1+T2               0                 8
  T3+T4               7                71
[1] 2 2
[1] FALSE
D72V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    2  5
  XQ LOSS WILD-TYPE 19 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2    5
  XQ LOSS WILD-TYPE   19   59
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0               2                19
  1               5                59
[1] 2 2
[1] FALSE
                   vv
clus                M0 M1 MX
  XQ LOSS MUTATED    5  0  2
  XQ LOSS WILD-TYPE 36  3 40
D72V6, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               5                36
  M1               0                 3
  MX               2                40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED    3  4
  XQ LOSS WILD-TYPE 41 38
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      3    4
  XQ LOSS WILD-TYPE   41   38
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE               3                41
  MALE                 4                38
[1] 2 2
[1] FALSE
                   vv
clus                PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  XQ LOSS MUTATED                                     6
  XQ LOSS WILD-TYPE                                  68
                   vv
clus                PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  XQ LOSS MUTATED                                       0
  XQ LOSS WILD-TYPE                                     8
                   vv
clus                PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  XQ LOSS MUTATED                                                  1
  XQ LOSS WILD-TYPE                                                2
D72V8, multiclass
                                                  clus
vv                                                 XQ LOSS MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                            6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                          0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA               1
                                                  clus
vv                                                 XQ LOSS WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                             68
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                            8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                 2
[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"
D72V9, continuous
                   vv
clus                R0 R1 R2 RX
  XQ LOSS MUTATED    4  3  0  0
  XQ LOSS WILD-TYPE 51 22  1  2
D72V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0               4                51
  R1               3                22
  R2               0                 1
  RX               0                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         1     5
  XQ LOSS WILD-TYPE     1                         5    69
D72V12, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 1
  BLACK OR AFRICAN AMERICAN               1                 5
  WHITE                                   5                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"
