[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"        "-oTKICH-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/KICH-TP/10005938/KICH-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/10685683/transformed.cor.cli.txt"

nPatients in clinical file=94, in cluster file=66, common to both=66
[1] "Reduce the number of clustering variables from 5 to 4."
[1]  4 66
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
  TP53 MUTATED TP53 WILD-TYPE 
            22             44 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
  PTEN MUTATED PTEN WILD-TYPE 
             6             60 
[1] "PABPC1 MUTATION ANALYSIS"
[1] 3
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               59 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               59 
[1] "URGCP MUTATION ANALYSIS"
[1] 3
  URGCP MUTATED URGCP WILD-TYPE 
              3              63 
  URGCP MUTATED URGCP WILD-TYPE 
              3              63 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "VITALSTATUS"                     
 [3] "DAYSTODEATH"                      "DAYSTOLASTFOLLOWUP"              
 [5] "PRIMARYSITEOFDESEASE"             "NEOPLASM.DISEASESTAGE"           
 [7] "PATHOLOGY.T.STAGE"                "PATHOLOGY.N.STAGE"               
 [9] "PATHOLOGY.M.STAGE"                "DCCUPLOADDATE"                   
[11] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
[13] "RADIATIONTHERAPY"                 "KARNOFSKYPERFORMANCESCORE"       
[15] "HISTOLOGICALTYPE"                 "NUMBERPACKYEARSSMOKED"           
[17] "YEAROFTOBACCOSMOKINGONSET"        "RACE"                            
[19] "ETHNICITY"                        "BATCHNUMBER"                     

Input Data has 20 rows and 66 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
          NA         4311           NA         3322         4169         3127 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
        2752         3304         3010         2582         2991         2949 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
        2815           NA         1364         2633           NA         2024 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
          NA         2248         1815          876         1665         1897 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
        4622          708         1366          400         1437         1520 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
        3745         1553          953         3474          714         2674 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
         775          788         1983         2211          108           18 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8430 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
          NA         2064           NA          712           76          341 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
        1125         2727          637         2304         2339           NA 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
        2279         2404         2820           NA         2445         2670 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        3141         2619         2368         1739         1873         1945 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=57,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	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=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=2,	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] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 66 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
21 25 18  2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   21    25    20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
21 25 18  2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   21    25    20 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
40  3  2 
[1] "table(vv)"
vv
   N0 N1+N2 
   40     5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
40  3  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 40

$Class1_nSamples
[1] 5

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   40     5 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=10, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   16  2
  TP53 WILD-TYPE 41  0
  TP53 MUTATED TP53 WILD-TYPE 
            18             41 
  TP53 MUTATED TP53 WILD-TYPE 
             2              0 
$`TP53 MUTATED`
TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8341 
        4311         2752         1961         1364         2633         1986 
TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
        3474          788         1983          712          341         1125 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
         637         2339         1971         2619         2368         1873 

$`TP53 WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
        3322         4169         3127         1977         3010         2582 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
        2991         2949         2024         2248         1815          876 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
        1665         1897         4622          708         1366          400 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
        1437         1520         3745         1553          953          714 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 
        2674          775         2211          108           18         2064 
TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
          76         2727         2304         2279         2404         2820 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8417 
        1997         2670         3141         1739         1945 

  TP53 MUTATED TP53 WILD-TYPE 
           341             18 
  TP53 MUTATED TP53 WILD-TYPE 
          4311           4622 
  TP53 MUTATED TP53 WILD-TYPE 
          1977           2024 
[1] "341.0 - 4311.0 (1977.0)" "18.0 - 4622.0 (2024.0)" 
[1] "hr="     "2.5e+09"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         5        8         5        4
  TP53 WILD-TYPE      16       17         9        2
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              5             16
  STAGE II             8             17
  STAGE III            5              9
  STAGE IV             4              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"
                vv
clus             T1 T2 T3+T4
  TP53 MUTATED    5  8     9
  TP53 WILD-TYPE 16 17    11
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               5             16
  T2               8             17
  T3+T4            9             11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  TP53 MUTATED   11     4
  TP53 WILD-TYPE 29     1
D1V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  N0              11             29
  N1+N2            4              1
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  TP53 MUTATED   10  1  0
  TP53 WILD-TYPE 24  1  9
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           10             24
  M1            1              1
  MX            0              9
[1] 3 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
  TP53 MUTATED    9 13
  TP53 WILD-TYPE 18 26
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      9   13
  TP53 WILD-TYPE   18   26
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            9             18
  MALE             13             26
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             10 
    TCGA-KM-8438     TCGA-KM-8439     TCGA-KM-8440     TCGA-KM-8441 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-KM-8442     TCGA-KM-8443     TCGA-KM-8476     TCGA-KM-8477 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-KM-8639     TCGA-KO-8411 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" 
D1V9, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         1    18
  TP53 WILD-TYPE     0                         3    40
D1V10, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2              0
  BLACK OR AFRICAN AMERICAN            1              3
  WHITE                               18             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"
D1V11, binary
                cls
clus              0  1
  TP53 MUTATED    1 10
  TP53 WILD-TYPE  3 22
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   10
  TP53 WILD-TYPE    3   22
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO           10             22
[1] 2 2
[1] FALSE

Clustering(2) Variable = PTEN MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    3  1
  PTEN WILD-TYPE 54  1
  PTEN MUTATED PTEN WILD-TYPE 
             4             55 
  PTEN MUTATED PTEN WILD-TYPE 
             1              1 
$`PTEN MUTATED`
TCGA-KL-8329 TCGA-KL-8345 TCGA-KO-8408 TCGA-KO-8415 
        2752         1665         1971         1739 

$`PTEN WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 
        4311         3322         4169         3127         1977         3010 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
        2582         2991         2949         1961         1364         2633 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 
        2024         1986         2248         1815          876         1897 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
        4622          708         1366          400         1437         1520 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
        3745         1553          953         3474          714         2674 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
         775          788         1983         2211          108           18 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
        2064          712           76          341         1125         2727 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
         637         2304         2339         2279         2404         2820 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
        1997         2670         3141         2619         2368         1873 
TCGA-KO-8417 
        1945 

  PTEN MUTATED PTEN WILD-TYPE 
          1665             18 
  PTEN MUTATED PTEN WILD-TYPE 
          2752           4622 
  PTEN MUTATED PTEN WILD-TYPE 
          1855           1997 
[1] "1665.0 - 2752.0 (1855.0)" "18.0 - 4622.0 (1997.0)"  
[1] "hr=" "21" 
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         2        0         3        1
  PTEN WILD-TYPE      19       25        11        5
D2V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              2             19
  STAGE II             0             25
  STAGE III            3             11
  STAGE IV             1              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3+T4
  PTEN MUTATED    2  0     4
  PTEN WILD-TYPE 19 25    16
D2V4, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  T1               2             19
  T2               0             25
  T3+T4            4             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1+N2
  PTEN MUTATED    3     2
  PTEN WILD-TYPE 37     3
D2V5, multiclass
       clus
vv      PTEN MUTATED PTEN WILD-TYPE
  N0               3             37
  N1+N2            2              3
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  PTEN MUTATED    5  0  0
  PTEN WILD-TYPE 29  2  9
D2V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  M0            5             29
  M1            0              2
  MX            0              9
[1] 3 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
  PTEN MUTATED    4  2
  PTEN WILD-TYPE 23 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      4    2
  PTEN WILD-TYPE   23   37
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            4             23
  MALE              2             37
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2              9 
    TCGA-KL-8324     TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-KM-8639     TCGA-KN-8428     TCGA-KN-8433     TCGA-KO-8409 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-KO-8416 
"PTEN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         0     5
  PTEN WILD-TYPE     1                         4    53
D2V10, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                1              1
  BLACK OR AFRICAN AMERICAN            0              4
  WHITE                                5             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                cls
clus              0  1
  PTEN MUTATED    1  1
  PTEN WILD-TYPE  3 31
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    1
  PTEN WILD-TYPE    3   31
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              3
  NOT HISPANIC OR LATINO            1             31
[1] 2 2
[1] FALSE

Clustering(3) Variable = PABPC1 MUTATION ANALYSIS
D3V1, survival
                  sevent
clus2               0  1
  PABPC1 MUTATED    5  1
  PABPC1 WILD-TYPE 52  1
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               6               53 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1                1 
$`PABPC1 MUTATED`
TCGA-KL-8329 TCGA-KL-8341 TCGA-KL-8343 TCGA-KM-8476 TCGA-KN-8425 TCGA-KN-8427 
        2752         1986         1815         3745         2211           18 

$`PABPC1 WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 
        4311         3322         4169         3127         1977         3010 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
        2582         2991         2949         1961         1364         2633 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
        2024         2248          876         1665         1897         4622 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 
         708         1366          400         1437         1520         1553 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
         953         3474          714         2674          775          788 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        1983          108         2064          712           76          341 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
        1125         2727          637         2304         2339         2279 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
        2404         2820         1971         1997         2670         3141 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        2619         2368         1739         1873         1945 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
              18               76 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
            3745             4622 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
          2098.5           1983.0 
[1] "18.0 - 3745.0 (2098.5)" "76.0 - 4622.0 (1983.0)"
[1] "hr=" "6.9"
D3V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PABPC1 MUTATED         3        0         1        3
  PABPC1 WILD-TYPE      18       25        13        3
D3V3, multiclass
           clus
vv          PABPC1 MUTATED PABPC1 WILD-TYPE
  STAGE I                3               18
  STAGE II               0               25
  STAGE III              1               13
  STAGE IV               3                3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3+T4
  PABPC1 MUTATED    3  0     4
  PABPC1 WILD-TYPE 18 25    16
D3V4, multiclass
       clus
vv      PABPC1 MUTATED PABPC1 WILD-TYPE
  T1                 3               18
  T2                 0               25
  T3+T4              4               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1+N2
  PABPC1 MUTATED    3     2
  PABPC1 WILD-TYPE 37     3
D3V5, multiclass
       clus
vv      PABPC1 MUTATED PABPC1 WILD-TYPE
  N0                 3               37
  N1+N2              2                3
[1] 2 2
[1] FALSE
                  vv
clus               M0 M1 MX
  PABPC1 MUTATED    3  0  1
  PABPC1 WILD-TYPE 31  2  8
D3V6, multiclass
    clus
vv   PABPC1 MUTATED PABPC1 WILD-TYPE
  M0              3               31
  M1              0                2
  MX              1                8
[1] 3 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
  PABPC1 MUTATED    1  6
  PABPC1 WILD-TYPE 26 33
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      1    6
  PABPC1 WILD-TYPE   26   33
        clus
vv       PABPC1 MUTATED PABPC1 WILD-TYPE
  FEMALE              1               26
  MALE                6               33
[1] 2 2
[1] FALSE
D3V8, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1               10 
      TCGA-KM-8438       TCGA-KM-8439       TCGA-KM-8440       TCGA-KM-8441 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KM-8442       TCGA-KM-8443       TCGA-KM-8477       TCGA-KM-8639 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KO-8411       TCGA-KO-8413 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
D3V9, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1               10 
      TCGA-KL-8324       TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8345 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KM-8639       TCGA-KN-8428       TCGA-KN-8433       TCGA-KO-8408 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KO-8409       TCGA-KO-8416 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PABPC1 MUTATED       2                         0     5
  PABPC1 WILD-TYPE     0                         4    53
D3V10, multiclass
                           clus
vv                          PABPC1 MUTATED PABPC1 WILD-TYPE
  ASIAN                                  2                0
  BLACK OR AFRICAN AMERICAN              0                4
  WHITE                                  5               53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
                  cls
clus                0  1
  PABPC1 MUTATED    0  3
  PABPC1 WILD-TYPE  4 29
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      0    3
  PABPC1 WILD-TYPE    4   29
                        clus
vv                       PABPC1 MUTATED PABPC1 WILD-TYPE
  HISPANIC OR LATINO                  0                4
  NOT HISPANIC OR LATINO              3               29
[1] 2 2
[1] FALSE

Clustering(4) Variable = URGCP MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  URGCP MUTATED    2  0
  URGCP WILD-TYPE 55  2
  URGCP MUTATED URGCP WILD-TYPE 
              2              57 
  URGCP MUTATED URGCP WILD-TYPE 
              0               2 
$`URGCP MUTATED`
TCGA-KL-8334 TCGA-KN-8425 
        2949         2211 

$`URGCP WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
        4311         3322         4169         3127         2752         1977 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
        3010         2582         2991         1961         1364         2633 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
        2024         1986         2248         1815          876         1665 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
        1897         4622          708         1366          400         1437 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
        1520         3745         1553          953         3474          714 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 
        2674          775          788         1983          108           18 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
        2064          712           76          341         1125         2727 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
         637         2304         2339         2279         2404         2820 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
        1971         1997         2670         3141         2619         2368 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
        1739         1873         1945 

  URGCP MUTATED URGCP WILD-TYPE 
           2211              18 
  URGCP MUTATED URGCP WILD-TYPE 
           2949            4622 
  URGCP MUTATED URGCP WILD-TYPE 
           2580            1983 
[1] "2211.0 - 2949.0 (2580.0)" "18.0 - 4622.0 (1983.0)"  
[1] "Remove cluster labels:" "URGCP MUTATED"         
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  URGCP MUTATED         1        1         1        0
  URGCP WILD-TYPE      20       24        13        6
D4V3, multiclass
           clus
vv          URGCP MUTATED URGCP WILD-TYPE
  STAGE I               1              20
  STAGE II              1              24
  STAGE III             1              13
  STAGE IV              0               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3+T4
  URGCP MUTATED    1  1     1
  URGCP WILD-TYPE 20 24    19
D4V4, multiclass
       clus
vv      URGCP MUTATED URGCP WILD-TYPE
  T1                1              20
  T2                1              24
  T3+T4             1              19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1+N2
  URGCP MUTATED    3     0
  URGCP WILD-TYPE 37     5
D4V5, multiclass
       clus
vv      URGCP MUTATED URGCP WILD-TYPE
  N0                3              37
  N1+N2             0               5
[1] 2 2
[1] FALSE
                 vv
clus              M0 M1 MX
  URGCP MUTATED    1  0  0
  URGCP WILD-TYPE 33  2  9
D4V6, multiclass
[1] "Remove cluster labels:" "URGCP MUTATED"         
clus
  URGCP MUTATED URGCP WILD-TYPE 
              1              44 
     TCGA-KL-8323      TCGA-KL-8324      TCGA-KL-8325      TCGA-KL-8326 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KL-8327      TCGA-KL-8328      TCGA-KL-8329      TCGA-KL-8330 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KL-8331      TCGA-KL-8332      TCGA-KL-8333      TCGA-KL-8335 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KL-8336      TCGA-KL-8337      TCGA-KL-8338      TCGA-KL-8339 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KL-8340      TCGA-KL-8341      TCGA-KL-8342      TCGA-KL-8343 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KL-8344      TCGA-KL-8345      TCGA-KL-8346      TCGA-KM-8438 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KM-8439      TCGA-KM-8440      TCGA-KM-8441      TCGA-KM-8442 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KM-8443      TCGA-KM-8476      TCGA-KM-8477      TCGA-KM-8639 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KN-8426      TCGA-KO-8405      TCGA-KO-8406      TCGA-KO-8407 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8410      TCGA-KO-8411      TCGA-KO-8413 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KO-8414      TCGA-KO-8415      TCGA-KO-8416      TCGA-KO-8417 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
D4V7, binary
                 cls
clus               0  1
  URGCP MUTATED    1  2
  URGCP WILD-TYPE 26 37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED      1    2
  URGCP WILD-TYPE   26   37
        clus
vv       URGCP MUTATED URGCP WILD-TYPE
  FEMALE             1              26
  MALE               2              37
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
[1] "Remove cluster labels:" "URGCP MUTATED"         
clus
  URGCP MUTATED URGCP WILD-TYPE 
              1              10 
     TCGA-KL-8324      TCGA-KL-8330      TCGA-KL-8335      TCGA-KL-8341 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KL-8345      TCGA-KM-8639      TCGA-KN-8433      TCGA-KO-8408 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" "URGCP WILD-TYPE" 
     TCGA-KO-8409      TCGA-KO-8416 
"URGCP WILD-TYPE" "URGCP WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  URGCP MUTATED       0                         0     3
  URGCP WILD-TYPE     2                         4    55
D4V10, multiclass
                           clus
vv                          URGCP MUTATED URGCP WILD-TYPE
  ASIAN                                 0               2
  BLACK OR AFRICAN AMERICAN             0               4
  WHITE                                 3              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"
D4V11, binary
                 cls
clus               0  1
  URGCP MUTATED    0  1
  URGCP WILD-TYPE  4 31
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED      0    1
  URGCP WILD-TYPE    4   31
                        clus
vv                       URGCP MUTATED URGCP WILD-TYPE
  HISPANIC OR LATINO                 0               4
  NOT HISPANIC OR LATINO             1              31
[1] 2 2
[1] FALSE
