[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/15080874/KICH-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/15174156/transformed.cor.cli.txt"

nPatients in clinical file=110, 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] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "RADIATION_THERAPY"                     
[14] "KARNOFSKY_PERFORMANCE_SCORE"           
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_PACK_YEARS_SMOKED"              
[18] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCH_NUMBER"                          

Input Data has 21 rows and 66 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
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.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH_NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER excluded in the analysis because there is no case of (both >= 3) in the table below"
              B226.47.0 B251.42.0
freq.values   "65"      "1"      
freq.contrast "1"       "65"     
both >= 3     "FALSE"   "FALSE"  
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 66 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, 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=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=4, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=10, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=8, 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  6
  TP53 WILD-TYPE 40  3
  TP53 MUTATED TP53 WILD-TYPE 
            22             43 
  TP53 MUTATED TP53 WILD-TYPE 
             6              3 
$`TP53 MUTATED`
TCGA-KL-8324 TCGA-KL-8329 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
      141.73        90.48        92.55        30.25        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8341 TCGA-KN-8418 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8428 
       28.11        24.79       129.37        25.91        65.19        52.27 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 
       19.33        11.21        59.08        42.35        76.90        10.68 
TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
       16.67        86.10        77.85        61.58 

$`TP53 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 
       38.07        23.84       109.22       137.06       102.81       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8340 TCGA-KL-8342 
       98.96        84.89        98.33        96.95        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8425 TCGA-KN-8426 
       31.33        23.47        87.91        25.48       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8405 
        0.99        87.12         2.50       115.00       100.87        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8415 
       79.04        92.71        80.38        87.78       103.27        57.17 
TCGA-KO-8417 
       63.95 

  TP53 MUTATED TP53 WILD-TYPE 
         10.68           0.99 
  TP53 MUTATED TP53 WILD-TYPE 
        141.73         151.96 
  TP53 MUTATED TP53 WILD-TYPE 
        55.675         73.910 
[1] "10.7 - 141.7 (55.7)" "1.0 - 152.0 (73.9)" 
[1] "hr=" "4.4"
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
D1V6, binary
                cls
clus              0  1
  TP53 MUTATED   10  1
  TP53 WILD-TYPE 24  1
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     10    1
  TP53 WILD-TYPE   24    1
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           10             24
  1            1              1
[1] 2 2
[1] FALSE
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
D1V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         1    18
  TP53 WILD-TYPE     0                         3    40
D1V11, 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"
D1V12, 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  3
  PTEN WILD-TYPE 53  6
  PTEN MUTATED PTEN WILD-TYPE 
             6             59 
  PTEN MUTATED PTEN WILD-TYPE 
             3              6 
$`PTEN MUTATED`
TCGA-KL-8323 TCGA-KL-8329 TCGA-KL-8336 TCGA-KL-8345 TCGA-KO-8408 TCGA-KO-8415 
       38.07        90.48        30.25        54.74        16.67        57.17 

$`PTEN WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8330 
      141.73        23.84       109.22       137.06       102.81       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       98.96        84.89        98.33        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       86.56        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
        3.55         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 
       10.68        74.93        79.04        92.71        80.38        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.10        77.85        61.58        63.95 

  PTEN MUTATED PTEN WILD-TYPE 
         16.67           0.99 
  PTEN MUTATED PTEN WILD-TYPE 
         90.48         151.96 
  PTEN MUTATED PTEN WILD-TYPE 
        46.405         71.410 
[1] "16.7 - 90.5 (46.4)" "1.0 - 152.0 (71.4)"
[1] "hr=" "5.5"
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
D2V6, binary
                cls
clus              0  1
  PTEN MUTATED    5  0
  PTEN WILD-TYPE 29  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      5    0
  PTEN WILD-TYPE   29    2
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            5             29
  1            0              2
[1] 2 2
[1] FALSE
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" 
D2V10, continuous
[1] "Remove cluster labels:" "PTEN MUTATED"          
clus
  PTEN MUTATED PTEN WILD-TYPE 
             2              6 
    TCGA-KL-8330     TCGA-KL-8335     TCGA-KL-8341     TCGA-KM-8639 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-KN-8433     TCGA-KO-8409 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       1                         0     5
  PTEN WILD-TYPE     1                         4    53
D2V11, 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"
D2V12, 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    4  3
  PABPC1 WILD-TYPE 52  6
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               7               58 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               3                6 
$`PABPC1 MUTATED`
TCGA-KL-8329 TCGA-KL-8341 TCGA-KL-8343 TCGA-KM-8476 TCGA-KN-8425 TCGA-KN-8427 
       90.48        24.79        71.41       123.12       104.52         0.99 
TCGA-KO-8404 
       10.68 

$`PABPC1 WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 
       30.25        44.84        86.56        28.11        66.54        73.91 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       28.80        47.24        49.97        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 
       23.47        87.91        25.48        25.91        65.19         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       77.85        57.17        61.58        63.95 

  PABPC1 MUTATED PABPC1 WILD-TYPE 
            0.99             2.50 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
          123.12           151.96 
  PABPC1 MUTATED PABPC1 WILD-TYPE 
           71.41            64.57 
[1] "1.0 - 123.1 (71.4)" "2.5 - 152.0 (64.6)"
[1] "hr=" "4.9"
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
D3V6, binary
                  cls
clus                0  1
  PABPC1 MUTATED    3  0
  PABPC1 WILD-TYPE 31  2
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PABPC1 MUTATED      3    0
  PABPC1 WILD-TYPE   31    2
   clus
vv  PABPC1 MUTATED PABPC1 WILD-TYPE
  0              3               31
  1              0                2
[1] 2 2
[1] FALSE
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" 
D3V10, continuous
[1] "Remove cluster labels:" "PABPC1 MUTATED"        
clus
  PABPC1 MUTATED PABPC1 WILD-TYPE 
               1                7 
      TCGA-KL-8330       TCGA-KL-8335       TCGA-KL-8345       TCGA-KM-8639 
"PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" "PABPC1 WILD-TYPE" 
      TCGA-KN-8433       TCGA-KO-8408       TCGA-KO-8409 
"PABPC1 WILD-TYPE" "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
D3V11, 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"
D3V12, 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  1
  URGCP WILD-TYPE 54  8
  URGCP MUTATED URGCP WILD-TYPE 
              3              62 
  URGCP MUTATED URGCP WILD-TYPE 
              1               8 
$`URGCP MUTATED`
TCGA-KL-8334 TCGA-KN-8425 TCGA-KN-8428 
       96.95       104.52        52.27 

$`URGCP WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8335 
       90.48       108.62        98.96        84.89        98.33        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19         3.55         0.99        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 
       61.58        63.95 

  URGCP MUTATED URGCP WILD-TYPE 
          52.27            0.99 
  URGCP MUTATED URGCP WILD-TYPE 
         104.52          151.96 
  URGCP MUTATED URGCP WILD-TYPE 
          96.95           64.57 
[1] "52.3 - 104.5 (97.0)" "1.0 - 152.0 (64.6)" 
[1] "hr=" "2"  
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
D4V6, binary
                 cls
clus               0  1
  URGCP MUTATED    1  0
  URGCP WILD-TYPE 33  2
[1] "tbl2"
                 cls
clus              [,1] [,2]
  URGCP MUTATED      1    0
  URGCP WILD-TYPE   33    2
   clus
vv  URGCP MUTATED URGCP WILD-TYPE
  0             1              33
  1             0               2
[1] 2 2
[1] FALSE
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" 
D4V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  URGCP MUTATED       0                         0     3
  URGCP WILD-TYPE     2                         4    55
D4V11, 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"
D4V12, 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
