
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.81.4078/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.81.4078/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/403963/SKCM-All_Primary.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-All_Primary/3180571/SKCM-All_Primary.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=31, in cluster file=38, common to both=23
[1] "Reduce the number of clustering variables from 20 to 15."
[1] 15 23
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            16              7 
  BRAF MUTATED BRAF WILD-TYPE 
            16              7 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             3             20 
  NRAS MUTATED NRAS WILD-TYPE 
             3             20 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             4             19 
  PRB2 MUTATED PRB2 WILD-TYPE 
             4             19 
[1] "FAM135B MUTATION ANALYSIS"
[1] 3
  FAM135B MUTATED FAM135B WILD-TYPE 
                6                17 
  FAM135B MUTATED FAM135B WILD-TYPE 
                6                17 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             4             19 
  PTEN MUTATED PTEN WILD-TYPE 
             4             19 
[1] "TLL1 MUTATION ANALYSIS"
[1] 3
  TLL1 MUTATED TLL1 WILD-TYPE 
             6             17 
  TLL1 MUTATED TLL1 WILD-TYPE 
             6             17 
[1] "ARID2 MUTATION ANALYSIS"
[1] 3
  ARID2 MUTATED ARID2 WILD-TYPE 
              4              19 
  ARID2 MUTATED ARID2 WILD-TYPE 
              4              19 
[1] "ZFHX4 MUTATION ANALYSIS"
[1] 3
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
              8              15 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
              8              15 
[1] "CFHR1 MUTATION ANALYSIS"
[1] 3
  CFHR1 MUTATED CFHR1 WILD-TYPE 
              5              18 
  CFHR1 MUTATED CFHR1 WILD-TYPE 
              5              18 
[1] "OR52M1 MUTATION ANALYSIS"
[1] 3
  OR52M1 MUTATED OR52M1 WILD-TYPE 
               3               20 
  OR52M1 MUTATED OR52M1 WILD-TYPE 
               3               20 
[1] "PPP6C MUTATION ANALYSIS"
[1] 3
  PPP6C MUTATED PPP6C WILD-TYPE 
              3              20 
  PPP6C MUTATED PPP6C WILD-TYPE 
              3              20 
[1] "RUNDC3B MUTATION ANALYSIS"
[1] 3
  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
                3                20 
  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
                3                20 
[1] "ADCYAP1R1 MUTATION ANALYSIS"
[1] 3
  ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE 
                  3                  20 
  ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE 
                  3                  20 
[1] "KCNC2 MUTATION ANALYSIS"
[1] 3
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              3              20 
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              3              20 
[1] "PIK3R1 MUTATION ANALYSIS"
[1] 3
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               4               19 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               4               19 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "DAYSTOSUBMITTEDSPECIMENDX"             
 [5] "VITALSTATUS"                           
 [6] "DCCUPLOADDATE"                         
 [7] "PRIMARYSITEOFDESEASE"                  
 [8] "GENDER"                                
 [9] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[10] "RADIATIONTHERAPY"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "TUMOR.STAGECODE"                       
[15] "NEOPLASM.DISEASESTAGE"                 
[16] "BATCHNUMBER"                           

Input Data has 16 rows and 23 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A299 
         237          118           16           13           41           NA 
TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XD TCGA-EB-A3XE TCGA-EB-A3XF 
          39           36            9           NA           NA            4 
TCGA-EB-A3Y6 TCGA-EB-A3Y7 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
          16           NA           NA           NA            1           NA 
TCGA-GN-A269 TCGA-GN-A26C TCGA-HR-A2OG TCGA-HR-A2OH TCGA-IH-A3EA 
          NA           NA           NA           NA          524 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 6:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
[3] "GENDER"                  "LYMPH.NODE.METASTASIS"  
[5] "TUMOR.STAGECODE"         "NEOPLASM.DISEASESTAGE"  
[1] "TUMOR.?STAGE" "5"           
[1] "stage2"
vv
T2A T3A T3B  T4 T4A T4B 
  1   2   1   1   1  16 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 23 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=7, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE

Clustering(1) Variable = BRAF MUTATION ANALYSIS
D1V1, survival
                sevent
clus2            0 1
  BRAF MUTATED   9 3
  BRAF WILD-TYPE 3 2
  BRAF MUTATED BRAF WILD-TYPE 
            12              5 
  BRAF MUTATED BRAF WILD-TYPE 
             3              2 
$`BRAF MUTATED`
TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF 
        0.43         1.35         1.28         1.18         0.30         0.13 
TCGA-EB-A3Y6 TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 TCGA-IH-A3EA 
        0.53        24.00         0.03        15.35         5.59        17.23 

$`BRAF WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-FR-A2OS TCGA-GN-A26C 
        7.79         3.88         0.53        12.10        26.99 

  BRAF MUTATED BRAF WILD-TYPE 
          0.03           0.53 
  BRAF MUTATED BRAF WILD-TYPE 
         24.00          26.99 
  BRAF MUTATED BRAF WILD-TYPE 
          1.23           7.79 
[1] "0.0 - 24.0 (1.2)" "0.5 - 27.0 (7.8)"
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
  "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
  "BRAF MUTATED"   "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
  "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-IH-A3EA 
  "BRAF MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
  "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
  "BRAF MUTATED"   "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
  "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-IH-A3EA 
  "BRAF MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
  "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
  "BRAF MUTATED"   "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
  "BRAF MUTATED"   "BRAF MUTATED"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-IH-A3EA 
  "BRAF MUTATED" 
[1] "hr=" "2"  
D1V2, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  BRAF MUTATED                    1            14
  BRAF WILD-TYPE                  1             5
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  BRAF MUTATED                                                                                          1
  BRAF WILD-TYPE                                                                                        1
D1V3, multiclass
                                                                                          clus
vv                                                                                         BRAF MUTATED
  DISTANT METASTASIS                                                                                  1
  PRIMARY TUMOR                                                                                      14
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
                                                                                          clus
vv                                                                                         BRAF WILD-TYPE
  DISTANT METASTASIS                                                                                    1
  PRIMARY TUMOR                                                                                         5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
D1V4, binary
                cls
clus              0  1
  BRAF MUTATED    4 12
  BRAF WILD-TYPE  3  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      4   12
  BRAF WILD-TYPE    3    4
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE            4              3
  MALE             12              4
                vv
clus             N0 N1A N2A N2B N2C N3 NX
  BRAF MUTATED    8   1   1   1   0  2  3
  BRAF WILD-TYPE  2   0   0   2   1  1  0
D1V5, multiclass
D1V6, continuous
                vv
clus             STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  BRAF MUTATED          1        1         1         8          1          2
  BRAF WILD-TYPE        0        0         0         2          0          1
                vv
clus             STAGE IIIC STAGE IV
  BRAF MUTATED            1        1
  BRAF WILD-TYPE          2        0
D1V7, multiclass

Clustering(2) Variable = NRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  NRAS MUTATED    2  0
  NRAS WILD-TYPE 10  5
  NRAS MUTATED NRAS WILD-TYPE 
             2             15 
  NRAS MUTATED NRAS WILD-TYPE 
             0              5 
$`NRAS MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A1NK 
        3.88         0.53 

$`NRAS WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        7.79         0.43         1.35         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.13         0.53        12.10        24.00         0.03        15.35 
TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        26.99        17.23 

  NRAS MUTATED NRAS WILD-TYPE 
          0.53           0.03 
  NRAS MUTATED NRAS WILD-TYPE 
          3.88          26.99 
  NRAS MUTATED NRAS WILD-TYPE 
         2.205          1.350 
[1] "0.5 - 3.9 (2.2)"  "0.0 - 27.0 (1.4)"
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"NRAS WILD-TYPE"   "NRAS MUTATED"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IH-A3EA 
"NRAS WILD-TYPE" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"NRAS WILD-TYPE"   "NRAS MUTATED"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IH-A3EA 
"NRAS WILD-TYPE" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"NRAS WILD-TYPE"   "NRAS MUTATED"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-IH-A3EA 
"NRAS WILD-TYPE" 
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             15 
    TCGA-D9-A1X3     TCGA-EB-A24C     TCGA-EB-A24D     TCGA-EB-A3HV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XB     TCGA-EB-A3XC     TCGA-EB-A3XF     TCGA-EB-A3Y6 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FR-A2OS     TCGA-FS-A1ZN     TCGA-GF-A2C7     TCGA-GN-A263 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GN-A269     TCGA-GN-A26C     TCGA-IH-A3EA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D2V2, continuous
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             19 
    TCGA-D9-A1X3     TCGA-EB-A24C     TCGA-EB-A24D     TCGA-EB-A299 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC     TCGA-EB-A3XD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XE     TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-EB-A3Y7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FR-A2OS     TCGA-FS-A1ZN     TCGA-GF-A2C7     TCGA-GN-A263 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GN-A269     TCGA-GN-A26C     TCGA-IH-A3EA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  NRAS MUTATED                    1             2
  NRAS WILD-TYPE                  1            17
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  NRAS MUTATED                                                                                          0
  NRAS WILD-TYPE                                                                                        2
D2V3, multiclass
                                                                                          clus
vv                                                                                         NRAS MUTATED
  DISTANT METASTASIS                                                                                  1
  PRIMARY TUMOR                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
                                                                                          clus
vv                                                                                         NRAS WILD-TYPE
  DISTANT METASTASIS                                                                                    1
  PRIMARY TUMOR                                                                                        17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
D2V4, binary
                cls
clus              0  1
  NRAS MUTATED    1  2
  NRAS WILD-TYPE  6 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      1    2
  NRAS WILD-TYPE    6   14
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            1              6
  MALE              2             14
                vv
clus             N0 N1A N2A N2B N2C N3 NX
  NRAS MUTATED    1   0   0   0   0  1  0
  NRAS WILD-TYPE  9   1   1   3   1  2  3
D2V5, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             20 
    TCGA-D9-A1X3     TCGA-EB-A24C     TCGA-EB-A24D     TCGA-EB-A299 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC     TCGA-EB-A3XD 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XE     TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-EB-A3Y7 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FR-A2OS     TCGA-FS-A1ZN     TCGA-GF-A2C7     TCGA-GN-A263 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GN-A269     TCGA-GN-A26C     TCGA-HR-A2OH     TCGA-IH-A3EA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
D2V6, continuous
                vv
clus             STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  NRAS MUTATED          0        0         0         1          0          0
  NRAS WILD-TYPE        1        1         1         9          1          3
                vv
clus             STAGE IIIC STAGE IV
  NRAS MUTATED            1        0
  NRAS WILD-TYPE          2        1
D2V7, multiclass
[1] "Remove cluster labels:" "NRAS MUTATED"          
clus
  NRAS MUTATED NRAS WILD-TYPE 
             2             19 
    TCGA-EB-A24C     TCGA-EB-A24D     TCGA-EB-A299     TCGA-EB-A3HV 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XB     TCGA-EB-A3XC     TCGA-EB-A3XD     TCGA-EB-A3XE 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-EB-A3Y7     TCGA-FR-A2OS 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-FS-A1ZN     TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-GN-A26C     TCGA-HR-A2OH     TCGA-IH-A3EA 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 

Clustering(3) Variable = PRB2 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  PRB2 MUTATED    2  0
  PRB2 WILD-TYPE 10  5
  PRB2 MUTATED PRB2 WILD-TYPE 
             2             15 
  PRB2 MUTATED PRB2 WILD-TYPE 
             0              5 
$`PRB2 MUTATED`
TCGA-EB-A3XB TCGA-IH-A3EA 
        1.18        17.23 

$`PRB2 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
        7.79         3.88         0.53         0.43         1.35         1.28 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 
        0.30         0.13         0.53        12.10        24.00         0.03 
TCGA-GN-A263 TCGA-GN-A269 TCGA-GN-A26C 
       15.35         5.59        26.99 

  PRB2 MUTATED PRB2 WILD-TYPE 
          1.18           0.03 
  PRB2 MUTATED PRB2 WILD-TYPE 
         17.23          26.99 
  PRB2 MUTATED PRB2 WILD-TYPE 
         9.205          1.350 
[1] "1.2 - 17.2 (9.2)" "0.0 - 27.0 (1.4)"
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" "PRB2 WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-IH-A3EA 
  "PRB2 MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" "PRB2 WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-IH-A3EA 
  "PRB2 MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED" "PRB2 WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-IH-A3EA 
  "PRB2 MUTATED" 
[1] "Remove cluster labels:" "PRB2 MUTATED"          
clus
  PRB2 MUTATED PRB2 WILD-TYPE 
             2             15 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XC     TCGA-EB-A3XF 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN     TCGA-GF-A2C7 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
D3V2, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  PRB2 MUTATED                    0             4
  PRB2 WILD-TYPE                  2            15
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PRB2 MUTATED                                                                                          0
  PRB2 WILD-TYPE                                                                                        2
D3V3, multiclass
                                                                                          clus
vv                                                                                         PRB2 MUTATED
  DISTANT METASTASIS                                                                                  0
  PRIMARY TUMOR                                                                                       4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
                                                                                          clus
vv                                                                                         PRB2 WILD-TYPE
  DISTANT METASTASIS                                                                                    2
  PRIMARY TUMOR                                                                                        15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
D3V4, binary
                cls
clus              0  1
  PRB2 MUTATED    2  2
  PRB2 WILD-TYPE  5 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      2    2
  PRB2 WILD-TYPE    5   14
        clus
vv       PRB2 MUTATED PRB2 WILD-TYPE
  FEMALE            2              5
  MALE              2             14
                vv
clus             N0 N1A N2A N2B N2C N3 NX
  PRB2 MUTATED    2   0   0   0   0  0  2
  PRB2 WILD-TYPE  8   1   1   3   1  3  1
D3V5, multiclass
D3V6, continuous
                vv
clus             STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  PRB2 MUTATED          0        1         1         2          0          0
  PRB2 WILD-TYPE        1        0         0         8          1          3
                vv
clus             STAGE IIIC STAGE IV
  PRB2 MUTATED            0        0
  PRB2 WILD-TYPE          3        1
D3V7, multiclass

Clustering(4) Variable = FAM135B MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2               0 1
  FAM135B MUTATED   4 1
  FAM135B WILD-TYPE 8 4
  FAM135B MUTATED FAM135B WILD-TYPE 
                5                12 
  FAM135B MUTATED FAM135B WILD-TYPE 
                1                 4 
$`FAM135B MUTATED`
TCGA-EB-A24D TCGA-EB-A3XB TCGA-EB-A3XC TCGA-GN-A269 TCGA-IH-A3EA 
        1.35         1.18         0.30         5.59        17.23 

$`FAM135B WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XF 
        7.79         3.88         0.53         0.43         1.28         0.13 
TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A26C 
        0.53        12.10        24.00         0.03        15.35        26.99 

  FAM135B MUTATED FAM135B WILD-TYPE 
             0.30              0.03 
  FAM135B MUTATED FAM135B WILD-TYPE 
            17.23             26.99 
  FAM135B MUTATED FAM135B WILD-TYPE 
             1.35              2.58 
[1] "0.3 - 17.2 (1.4)" "0.0 - 27.0 (2.6)"
       TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-EB-A1NK        TCGA-EB-A24C 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "FAM135B MUTATED" "FAM135B WILD-TYPE"   "FAM135B MUTATED"   "FAM135B MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-FR-A2OS        TCGA-FS-A1ZN 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" 
       TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269        TCGA-GN-A26C 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE"   "FAM135B MUTATED" "FAM135B WILD-TYPE" 
       TCGA-IH-A3EA 
  "FAM135B MUTATED" 
       TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-EB-A1NK        TCGA-EB-A24C 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "FAM135B MUTATED" "FAM135B WILD-TYPE"   "FAM135B MUTATED"   "FAM135B MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-FR-A2OS        TCGA-FS-A1ZN 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" 
       TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269        TCGA-GN-A26C 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE"   "FAM135B MUTATED" "FAM135B WILD-TYPE" 
       TCGA-IH-A3EA 
  "FAM135B MUTATED" 
       TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-EB-A1NK        TCGA-EB-A24C 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "FAM135B MUTATED" "FAM135B WILD-TYPE"   "FAM135B MUTATED"   "FAM135B MUTATED" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-FR-A2OS        TCGA-FS-A1ZN 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" "FAM135B WILD-TYPE" 
       TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269        TCGA-GN-A26C 
"FAM135B WILD-TYPE" "FAM135B WILD-TYPE"   "FAM135B MUTATED" "FAM135B WILD-TYPE" 
       TCGA-IH-A3EA 
  "FAM135B MUTATED" 
[1] "hr=" "1.5"
D4V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  FAM135B MUTATED                    0             6
  FAM135B WILD-TYPE                  2            13
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  FAM135B MUTATED                                                                                          0
  FAM135B WILD-TYPE                                                                                        2
D4V3, multiclass
                                                                                          clus
vv                                                                                         FAM135B MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
                                                                                          clus
vv                                                                                         FAM135B WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  PRIMARY TUMOR                                                                                           13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 2
D4V4, binary
                   cls
clus                 0  1
  FAM135B MUTATED    1  5
  FAM135B WILD-TYPE  6 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM135B MUTATED      1    5
  FAM135B WILD-TYPE    6   11
        clus
vv       FAM135B MUTATED FAM135B WILD-TYPE
  FEMALE               1                 6
  MALE                 5                11
                   vv
clus                N0 N1A N2A N2B N2C N3 NX
  FAM135B MUTATED    2   0   0   1   1  1  1
  FAM135B WILD-TYPE  8   1   1   2   0  2  2
D4V5, multiclass
D4V6, continuous
                   vv
clus                STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  FAM135B MUTATED          0        1         0         2          0          2
  FAM135B WILD-TYPE        1        0         1         8          1          1
                   vv
clus                STAGE IIIC STAGE IV
  FAM135B MUTATED            1        0
  FAM135B WILD-TYPE          2        1
D4V7, multiclass

Clustering(5) Variable = PTEN MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    2  1
  PTEN WILD-TYPE 10  4
  PTEN MUTATED PTEN WILD-TYPE 
             3             14 
  PTEN MUTATED PTEN WILD-TYPE 
             1              4 
$`PTEN MUTATED`
TCGA-GF-A2C7 TCGA-GN-A26C TCGA-IH-A3EA 
        0.03        26.99        17.23 

$`PTEN WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
        7.79         3.88         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN 
        1.18         0.30         0.13         0.53        12.10        24.00 
TCGA-GN-A263 TCGA-GN-A269 
       15.35         5.59 

  PTEN MUTATED PTEN WILD-TYPE 
          0.03           0.13 
  PTEN MUTATED PTEN WILD-TYPE 
         26.99          24.00 
  PTEN MUTATED PTEN WILD-TYPE 
        17.230          1.315 
[1] "0.0 - 27.0 (17.2)" "0.1 - 24.0 (1.3)" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
  "PTEN MUTATED" "PTEN WILD-TYPE" "PTEN WILD-TYPE"   "PTEN MUTATED" 
    TCGA-IH-A3EA 
  "PTEN MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
  "PTEN MUTATED" "PTEN WILD-TYPE" "PTEN WILD-TYPE"   "PTEN MUTATED" 
    TCGA-IH-A3EA 
  "PTEN MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" "PTEN WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
  "PTEN MUTATED" "PTEN WILD-TYPE" "PTEN WILD-TYPE"   "PTEN MUTATED" 
    TCGA-IH-A3EA 
  "PTEN MUTATED" 
[1] "hr="     "1.3e+09"
D5V2, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  PTEN MUTATED                    1             2
  PTEN WILD-TYPE                  1            17
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PTEN MUTATED                                                                                          1
  PTEN WILD-TYPE                                                                                        1
D5V3, multiclass
                                                                                          clus
vv                                                                                         PTEN MUTATED
  DISTANT METASTASIS                                                                                  1
  PRIMARY TUMOR                                                                                       2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            1
                                                                                          clus
vv                                                                                         PTEN WILD-TYPE
  DISTANT METASTASIS                                                                                    1
  PRIMARY TUMOR                                                                                        17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              1
D5V4, binary
                cls
clus              0  1
  PTEN MUTATED    1  3
  PTEN WILD-TYPE  6 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    3
  PTEN WILD-TYPE    6   13
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            1              6
  MALE              3             13
                vv
clus             N0 N1A N2A N2B N2C N3 NX
  PTEN MUTATED    2   0   1   1   0  0  0
  PTEN WILD-TYPE  8   1   0   2   1  3  3
D5V5, multiclass
D5V6, continuous
                vv
clus             STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  PTEN MUTATED          0        0         0         2          0          1
  PTEN WILD-TYPE        1        1         1         8          1          2
                vv
clus             STAGE IIIC STAGE IV
  PTEN MUTATED            1        0
  PTEN WILD-TYPE          2        1
D5V7, multiclass

Clustering(6) Variable = TLL1 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2            0 1
  TLL1 MUTATED   4 1
  TLL1 WILD-TYPE 8 4
  TLL1 MUTATED TLL1 WILD-TYPE 
             5             12 
  TLL1 MUTATED TLL1 WILD-TYPE 
             1              4 
$`TLL1 MUTATED`
TCGA-D9-A3Z4 TCGA-EB-A24D TCGA-EB-A3Y6 TCGA-GN-A26C TCGA-IH-A3EA 
        3.88         1.35         0.53        26.99        17.23 

$`TLL1 WILD-TYPE`
TCGA-D9-A1X3 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        7.79         0.53         0.43         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 
        0.13        12.10        24.00         0.03        15.35         5.59 

  TLL1 MUTATED TLL1 WILD-TYPE 
          0.53           0.03 
  TLL1 MUTATED TLL1 WILD-TYPE 
         26.99          24.00 
  TLL1 MUTATED TLL1 WILD-TYPE 
          3.88           1.23 
[1] "0.5 - 27.0 (3.9)" "0.0 - 24.0 (1.2)"
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"TLL1 WILD-TYPE"   "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
  "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"TLL1 WILD-TYPE"   "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"TLL1 WILD-TYPE" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE"   "TLL1 MUTATED" 
    TCGA-IH-A3EA 
  "TLL1 MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"TLL1 WILD-TYPE"   "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
  "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"TLL1 WILD-TYPE"   "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"TLL1 WILD-TYPE" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE"   "TLL1 MUTATED" 
    TCGA-IH-A3EA 
  "TLL1 MUTATED" 
    TCGA-D9-A1X3     TCGA-D9-A3Z4     TCGA-EB-A1NK     TCGA-EB-A24C 
"TLL1 WILD-TYPE"   "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-EB-A24D     TCGA-EB-A3HV     TCGA-EB-A3XB     TCGA-EB-A3XC 
  "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-EB-A3XF     TCGA-EB-A3Y6     TCGA-FR-A2OS     TCGA-FS-A1ZN 
"TLL1 WILD-TYPE"   "TLL1 MUTATED" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE" 
    TCGA-GF-A2C7     TCGA-GN-A263     TCGA-GN-A269     TCGA-GN-A26C 
"TLL1 WILD-TYPE" "TLL1 WILD-TYPE" "TLL1 WILD-TYPE"   "TLL1 MUTATED" 
    TCGA-IH-A3EA 
  "TLL1 MUTATED" 
[1] "hr="     "1.3e+09"
D6V2, continuous
                vv
clus             DISTANT METASTASIS PRIMARY TUMOR
  TLL1 MUTATED                    0             6
  TLL1 WILD-TYPE                  2            13
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  TLL1 MUTATED                                                                                          0
  TLL1 WILD-TYPE                                                                                        2
D6V3, multiclass
                                                                                          clus
vv                                                                                         TLL1 MUTATED
  DISTANT METASTASIS                                                                                  0
  PRIMARY TUMOR                                                                                       6
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
                                                                                          clus
vv                                                                                         TLL1 WILD-TYPE
  DISTANT METASTASIS                                                                                    2
  PRIMARY TUMOR                                                                                        13
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              2
D6V4, binary
                cls
clus              0  1
  TLL1 MUTATED    2  4
  TLL1 WILD-TYPE  5 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  TLL1 MUTATED      2    4
  TLL1 WILD-TYPE    5   12
        clus
vv       TLL1 MUTATED TLL1 WILD-TYPE
  FEMALE            2              5
  MALE              4             12
                vv
clus             N0 N1A N2A N2B N2C N3 NX
  TLL1 MUTATED    2   0   0   2   1  1  0
  TLL1 WILD-TYPE  8   1   1   1   0  2  3
D6V5, multiclass
D6V6, continuous
                vv
clus             STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  TLL1 MUTATED          0        0         0         2          0          2
  TLL1 WILD-TYPE        1        1         1         8          1          1
                vv
clus             STAGE IIIC STAGE IV
  TLL1 MUTATED            2        0
  TLL1 WILD-TYPE          1        1
D6V7, multiclass

Clustering(7) Variable = ARID2 MUTATION ANALYSIS
D7V1, survival
                 sevent
clus2             0 1
  ARID2 MUTATED   3 1
  ARID2 WILD-TYPE 9 4
  ARID2 MUTATED ARID2 WILD-TYPE 
              4              13 
  ARID2 MUTATED ARID2 WILD-TYPE 
              1               4 
$`ARID2 MUTATED`
TCGA-EB-A1NK TCGA-EB-A24D TCGA-GN-A26C TCGA-IH-A3EA 
        0.53         1.35        26.99        17.23 

$`ARID2 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        7.79         3.88         0.43         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.13         0.53        12.10        24.00         0.03        15.35 
TCGA-GN-A269 
        5.59 

  ARID2 MUTATED ARID2 WILD-TYPE 
           0.53            0.03 
  ARID2 MUTATED ARID2 WILD-TYPE 
          26.99           24.00 
  ARID2 MUTATED ARID2 WILD-TYPE 
           9.29            1.28 
[1] "0.5 - 27.0 (9.3)" "0.0 - 24.0 (1.3)"
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE"   "ARID2 MUTATED" "ARID2 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE"   "ARID2 MUTATED" 
     TCGA-IH-A3EA 
  "ARID2 MUTATED" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE"   "ARID2 MUTATED" "ARID2 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE"   "ARID2 MUTATED" 
     TCGA-IH-A3EA 
  "ARID2 MUTATED" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE"   "ARID2 MUTATED" "ARID2 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
  "ARID2 MUTATED" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"ARID2 WILD-TYPE" "ARID2 WILD-TYPE" "ARID2 WILD-TYPE"   "ARID2 MUTATED" 
     TCGA-IH-A3EA 
  "ARID2 MUTATED" 
[1] "hr="     "1.3e+09"
D7V2, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ARID2 MUTATED                    0             4
  ARID2 WILD-TYPE                  2            15
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ARID2 MUTATED                                                                                          0
  ARID2 WILD-TYPE                                                                                        2
D7V3, multiclass
                                                                                          clus
vv                                                                                         ARID2 MUTATED
  DISTANT METASTASIS                                                                                   0
  PRIMARY TUMOR                                                                                        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
                                                                                          clus
vv                                                                                         ARID2 WILD-TYPE
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                         15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
D7V4, binary
                 cls
clus               0  1
  ARID2 MUTATED    0  4
  ARID2 WILD-TYPE  7 12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARID2 MUTATED      0    4
  ARID2 WILD-TYPE    7   12
        clus
vv       ARID2 MUTATED ARID2 WILD-TYPE
  FEMALE             0               7
  MALE               4              12
                 vv
clus              N0 N1A N2A N2B N2C N3 NX
  ARID2 MUTATED    2   0   0   2   0  0  0
  ARID2 WILD-TYPE  8   1   1   1   1  3  3
D7V5, multiclass
D7V6, continuous
                 vv
clus              STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  ARID2 MUTATED          0        0         0         2          0          1
  ARID2 WILD-TYPE        1        1         1         8          1          2
                 vv
clus              STAGE IIIC STAGE IV
  ARID2 MUTATED            1        0
  ARID2 WILD-TYPE          2        1
D7V7, multiclass

Clustering(8) Variable = ZFHX4 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2             0 1
  ZFHX4 MUTATED   3 3
  ZFHX4 WILD-TYPE 9 2
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
              6              11 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
              3               2 
$`ZFHX4 MUTATED`
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-FS-A1ZN TCGA-GN-A263 TCGA-GN-A269 TCGA-IH-A3EA 
        1.18         0.30        24.00        15.35         5.59        17.23 

$`ZFHX4 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
        7.79         3.88         0.53         0.43         1.35         1.28 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-GF-A2C7 TCGA-GN-A26C 
        0.13         0.53        12.10         0.03        26.99 

  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
           0.30            0.03 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
          24.00           26.99 
  ZFHX4 MUTATED ZFHX4 WILD-TYPE 
          10.47            1.28 
[1] "0.3 - 24.0 (10.5)" "0.0 - 27.0 (1.3)" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED"   "ZFHX4 MUTATED" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED"   "ZFHX4 MUTATED" "ZFHX4 WILD-TYPE" 
     TCGA-IH-A3EA 
  "ZFHX4 MUTATED" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED"   "ZFHX4 MUTATED" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED"   "ZFHX4 MUTATED" "ZFHX4 WILD-TYPE" 
     TCGA-IH-A3EA 
  "ZFHX4 MUTATED" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED"   "ZFHX4 MUTATED" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE" "ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"ZFHX4 WILD-TYPE"   "ZFHX4 MUTATED"   "ZFHX4 MUTATED" "ZFHX4 WILD-TYPE" 
     TCGA-IH-A3EA 
  "ZFHX4 MUTATED" 
[1] "hr=" "2"  
D8V2, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  ZFHX4 MUTATED                    1             7
  ZFHX4 WILD-TYPE                  1            12
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ZFHX4 MUTATED                                                                                          0
  ZFHX4 WILD-TYPE                                                                                        2
D8V3, multiclass
                                                                                          clus
vv                                                                                         ZFHX4 MUTATED
  DISTANT METASTASIS                                                                                   1
  PRIMARY TUMOR                                                                                        7
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
                                                                                          clus
vv                                                                                         ZFHX4 WILD-TYPE
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                         12
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
D8V4, binary
                 cls
clus              0 1
  ZFHX4 MUTATED   1 7
  ZFHX4 WILD-TYPE 6 9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ZFHX4 MUTATED      1    7
  ZFHX4 WILD-TYPE    6    9
        clus
vv       ZFHX4 MUTATED ZFHX4 WILD-TYPE
  FEMALE             1               6
  MALE               7               9
                 vv
clus              N0 N1A N2A N2B N2C N3 NX
  ZFHX4 MUTATED    3   1   0   0   0  2  1
  ZFHX4 WILD-TYPE  7   0   1   3   1  1  2
D8V5, multiclass
D8V6, continuous
                 vv
clus              STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  ZFHX4 MUTATED          1        1         0         2          1          0
  ZFHX4 WILD-TYPE        0        0         1         8          0          3
                 vv
clus              STAGE IIIC STAGE IV
  ZFHX4 MUTATED            1        1
  ZFHX4 WILD-TYPE          2        0
D8V7, multiclass

Clustering(9) Variable = CFHR1 MUTATION ANALYSIS
D9V1, survival
                 sevent
clus2             0 1
  CFHR1 MUTATED   3 2
  CFHR1 WILD-TYPE 9 3
  CFHR1 MUTATED CFHR1 WILD-TYPE 
              5              12 
  CFHR1 MUTATED CFHR1 WILD-TYPE 
              2               3 
$`CFHR1 MUTATED`
TCGA-EB-A1NK TCGA-EB-A3XB TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        0.53         1.18         5.59        26.99        17.23 

$`CFHR1 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XC 
        7.79         3.88         0.43         1.35         1.28         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.13         0.53        12.10        24.00         0.03        15.35 

  CFHR1 MUTATED CFHR1 WILD-TYPE 
           0.53            0.03 
  CFHR1 MUTATED CFHR1 WILD-TYPE 
          26.99           24.00 
  CFHR1 MUTATED CFHR1 WILD-TYPE 
          5.590           1.315 
[1] "0.5 - 27.0 (5.6)" "0.0 - 24.0 (1.3)"
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED" "CFHR1 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED" "CFHR1 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED"   "CFHR1 MUTATED" 
     TCGA-IH-A3EA 
  "CFHR1 MUTATED" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED" "CFHR1 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED" "CFHR1 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED"   "CFHR1 MUTATED" 
     TCGA-IH-A3EA 
  "CFHR1 MUTATED" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED" "CFHR1 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED" "CFHR1 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"CFHR1 WILD-TYPE" "CFHR1 WILD-TYPE"   "CFHR1 MUTATED"   "CFHR1 MUTATED" 
     TCGA-IH-A3EA 
  "CFHR1 MUTATED" 
[1] "hr=" "2.5"
D9V2, continuous
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  CFHR1 MUTATED                    0             5
  CFHR1 WILD-TYPE                  2            14
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  CFHR1 MUTATED                                                                                          0
  CFHR1 WILD-TYPE                                                                                        2
D9V3, multiclass
                                                                                          clus
vv                                                                                         CFHR1 MUTATED
  DISTANT METASTASIS                                                                                   0
  PRIMARY TUMOR                                                                                        5
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
                                                                                          clus
vv                                                                                         CFHR1 WILD-TYPE
  DISTANT METASTASIS                                                                                     2
  PRIMARY TUMOR                                                                                         14
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
D9V4, binary
                 cls
clus               0  1
  CFHR1 MUTATED    0  5
  CFHR1 WILD-TYPE  7 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CFHR1 MUTATED      0    5
  CFHR1 WILD-TYPE    7   11
        clus
vv       CFHR1 MUTATED CFHR1 WILD-TYPE
  FEMALE             0               7
  MALE               5              11
                 vv
clus              N0 N1A N2A N2B N2C N3 NX
  CFHR1 MUTATED    2   0   0   1   0  1  1
  CFHR1 WILD-TYPE  8   1   1   2   1  2  2
D9V5, multiclass
D9V6, continuous
                 vv
clus              STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  CFHR1 MUTATED          0        1         0         2          0          0
  CFHR1 WILD-TYPE        1        0         1         8          1          3
                 vv
clus              STAGE IIIC STAGE IV
  CFHR1 MUTATED            2        0
  CFHR1 WILD-TYPE          1        1
D9V7, multiclass

Clustering(10) Variable = OR52M1 MUTATION ANALYSIS
D10V1, survival
                  sevent
clus2               0  1
  OR52M1 MUTATED    1  1
  OR52M1 WILD-TYPE 11  4
  OR52M1 MUTATED OR52M1 WILD-TYPE 
               2               15 
  OR52M1 MUTATED OR52M1 WILD-TYPE 
               1                4 
$`OR52M1 MUTATED`
TCGA-GN-A263 TCGA-IH-A3EA 
       15.35        17.23 

$`OR52M1 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
        7.79         3.88         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XC TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN 
        1.18         0.30         0.13         0.53        12.10        24.00 
TCGA-GF-A2C7 TCGA-GN-A269 TCGA-GN-A26C 
        0.03         5.59        26.99 

  OR52M1 MUTATED OR52M1 WILD-TYPE 
           15.35             0.03 
  OR52M1 MUTATED OR52M1 WILD-TYPE 
           17.23            26.99 
  OR52M1 MUTATED OR52M1 WILD-TYPE 
           16.29             1.28 
[1] "15.3 - 17.2 (16.3)" "0.0 - 27.0 (1.3)"  
      TCGA-D9-A1X3       TCGA-D9-A3Z4       TCGA-EB-A1NK       TCGA-EB-A24C 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A24D       TCGA-EB-A3HV       TCGA-EB-A3XB       TCGA-EB-A3XC 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A3XF       TCGA-EB-A3Y6       TCGA-FR-A2OS       TCGA-FS-A1ZN 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-GF-A2C7       TCGA-GN-A263       TCGA-GN-A269       TCGA-GN-A26C 
"OR52M1 WILD-TYPE"   "OR52M1 MUTATED" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-IH-A3EA 
  "OR52M1 MUTATED" 
      TCGA-D9-A1X3       TCGA-D9-A3Z4       TCGA-EB-A1NK       TCGA-EB-A24C 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A24D       TCGA-EB-A3HV       TCGA-EB-A3XB       TCGA-EB-A3XC 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A3XF       TCGA-EB-A3Y6       TCGA-FR-A2OS       TCGA-FS-A1ZN 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-GF-A2C7       TCGA-GN-A263       TCGA-GN-A269       TCGA-GN-A26C 
"OR52M1 WILD-TYPE"   "OR52M1 MUTATED" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-IH-A3EA 
  "OR52M1 MUTATED" 
      TCGA-D9-A1X3       TCGA-D9-A3Z4       TCGA-EB-A1NK       TCGA-EB-A24C 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A24D       TCGA-EB-A3HV       TCGA-EB-A3XB       TCGA-EB-A3XC 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A3XF       TCGA-EB-A3Y6       TCGA-FR-A2OS       TCGA-FS-A1ZN 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-GF-A2C7       TCGA-GN-A263       TCGA-GN-A269       TCGA-GN-A26C 
"OR52M1 WILD-TYPE"   "OR52M1 MUTATED" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-IH-A3EA 
  "OR52M1 MUTATED" 
[1] "Remove cluster labels:" "OR52M1 MUTATED"        
clus
  OR52M1 MUTATED OR52M1 WILD-TYPE 
               2               15 
      TCGA-D9-A1X3       TCGA-D9-A3Z4       TCGA-EB-A1NK       TCGA-EB-A24C 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A24D       TCGA-EB-A3HV       TCGA-EB-A3XB       TCGA-EB-A3XC 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-EB-A3XF       TCGA-EB-A3Y6       TCGA-FR-A2OS       TCGA-FS-A1ZN 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
      TCGA-GF-A2C7       TCGA-GN-A269       TCGA-GN-A26C 
"OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" "OR52M1 WILD-TYPE" 
D10V2, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  OR52M1 MUTATED                    0             3
  OR52M1 WILD-TYPE                  2            16
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  OR52M1 MUTATED                                                                                          0
  OR52M1 WILD-TYPE                                                                                        2
D10V3, multiclass
                                                                                          clus
vv                                                                                         OR52M1 MUTATED
  DISTANT METASTASIS                                                                                    0
  PRIMARY TUMOR                                                                                         3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
                                                                                          clus
vv                                                                                         OR52M1 WILD-TYPE
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                          16
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
D10V4, binary
                  cls
clus                0  1
  OR52M1 MUTATED    1  2
  OR52M1 WILD-TYPE  6 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  OR52M1 MUTATED      1    2
  OR52M1 WILD-TYPE    6   14
        clus
vv       OR52M1 MUTATED OR52M1 WILD-TYPE
  FEMALE              1                6
  MALE                2               14
                  vv
clus               N0 N1A N2A N2B N2C N3 NX
  OR52M1 MUTATED    1   0   0   0   0  1  1
  OR52M1 WILD-TYPE  9   1   1   3   1  2  2
D10V5, multiclass
D10V6, continuous
                  vv
clus               STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  OR52M1 MUTATED          0        0         0         2          0          0
  OR52M1 WILD-TYPE        1        1         1         8          1          3
                  vv
clus               STAGE IIIC STAGE IV
  OR52M1 MUTATED            0        1
  OR52M1 WILD-TYPE          3        0
D10V7, multiclass

Clustering(11) Variable = PPP6C MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  PPP6C MUTATED    2  0
  PPP6C WILD-TYPE 10  5
  PPP6C MUTATED PPP6C WILD-TYPE 
              2              15 
  PPP6C MUTATED PPP6C WILD-TYPE 
              0               5 
$`PPP6C MUTATED`
TCGA-EB-A3XB TCGA-EB-A3XC 
        1.18         0.30 

$`PPP6C WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
        7.79         3.88         0.53         0.43         1.35         1.28 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.13         0.53        12.10        24.00         0.03        15.35 
TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        26.99        17.23 

  PPP6C MUTATED PPP6C WILD-TYPE 
           0.30            0.03 
  PPP6C MUTATED PPP6C WILD-TYPE 
           1.18           26.99 
  PPP6C MUTATED PPP6C WILD-TYPE 
           0.74            3.88 
[1] "0.3 - 1.2 (0.7)"  "0.0 - 27.0 (3.9)"
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE"   "PPP6C MUTATED"   "PPP6C MUTATED" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-IH-A3EA 
"PPP6C WILD-TYPE" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE"   "PPP6C MUTATED"   "PPP6C MUTATED" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-IH-A3EA 
"PPP6C WILD-TYPE" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE"   "PPP6C MUTATED"   "PPP6C MUTATED" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-IH-A3EA 
"PPP6C WILD-TYPE" 
[1] "Remove cluster labels:" "PPP6C MUTATED"         
clus
  PPP6C MUTATED PPP6C WILD-TYPE 
              2              15 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XF      TCGA-EB-A3Y6 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-FR-A2OS      TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GN-A269      TCGA-GN-A26C      TCGA-IH-A3EA 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
D11V2, continuous
[1] "Remove cluster labels:" "PPP6C MUTATED"         
clus
  PPP6C MUTATED PPP6C WILD-TYPE 
              2              19 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A299      TCGA-EB-A3HV      TCGA-EB-A3XD 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A3XE      TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-EB-A3Y7 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-FR-A2OS      TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GN-A269      TCGA-GN-A26C      TCGA-IH-A3EA 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  PPP6C MUTATED                    1             2
  PPP6C WILD-TYPE                  1            17
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PPP6C MUTATED                                                                                          0
  PPP6C WILD-TYPE                                                                                        2
D11V3, multiclass
                                                                                          clus
vv                                                                                         PPP6C MUTATED
  DISTANT METASTASIS                                                                                   1
  PRIMARY TUMOR                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
                                                                                          clus
vv                                                                                         PPP6C WILD-TYPE
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                         17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
D11V4, binary
                 cls
clus               0  1
  PPP6C MUTATED    1  2
  PPP6C WILD-TYPE  6 14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PPP6C MUTATED      1    2
  PPP6C WILD-TYPE    6   14
        clus
vv       PPP6C MUTATED PPP6C WILD-TYPE
  FEMALE             1               6
  MALE               2              14
                 vv
clus              N0 N1A N2A N2B N2C N3 NX
  PPP6C MUTATED    1   0   0   0   0  0  1
  PPP6C WILD-TYPE  9   1   1   3   1  3  2
D11V5, multiclass
[1] "Remove cluster labels:" "PPP6C MUTATED"         
clus
  PPP6C MUTATED PPP6C WILD-TYPE 
              2              20 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A299      TCGA-EB-A3HV      TCGA-EB-A3XD 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A3XE      TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-EB-A3Y7 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-FR-A2OS      TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GN-A269      TCGA-GN-A26C      TCGA-HR-A2OH      TCGA-IH-A3EA 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
D11V6, continuous
                 vv
clus              STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  PPP6C MUTATED          0        1         0         1          0          0
  PPP6C WILD-TYPE        1        0         1         9          1          3
                 vv
clus              STAGE IIIC STAGE IV
  PPP6C MUTATED            0        0
  PPP6C WILD-TYPE          3        1
D11V7, multiclass
[1] "Remove cluster labels:" "PPP6C MUTATED"         
clus
  PPP6C MUTATED PPP6C WILD-TYPE 
              2              19 
     TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C      TCGA-EB-A24D 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A299      TCGA-EB-A3HV      TCGA-EB-A3XD      TCGA-EB-A3XE 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-EB-A3Y7      TCGA-FR-A2OS 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 
     TCGA-GN-A26C      TCGA-HR-A2OH      TCGA-IH-A3EA 
"PPP6C WILD-TYPE" "PPP6C WILD-TYPE" "PPP6C WILD-TYPE" 

Clustering(12) Variable = RUNDC3B MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2               0 1
  RUNDC3B MUTATED   3 0
  RUNDC3B WILD-TYPE 9 5
  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
                3                14 
  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
                0                 5 
$`RUNDC3B MUTATED`
TCGA-D9-A1X3 TCGA-EB-A24D TCGA-IH-A3EA 
        7.79         1.35        17.23 

$`RUNDC3B WILD-TYPE`
TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A3HV TCGA-EB-A3XB TCGA-EB-A3XC 
        3.88         0.53         0.43         1.28         1.18         0.30 
TCGA-EB-A3XF TCGA-EB-A3Y6 TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.13         0.53        12.10        24.00         0.03        15.35 
TCGA-GN-A269 TCGA-GN-A26C 
        5.59        26.99 

  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
             1.35              0.03 
  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
            17.23             26.99 
  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
             7.79              1.23 
[1] "1.4 - 17.2 (7.8)" "0.0 - 27.0 (1.2)"
       TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-EB-A1NK        TCGA-EB-A24C 
  "RUNDC3B MUTATED" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "RUNDC3B MUTATED" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-FR-A2OS        TCGA-FS-A1ZN 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269        TCGA-GN-A26C 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-IH-A3EA 
  "RUNDC3B MUTATED" 
       TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-EB-A1NK        TCGA-EB-A24C 
  "RUNDC3B MUTATED" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "RUNDC3B MUTATED" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-FR-A2OS        TCGA-FS-A1ZN 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269        TCGA-GN-A26C 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-IH-A3EA 
  "RUNDC3B MUTATED" 
       TCGA-D9-A1X3        TCGA-D9-A3Z4        TCGA-EB-A1NK        TCGA-EB-A24C 
  "RUNDC3B MUTATED" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A24D        TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC 
  "RUNDC3B MUTATED" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-FR-A2OS        TCGA-FS-A1ZN 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-GF-A2C7        TCGA-GN-A263        TCGA-GN-A269        TCGA-GN-A26C 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-IH-A3EA 
  "RUNDC3B MUTATED" 
[1] "hr="     "7.8e+08"
D12V2, continuous
                   vv
clus                DISTANT METASTASIS PRIMARY TUMOR
  RUNDC3B MUTATED                    0             2
  RUNDC3B WILD-TYPE                  2            17
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  RUNDC3B MUTATED                                                                                          1
  RUNDC3B WILD-TYPE                                                                                        1
D12V3, multiclass
                                                                                          clus
vv                                                                                         RUNDC3B MUTATED
  DISTANT METASTASIS                                                                                     0
  PRIMARY TUMOR                                                                                          2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               1
                                                                                          clus
vv                                                                                         RUNDC3B WILD-TYPE
  DISTANT METASTASIS                                                                                       2
  PRIMARY TUMOR                                                                                           17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 1
D12V4, binary
                   cls
clus                 0  1
  RUNDC3B MUTATED    0  3
  RUNDC3B WILD-TYPE  7 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  RUNDC3B MUTATED      0    3
  RUNDC3B WILD-TYPE    7   13
        clus
vv       RUNDC3B MUTATED RUNDC3B WILD-TYPE
  FEMALE               0                 7
  MALE                 3                13
                   vv
clus                N0 N1A N2A N2B N2C N3 NX
  RUNDC3B MUTATED    1   0   0   2   0  0  0
  RUNDC3B WILD-TYPE  9   1   1   1   1  3  3
D12V5, multiclass
D12V6, continuous
                   vv
clus                STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  RUNDC3B MUTATED          0        0         0         1          0          1
  RUNDC3B WILD-TYPE        1        1         1         9          1          2
                   vv
clus                STAGE IIIC STAGE IV
  RUNDC3B MUTATED            0        0
  RUNDC3B WILD-TYPE          3        1
D12V7, multiclass
[1] "Remove cluster labels:" "RUNDC3B MUTATED"       
clus
  RUNDC3B MUTATED RUNDC3B WILD-TYPE 
                2                19 
       TCGA-D9-A3Z4        TCGA-EB-A1NK        TCGA-EB-A24C        TCGA-EB-A299 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A3HV        TCGA-EB-A3XB        TCGA-EB-A3XC        TCGA-EB-A3XD 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-EB-A3XE        TCGA-EB-A3XF        TCGA-EB-A3Y6        TCGA-EB-A3Y7 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-FR-A2OS        TCGA-FS-A1ZN        TCGA-GF-A2C7        TCGA-GN-A263 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 
       TCGA-GN-A269        TCGA-GN-A26C        TCGA-HR-A2OH 
"RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" "RUNDC3B WILD-TYPE" 

Clustering(13) Variable = ADCYAP1R1 MUTATION ANALYSIS
D13V1, survival
                     sevent
clus2                  0  1
  ADCYAP1R1 MUTATED    2  1
  ADCYAP1R1 WILD-TYPE 10  4
  ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE 
                  3                  14 
  ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE 
                  1                   4 
$`ADCYAP1R1 MUTATED`
TCGA-EB-A3XC TCGA-EB-A3Y6 TCGA-GN-A269 
        0.30         0.53         5.59 

$`ADCYAP1R1 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV 
        7.79         3.88         0.53         0.43         1.35         1.28 
TCGA-EB-A3XB TCGA-EB-A3XF TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        1.18         0.13        12.10        24.00         0.03        15.35 
TCGA-GN-A26C TCGA-IH-A3EA 
       26.99        17.23 

  ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE 
               0.30                0.03 
  ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE 
               5.59               26.99 
  ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE 
              0.530               2.615 
[1] "0.3 - 5.6 (0.5)"  "0.0 - 27.0 (2.6)"
         TCGA-D9-A1X3          TCGA-D9-A3Z4          TCGA-EB-A1NK 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A24C          TCGA-EB-A24D          TCGA-EB-A3HV 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A3XB          TCGA-EB-A3XC          TCGA-EB-A3XF 
"ADCYAP1R1 WILD-TYPE"   "ADCYAP1R1 MUTATED" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A3Y6          TCGA-FR-A2OS          TCGA-FS-A1ZN 
  "ADCYAP1R1 MUTATED" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-GF-A2C7          TCGA-GN-A263          TCGA-GN-A269 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE"   "ADCYAP1R1 MUTATED" 
         TCGA-GN-A26C          TCGA-IH-A3EA 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-D9-A1X3          TCGA-D9-A3Z4          TCGA-EB-A1NK 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A24C          TCGA-EB-A24D          TCGA-EB-A3HV 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A3XB          TCGA-EB-A3XC          TCGA-EB-A3XF 
"ADCYAP1R1 WILD-TYPE"   "ADCYAP1R1 MUTATED" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A3Y6          TCGA-FR-A2OS          TCGA-FS-A1ZN 
  "ADCYAP1R1 MUTATED" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-GF-A2C7          TCGA-GN-A263          TCGA-GN-A269 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE"   "ADCYAP1R1 MUTATED" 
         TCGA-GN-A26C          TCGA-IH-A3EA 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-D9-A1X3          TCGA-D9-A3Z4          TCGA-EB-A1NK 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A24C          TCGA-EB-A24D          TCGA-EB-A3HV 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A3XB          TCGA-EB-A3XC          TCGA-EB-A3XF 
"ADCYAP1R1 WILD-TYPE"   "ADCYAP1R1 MUTATED" "ADCYAP1R1 WILD-TYPE" 
         TCGA-EB-A3Y6          TCGA-FR-A2OS          TCGA-FS-A1ZN 
  "ADCYAP1R1 MUTATED" "ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
         TCGA-GF-A2C7          TCGA-GN-A263          TCGA-GN-A269 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE"   "ADCYAP1R1 MUTATED" 
         TCGA-GN-A26C          TCGA-IH-A3EA 
"ADCYAP1R1 WILD-TYPE" "ADCYAP1R1 WILD-TYPE" 
[1] "hr="     "3.6e+09"
D13V2, continuous
                     vv
clus                  DISTANT METASTASIS PRIMARY TUMOR
  ADCYAP1R1 MUTATED                    0             3
  ADCYAP1R1 WILD-TYPE                  2            16
                     vv
clus                  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ADCYAP1R1 MUTATED                                                                                          0
  ADCYAP1R1 WILD-TYPE                                                                                        2
D13V3, multiclass
                                                                                          clus
vv                                                                                         ADCYAP1R1 MUTATED
  DISTANT METASTASIS                                                                                       0
  PRIMARY TUMOR                                                                                            3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 0
                                                                                          clus
vv                                                                                         ADCYAP1R1 WILD-TYPE
  DISTANT METASTASIS                                                                                         2
  PRIMARY TUMOR                                                                                             16
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                   2
D13V4, binary
                     cls
clus                   0  1
  ADCYAP1R1 MUTATED    1  2
  ADCYAP1R1 WILD-TYPE  6 14
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  ADCYAP1R1 MUTATED      1    2
  ADCYAP1R1 WILD-TYPE    6   14
        clus
vv       ADCYAP1R1 MUTATED ADCYAP1R1 WILD-TYPE
  FEMALE                 1                   6
  MALE                   2                  14
                     vv
clus                  N0 N1A N2A N2B N2C N3 NX
  ADCYAP1R1 MUTATED    2   0   0   0   0  1  0
  ADCYAP1R1 WILD-TYPE  8   1   1   3   1  2  3
D13V5, multiclass
D13V6, continuous
                     vv
clus                  STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA
  ADCYAP1R1 MUTATED          0        0         0         2          0
  ADCYAP1R1 WILD-TYPE        1        1         1         8          1
                     vv
clus                  STAGE IIIB STAGE IIIC STAGE IV
  ADCYAP1R1 MUTATED            0          1        0
  ADCYAP1R1 WILD-TYPE          3          2        1
D13V7, multiclass

Clustering(14) Variable = KCNC2 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2              0  1
  KCNC2 MUTATED    2  0
  KCNC2 WILD-TYPE 10  5
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              2              15 
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              0               5 
$`KCNC2 MUTATED`
TCGA-EB-A1NK TCGA-EB-A3Y6 
        0.53         0.53 

$`KCNC2 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3HV TCGA-EB-A3XB 
        7.79         3.88         0.43         1.35         1.28         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-FR-A2OS TCGA-FS-A1ZN TCGA-GF-A2C7 TCGA-GN-A263 
        0.30         0.13        12.10        24.00         0.03        15.35 
TCGA-GN-A269 TCGA-GN-A26C TCGA-IH-A3EA 
        5.59        26.99        17.23 

  KCNC2 MUTATED KCNC2 WILD-TYPE 
           0.53            0.03 
  KCNC2 MUTATED KCNC2 WILD-TYPE 
           0.53           26.99 
  KCNC2 MUTATED KCNC2 WILD-TYPE 
           0.53            3.88 
[1] "0.5 - 0.5 (0.5)"  "0.0 - 27.0 (3.9)"
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE"   "KCNC2 MUTATED" "KCNC2 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"KCNC2 WILD-TYPE"   "KCNC2 MUTATED" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-IH-A3EA 
"KCNC2 WILD-TYPE" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE"   "KCNC2 MUTATED" "KCNC2 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"KCNC2 WILD-TYPE"   "KCNC2 MUTATED" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-IH-A3EA 
"KCNC2 WILD-TYPE" 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A1NK      TCGA-EB-A24C 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE"   "KCNC2 MUTATED" "KCNC2 WILD-TYPE" 
     TCGA-EB-A24D      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3XF      TCGA-EB-A3Y6      TCGA-FR-A2OS      TCGA-FS-A1ZN 
"KCNC2 WILD-TYPE"   "KCNC2 MUTATED" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269      TCGA-GN-A26C 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-IH-A3EA 
"KCNC2 WILD-TYPE" 
[1] "Remove cluster labels:" "KCNC2 MUTATED"         
clus
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              2              15 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A24C      TCGA-EB-A24D 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC      TCGA-EB-A3XF 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-FR-A2OS      TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-GN-A269      TCGA-GN-A26C      TCGA-IH-A3EA 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
D14V2, continuous
[1] "Remove cluster labels:" "KCNC2 MUTATED"         
clus
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              2              19 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A24C      TCGA-EB-A24D 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A299      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3XD      TCGA-EB-A3XE      TCGA-EB-A3XF      TCGA-EB-A3Y7 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-FR-A2OS      TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-GN-A269      TCGA-GN-A26C      TCGA-IH-A3EA 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
                 vv
clus              DISTANT METASTASIS PRIMARY TUMOR
  KCNC2 MUTATED                    1             2
  KCNC2 WILD-TYPE                  1            17
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  KCNC2 MUTATED                                                                                          0
  KCNC2 WILD-TYPE                                                                                        2
D14V3, multiclass
                                                                                          clus
vv                                                                                         KCNC2 MUTATED
  DISTANT METASTASIS                                                                                   1
  PRIMARY TUMOR                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
                                                                                          clus
vv                                                                                         KCNC2 WILD-TYPE
  DISTANT METASTASIS                                                                                     1
  PRIMARY TUMOR                                                                                         17
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               2
D14V4, binary
                 cls
clus               0  1
  KCNC2 MUTATED    2  1
  KCNC2 WILD-TYPE  5 15
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KCNC2 MUTATED      2    1
  KCNC2 WILD-TYPE    5   15
        clus
vv       KCNC2 MUTATED KCNC2 WILD-TYPE
  FEMALE             2               5
  MALE               1              15
                 vv
clus              N0 N1A N2A N2B N2C N3 NX
  KCNC2 MUTATED    2   0   0   0   0  0  0
  KCNC2 WILD-TYPE  8   1   1   3   1  3  3
D14V5, multiclass
[1] "Remove cluster labels:" "KCNC2 MUTATED"         
clus
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              2              20 
     TCGA-D9-A1X3      TCGA-D9-A3Z4      TCGA-EB-A24C      TCGA-EB-A24D 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A299      TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3XD      TCGA-EB-A3XE      TCGA-EB-A3XF      TCGA-EB-A3Y7 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-FR-A2OS      TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-GN-A269      TCGA-GN-A26C      TCGA-HR-A2OH      TCGA-IH-A3EA 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
D14V6, continuous
                 vv
clus              STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  KCNC2 MUTATED          0        0         0         2          0          0
  KCNC2 WILD-TYPE        1        1         1         8          1          3
                 vv
clus              STAGE IIIC STAGE IV
  KCNC2 MUTATED            0        0
  KCNC2 WILD-TYPE          3        1
D14V7, multiclass
[1] "Remove cluster labels:" "KCNC2 MUTATED"         
clus
  KCNC2 MUTATED KCNC2 WILD-TYPE 
              2              19 
     TCGA-D9-A3Z4      TCGA-EB-A24C      TCGA-EB-A24D      TCGA-EB-A299 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3HV      TCGA-EB-A3XB      TCGA-EB-A3XC      TCGA-EB-A3XD 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-EB-A3XE      TCGA-EB-A3XF      TCGA-EB-A3Y7      TCGA-FR-A2OS 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-FS-A1ZN      TCGA-GF-A2C7      TCGA-GN-A263      TCGA-GN-A269 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 
     TCGA-GN-A26C      TCGA-HR-A2OH      TCGA-IH-A3EA 
"KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" "KCNC2 WILD-TYPE" 

Clustering(15) Variable = PIK3R1 MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2               0  1
  PIK3R1 MUTATED    2  1
  PIK3R1 WILD-TYPE 10  4
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               3               14 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
               1                4 
$`PIK3R1 MUTATED`
TCGA-EB-A3HV TCGA-EB-A3Y6 TCGA-FS-A1ZN 
        1.28         0.53        24.00 

$`PIK3R1 WILD-TYPE`
TCGA-D9-A1X3 TCGA-D9-A3Z4 TCGA-EB-A1NK TCGA-EB-A24C TCGA-EB-A24D TCGA-EB-A3XB 
        7.79         3.88         0.53         0.43         1.35         1.18 
TCGA-EB-A3XC TCGA-EB-A3XF TCGA-FR-A2OS TCGA-GF-A2C7 TCGA-GN-A263 TCGA-GN-A269 
        0.30         0.13        12.10         0.03        15.35         5.59 
TCGA-GN-A26C TCGA-IH-A3EA 
       26.99        17.23 

  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
            0.53             0.03 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           24.00            26.99 
  PIK3R1 MUTATED PIK3R1 WILD-TYPE 
           1.280            2.615 
[1] "0.5 - 24.0 (1.3)" "0.0 - 27.0 (2.6)"
      TCGA-D9-A1X3       TCGA-D9-A3Z4       TCGA-EB-A1NK       TCGA-EB-A24C 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-EB-A24D       TCGA-EB-A3HV       TCGA-EB-A3XB       TCGA-EB-A3XC 
"PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-EB-A3XF       TCGA-EB-A3Y6       TCGA-FR-A2OS       TCGA-FS-A1ZN 
"PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" "PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" 
      TCGA-GF-A2C7       TCGA-GN-A263       TCGA-GN-A269       TCGA-GN-A26C 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IH-A3EA 
"PIK3R1 WILD-TYPE" 
      TCGA-D9-A1X3       TCGA-D9-A3Z4       TCGA-EB-A1NK       TCGA-EB-A24C 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-EB-A24D       TCGA-EB-A3HV       TCGA-EB-A3XB       TCGA-EB-A3XC 
"PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-EB-A3XF       TCGA-EB-A3Y6       TCGA-FR-A2OS       TCGA-FS-A1ZN 
"PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" "PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" 
      TCGA-GF-A2C7       TCGA-GN-A263       TCGA-GN-A269       TCGA-GN-A26C 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IH-A3EA 
"PIK3R1 WILD-TYPE" 
      TCGA-D9-A1X3       TCGA-D9-A3Z4       TCGA-EB-A1NK       TCGA-EB-A24C 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-EB-A24D       TCGA-EB-A3HV       TCGA-EB-A3XB       TCGA-EB-A3XC 
"PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-EB-A3XF       TCGA-EB-A3Y6       TCGA-FR-A2OS       TCGA-FS-A1ZN 
"PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" "PIK3R1 WILD-TYPE"   "PIK3R1 MUTATED" 
      TCGA-GF-A2C7       TCGA-GN-A263       TCGA-GN-A269       TCGA-GN-A26C 
"PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" "PIK3R1 WILD-TYPE" 
      TCGA-IH-A3EA 
"PIK3R1 WILD-TYPE" 
[1] "hr=" "1.1"
D15V2, continuous
                  vv
clus               DISTANT METASTASIS PRIMARY TUMOR
  PIK3R1 MUTATED                    0             4
  PIK3R1 WILD-TYPE                  2            15
                  vv
clus               REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PIK3R1 MUTATED                                                                                          0
  PIK3R1 WILD-TYPE                                                                                        2
D15V3, multiclass
                                                                                          clus
vv                                                                                         PIK3R1 MUTATED
  DISTANT METASTASIS                                                                                    0
  PRIMARY TUMOR                                                                                         4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              0
                                                                                          clus
vv                                                                                         PIK3R1 WILD-TYPE
  DISTANT METASTASIS                                                                                      2
  PRIMARY TUMOR                                                                                          15
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                2
D15V4, binary
                  cls
clus                0  1
  PIK3R1 MUTATED    2  2
  PIK3R1 WILD-TYPE  5 14
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3R1 MUTATED      2    2
  PIK3R1 WILD-TYPE    5   14
        clus
vv       PIK3R1 MUTATED PIK3R1 WILD-TYPE
  FEMALE              2                5
  MALE                2               14
                  vv
clus               N0 N1A N2A N2B N2C N3 NX
  PIK3R1 MUTATED    2   1   0   0   1  0  0
  PIK3R1 WILD-TYPE  8   0   1   3   0  3  3
D15V5, multiclass
D15V6, continuous
                  vv
clus               STAGE IB STAGE II STAGE IIA STAGE IIC STAGE IIIA STAGE IIIB
  PIK3R1 MUTATED          0        0         0         2          1          1
  PIK3R1 WILD-TYPE        1        1         1         8          0          2
                  vv
clus               STAGE IIIC STAGE IV
  PIK3R1 MUTATED            0        0
  PIK3R1 WILD-TYPE          3        1
D15V7, multiclass
                     V1.D                        V2                        V3 
          "Time to Death"                     "AGE" "PRIMARY.SITE.OF.DISEASE" 
                       V4                        V5                        V6 
                 "GENDER"   "LYMPH.NODE.METASTASIS"         "TUMOR.STAGECODE" 
                       V7 
  "NEOPLASM.DISEASESTAGE" 
> q(save="no")
