
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/404093/SKCM-WT.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-WT/3215660/SKCM-WT.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=23, in cluster file=34, common to both=22
[1] "Reduce the number of clustering variables from 8 to 5."
[1]  5 22
[1] "ADAMTS9 MUTATION ANALYSIS"
[1] 3
  ADAMTS9 MUTATED ADAMTS9 WILD-TYPE 
                5                17 
  ADAMTS9 MUTATED ADAMTS9 WILD-TYPE 
                5                17 
[1] "RAC1 MUTATION ANALYSIS"
[1] 3
  RAC1 MUTATED RAC1 WILD-TYPE 
             4             18 
  RAC1 MUTATED RAC1 WILD-TYPE 
             4             18 
[1] "SERPINI2 MUTATION ANALYSIS"
[1] 3
  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
                 3                 19 
  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
                 3                 19 
[1] "ESRP1 MUTATION ANALYSIS"
[1] 3
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              4              18 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              4              18 
[1] "PLCB4 MUTATION ANALYSIS"
[1] 3
  PLCB4 MUTATED PLCB4 WILD-TYPE 
              4              18 
  PLCB4 MUTATED PLCB4 WILD-TYPE 
              4              18 
[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 22 columns.

[1] "Batch" "16"   
[1] "Last Follow UP"
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D9-A149 TCGA-DA-A1IA TCGA-DA-A3F2 
          NA         1390           NA           NA           NA          589 
TCGA-EE-A17Z TCGA-EE-A29D TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2MR TCGA-ER-A19L 
          NA           NA           NA           NA           NA           NA 
TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-FS-A1Z4 TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZU 
        2386          200           NA           NA           NA           NA 
TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
          NA           NA           NA          447 
Variable 1:'AGE':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=14,	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=11,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=2,	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
 T1 T1A  T2 T2A T3A T3B  T4 T4A T4B  TX 
  2   1   1   1   3   2   1   2   5   2 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 22 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=19, 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=6, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE

Clustering(1) Variable = ADAMTS9 MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2               0 1
  ADAMTS9 MUTATED   1 2
  ADAMTS9 WILD-TYPE 4 7
  ADAMTS9 MUTATED ADAMTS9 WILD-TYPE 
                3                11 
  ADAMTS9 MUTATED ADAMTS9 WILD-TYPE 
                2                 7 
$`ADAMTS9 MUTATED`
TCGA-D3-A2J6 TCGA-EE-A29D TCGA-ER-A1A1 
       10.26        11.15        78.44 

$`ADAMTS9 WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-ER-A19L 
       45.70        24.00         4.93        19.36         6.31        12.99 
TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
        6.58        15.35        31.33        12.16        14.70 

  ADAMTS9 MUTATED ADAMTS9 WILD-TYPE 
            10.26              4.93 
  ADAMTS9 MUTATED ADAMTS9 WILD-TYPE 
            78.44             45.70 
  ADAMTS9 MUTATED ADAMTS9 WILD-TYPE 
            11.15             14.70 
[1] "10.3 - 78.4 (11.2)" "4.9 - 45.7 (14.7)" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE"   "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
  "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE"   "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
  "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-D3-A2J6        TCGA-D3-A3CC        TCGA-D3-A3CF        TCGA-DA-A1IA 
  "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-DA-A3F2        TCGA-EE-A17Z        TCGA-EE-A29D        TCGA-ER-A19L 
"ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE"   "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" 
       TCGA-ER-A1A1        TCGA-ER-A3ET        TCGA-GN-A261        TCGA-GN-A264 
  "ADAMTS9 MUTATED" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
       TCGA-GN-A26A        TCGA-GN-A26D 
"ADAMTS9 WILD-TYPE" "ADAMTS9 WILD-TYPE" 
[1] "hr=" "1.1"
D1V2, continuous
                   vv
clus                DISTANT METASTASIS
  ADAMTS9 MUTATED                    0
  ADAMTS9 WILD-TYPE                  3
                   vv
clus                REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ADAMTS9 MUTATED                                                                                          0
  ADAMTS9 WILD-TYPE                                                                                        6
                   vv
clus                REGIONAL LYMPH NODE
  ADAMTS9 MUTATED                     5
  ADAMTS9 WILD-TYPE                   8
D1V3, multiclass
                                                                                          clus
vv                                                                                         ADAMTS9 MUTATED
  DISTANT METASTASIS                                                                                     0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               0
  REGIONAL LYMPH NODE                                                                                    5
                                                                                          clus
vv                                                                                         ADAMTS9 WILD-TYPE
  DISTANT METASTASIS                                                                                       3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                 6
  REGIONAL LYMPH NODE                                                                                      8
D1V4, binary
                   cls
clus                 0  1
  ADAMTS9 MUTATED    0  5
  ADAMTS9 WILD-TYPE 11  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  ADAMTS9 MUTATED      0    5
  ADAMTS9 WILD-TYPE   11    6
        clus
vv       ADAMTS9 MUTATED ADAMTS9 WILD-TYPE
  FEMALE               0                11
  MALE                 5                 6
                   vv
clus                N0 N1 N1A N1B N2B N3
  ADAMTS9 MUTATED    3  0   0   1   0  1
  ADAMTS9 WILD-TYPE  7  1   2   2   2  1
D1V5, multiclass
D1V6, continuous
                   vv
clus                STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  ADAMTS9 MUTATED         1        1        0         1         0         0
  ADAMTS9 WILD-TYPE       2        0        1         1         3         1
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC
  ADAMTS9 MUTATED            0          0          2
  ADAMTS9 WILD-TYPE          2          2          2
D1V7, multiclass

Clustering(2) Variable = RAC1 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2            0 1
  RAC1 MUTATED   1 1
  RAC1 WILD-TYPE 4 8
  RAC1 MUTATED RAC1 WILD-TYPE 
             2             12 
  RAC1 MUTATED RAC1 WILD-TYPE 
             1              8 
$`RAC1 MUTATED`
TCGA-EE-A29D TCGA-ER-A1A1 
       11.15        78.44 

$`RAC1 WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       12.99         6.58        15.35        31.33        12.16        14.70 

  RAC1 MUTATED RAC1 WILD-TYPE 
         11.15           4.93 
  RAC1 MUTATED RAC1 WILD-TYPE 
         78.44          45.70 
  RAC1 MUTATED RAC1 WILD-TYPE 
        44.795         13.845 
[1] "11.2 - 78.4 (44.8)" "4.9 - 45.7 (13.8)" 
    TCGA-D3-A2J6     TCGA-D3-A3CC     TCGA-D3-A3CF     TCGA-DA-A1IA 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-DA-A3F2     TCGA-EE-A17Z     TCGA-EE-A29D     TCGA-ER-A19L 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE"   "RAC1 MUTATED" "RAC1 WILD-TYPE" 
    TCGA-ER-A1A1     TCGA-ER-A3ET     TCGA-GN-A261     TCGA-GN-A264 
  "RAC1 MUTATED" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-GN-A26A     TCGA-GN-A26D 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-D3-A2J6     TCGA-D3-A3CC     TCGA-D3-A3CF     TCGA-DA-A1IA 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-DA-A3F2     TCGA-EE-A17Z     TCGA-EE-A29D     TCGA-ER-A19L 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE"   "RAC1 MUTATED" "RAC1 WILD-TYPE" 
    TCGA-ER-A1A1     TCGA-ER-A3ET     TCGA-GN-A261     TCGA-GN-A264 
  "RAC1 MUTATED" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-GN-A26A     TCGA-GN-A26D 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-D3-A2J6     TCGA-D3-A3CC     TCGA-D3-A3CF     TCGA-DA-A1IA 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-DA-A3F2     TCGA-EE-A17Z     TCGA-EE-A29D     TCGA-ER-A19L 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE"   "RAC1 MUTATED" "RAC1 WILD-TYPE" 
    TCGA-ER-A1A1     TCGA-ER-A3ET     TCGA-GN-A261     TCGA-GN-A264 
  "RAC1 MUTATED" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-GN-A26A     TCGA-GN-A26D 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
[1] "Remove cluster labels:" "RAC1 MUTATED"          
clus
  RAC1 MUTATED RAC1 WILD-TYPE 
             2             12 
    TCGA-D3-A2J6     TCGA-D3-A3CC     TCGA-D3-A3CF     TCGA-DA-A1IA 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-DA-A3F2     TCGA-EE-A17Z     TCGA-ER-A19L     TCGA-ER-A3ET 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
    TCGA-GN-A261     TCGA-GN-A264     TCGA-GN-A26A     TCGA-GN-A26D 
"RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" "RAC1 WILD-TYPE" 
D2V2, continuous
                vv
clus             DISTANT METASTASIS
  RAC1 MUTATED                    2
  RAC1 WILD-TYPE                  1
                vv
clus             REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  RAC1 MUTATED                                                                                          0
  RAC1 WILD-TYPE                                                                                        6
                vv
clus             REGIONAL LYMPH NODE
  RAC1 MUTATED                     2
  RAC1 WILD-TYPE                  11
D2V3, multiclass
                                                                                          clus
vv                                                                                         RAC1 MUTATED
  DISTANT METASTASIS                                                                                  2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)            0
  REGIONAL LYMPH NODE                                                                                 2
                                                                                          clus
vv                                                                                         RAC1 WILD-TYPE
  DISTANT METASTASIS                                                                                    1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)              6
  REGIONAL LYMPH NODE                                                                                  11
D2V4, binary
                cls
clus              0  1
  RAC1 MUTATED    1  3
  RAC1 WILD-TYPE 10  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  RAC1 MUTATED      1    3
  RAC1 WILD-TYPE   10    8
        clus
vv       RAC1 MUTATED RAC1 WILD-TYPE
  FEMALE            1             10
  MALE              3              8
                vv
clus             N0 N1 N1A N1B N2B N3
  RAC1 MUTATED    2  0   0   1   0  1
  RAC1 WILD-TYPE  8  1   2   2   2  1
D2V5, multiclass
D2V6, continuous
                vv
clus             STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  RAC1 MUTATED         0        0        1         0         1         0
  RAC1 WILD-TYPE       3        1        0         2         2         1
                vv
clus             STAGE IIIA STAGE IIIB STAGE IIIC
  RAC1 MUTATED            0          0          2
  RAC1 WILD-TYPE          2          2          2
D2V7, multiclass

Clustering(3) Variable = SERPINI2 MUTATION ANALYSIS
D3V1, survival
                    sevent
clus2                0 1
  SERPINI2 MUTATED   0 2
  SERPINI2 WILD-TYPE 5 7
  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
                 2                 12 
  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
                 2                  7 
$`SERPINI2 MUTATED`
TCGA-EE-A29D TCGA-GN-A26A 
       11.15        12.16 

$`SERPINI2 WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-ER-A19L TCGA-ER-A1A1 TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26D 
       12.99        78.44         6.58        15.35        31.33        14.70 

  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
             11.15               4.93 
  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
             12.16              78.44 
  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
            11.655             15.025 
[1] "11.2 - 12.2 (11.7)" "4.9 - 78.4 (15.0)" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "SERPINI2 MUTATED" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "SERPINI2 MUTATED" "SERPINI2 WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "SERPINI2 MUTATED" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "SERPINI2 MUTATED" "SERPINI2 WILD-TYPE" 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-EE-A29D         TCGA-ER-A19L         TCGA-ER-A1A1 
  "SERPINI2 MUTATED" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-ER-A3ET         TCGA-GN-A261         TCGA-GN-A264 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-GN-A26A         TCGA-GN-A26D 
  "SERPINI2 MUTATED" "SERPINI2 WILD-TYPE" 
[1] "Remove cluster labels:" "SERPINI2 MUTATED"      
clus
  SERPINI2 MUTATED SERPINI2 WILD-TYPE 
                 2                 12 
        TCGA-D3-A2J6         TCGA-D3-A3CC         TCGA-D3-A3CF 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-DA-A1IA         TCGA-DA-A3F2         TCGA-EE-A17Z 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-ER-A19L         TCGA-ER-A1A1         TCGA-ER-A3ET 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
        TCGA-GN-A261         TCGA-GN-A264         TCGA-GN-A26D 
"SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" "SERPINI2 WILD-TYPE" 
D3V2, continuous
                    vv
clus                 DISTANT METASTASIS
  SERPINI2 MUTATED                    1
  SERPINI2 WILD-TYPE                  2
                    vv
clus                 REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  SERPINI2 MUTATED                                                                                          1
  SERPINI2 WILD-TYPE                                                                                        5
                    vv
clus                 REGIONAL LYMPH NODE
  SERPINI2 MUTATED                     1
  SERPINI2 WILD-TYPE                  12
D3V3, multiclass
                                                                                          clus
vv                                                                                         SERPINI2 MUTATED
  DISTANT METASTASIS                                                                                      1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                1
  REGIONAL LYMPH NODE                                                                                     1
                                                                                          clus
vv                                                                                         SERPINI2 WILD-TYPE
  DISTANT METASTASIS                                                                                        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)                  5
  REGIONAL LYMPH NODE                                                                                      12
D3V4, binary
                    cls
clus                  0  1
  SERPINI2 MUTATED    2  1
  SERPINI2 WILD-TYPE  9 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  SERPINI2 MUTATED      2    1
  SERPINI2 WILD-TYPE    9   10
        clus
vv       SERPINI2 MUTATED SERPINI2 WILD-TYPE
  FEMALE                2                  9
  MALE                  1                 10
                    vv
clus                 N0 N1 N1A N1B N2B N3
  SERPINI2 MUTATED    1  0   1   1   0  0
  SERPINI2 WILD-TYPE  9  1   1   2   2  2
D3V5, multiclass
D3V6, continuous
                    vv
clus                 STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  SERPINI2 MUTATED         0        0        0         0         1         0
  SERPINI2 WILD-TYPE       3        1        1         2         2         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC
  SERPINI2 MUTATED            1          0          1
  SERPINI2 WILD-TYPE          1          2          3
D3V7, multiclass

Clustering(4) Variable = ESRP1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2             0 1
  ESRP1 MUTATED   1 1
  ESRP1 WILD-TYPE 4 8
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              2              12 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              1               8 
$`ESRP1 MUTATED`
TCGA-D3-A2J6 TCGA-ER-A1A1 
       10.26        78.44 

$`ESRP1 WILD-TYPE`
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z TCGA-EE-A29D 
       45.70        24.00         4.93        19.36         6.31        11.15 
TCGA-ER-A19L TCGA-ER-A3ET TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       12.99         6.58        15.35        31.33        12.16        14.70 

  ESRP1 MUTATED ESRP1 WILD-TYPE 
          10.26            4.93 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
          78.44           45.70 
  ESRP1 MUTATED ESRP1 WILD-TYPE 
         44.350          13.845 
[1] "10.3 - 78.4 (44.4)" "4.9 - 45.7 (13.8)" 
     TCGA-D3-A2J6      TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-DA-A1IA 
  "ESRP1 MUTATED" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-DA-A3F2      TCGA-EE-A17Z      TCGA-EE-A29D      TCGA-ER-A19L 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-ER-A1A1      TCGA-ER-A3ET      TCGA-GN-A261      TCGA-GN-A264 
  "ESRP1 MUTATED" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-D3-A2J6      TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-DA-A1IA 
  "ESRP1 MUTATED" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-DA-A3F2      TCGA-EE-A17Z      TCGA-EE-A29D      TCGA-ER-A19L 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-ER-A1A1      TCGA-ER-A3ET      TCGA-GN-A261      TCGA-GN-A264 
  "ESRP1 MUTATED" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-D3-A2J6      TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-DA-A1IA 
  "ESRP1 MUTATED" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-DA-A3F2      TCGA-EE-A17Z      TCGA-EE-A29D      TCGA-ER-A19L 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-ER-A1A1      TCGA-ER-A3ET      TCGA-GN-A261      TCGA-GN-A264 
  "ESRP1 MUTATED" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
[1] "Remove cluster labels:" "ESRP1 MUTATED"         
clus
  ESRP1 MUTATED ESRP1 WILD-TYPE 
              2              12 
     TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-DA-A1IA      TCGA-DA-A3F2 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-EE-A17Z      TCGA-EE-A29D      TCGA-ER-A19L      TCGA-ER-A3ET 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
     TCGA-GN-A261      TCGA-GN-A264      TCGA-GN-A26A      TCGA-GN-A26D 
"ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" "ESRP1 WILD-TYPE" 
D4V2, continuous
                 vv
clus              DISTANT METASTASIS
  ESRP1 MUTATED                    1
  ESRP1 WILD-TYPE                  2
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  ESRP1 MUTATED                                                                                          0
  ESRP1 WILD-TYPE                                                                                        6
                 vv
clus              REGIONAL LYMPH NODE
  ESRP1 MUTATED                     3
  ESRP1 WILD-TYPE                  10
D4V3, multiclass
                                                                                          clus
vv                                                                                         ESRP1 MUTATED
  DISTANT METASTASIS                                                                                   1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             0
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         ESRP1 WILD-TYPE
  DISTANT METASTASIS                                                                                     2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               6
  REGIONAL LYMPH NODE                                                                                   10
D4V4, binary
                 cls
clus               0  1
  ESRP1 MUTATED    0  4
  ESRP1 WILD-TYPE 11  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ESRP1 MUTATED      0    4
  ESRP1 WILD-TYPE   11    7
        clus
vv       ESRP1 MUTATED ESRP1 WILD-TYPE
  FEMALE             0              11
  MALE               4               7
                 vv
clus              N0 N1 N1A N1B N2B N3
  ESRP1 MUTATED    3  0   0   0   0  1
  ESRP1 WILD-TYPE  7  1   2   3   2  1
D4V5, multiclass
D4V6, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  ESRP1 MUTATED         1        0        1         1         0         0
  ESRP1 WILD-TYPE       2        1        0         1         3         1
                 vv
clus              STAGE IIIA STAGE IIIB STAGE IIIC
  ESRP1 MUTATED            0          0          1
  ESRP1 WILD-TYPE          2          2          3
D4V7, multiclass

Clustering(5) Variable = PLCB4 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2             0 1
  PLCB4 MUTATED   2 1
  PLCB4 WILD-TYPE 3 8
  PLCB4 MUTATED PLCB4 WILD-TYPE 
              3              11 
  PLCB4 MUTATED PLCB4 WILD-TYPE 
              1               8 
$`PLCB4 MUTATED`
TCGA-EE-A29D TCGA-ER-A1A1 TCGA-ER-A3ET 
       11.15        78.44         6.58 

$`PLCB4 WILD-TYPE`
TCGA-D3-A2J6 TCGA-D3-A3CC TCGA-D3-A3CF TCGA-DA-A1IA TCGA-DA-A3F2 TCGA-EE-A17Z 
       10.26        45.70        24.00         4.93        19.36         6.31 
TCGA-ER-A19L TCGA-GN-A261 TCGA-GN-A264 TCGA-GN-A26A TCGA-GN-A26D 
       12.99        15.35        31.33        12.16        14.70 

  PLCB4 MUTATED PLCB4 WILD-TYPE 
           6.58            4.93 
  PLCB4 MUTATED PLCB4 WILD-TYPE 
          78.44           45.70 
  PLCB4 MUTATED PLCB4 WILD-TYPE 
          11.15           14.70 
[1] "6.6 - 78.4 (11.2)" "4.9 - 45.7 (14.7)"
     TCGA-D3-A2J6      TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-DA-A1IA 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-DA-A3F2      TCGA-EE-A17Z      TCGA-EE-A29D      TCGA-ER-A19L 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE"   "PLCB4 MUTATED" "PLCB4 WILD-TYPE" 
     TCGA-ER-A1A1      TCGA-ER-A3ET      TCGA-GN-A261      TCGA-GN-A264 
  "PLCB4 MUTATED"   "PLCB4 MUTATED" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-D3-A2J6      TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-DA-A1IA 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-DA-A3F2      TCGA-EE-A17Z      TCGA-EE-A29D      TCGA-ER-A19L 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE"   "PLCB4 MUTATED" "PLCB4 WILD-TYPE" 
     TCGA-ER-A1A1      TCGA-ER-A3ET      TCGA-GN-A261      TCGA-GN-A264 
  "PLCB4 MUTATED"   "PLCB4 MUTATED" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-D3-A2J6      TCGA-D3-A3CC      TCGA-D3-A3CF      TCGA-DA-A1IA 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-DA-A3F2      TCGA-EE-A17Z      TCGA-EE-A29D      TCGA-ER-A19L 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE"   "PLCB4 MUTATED" "PLCB4 WILD-TYPE" 
     TCGA-ER-A1A1      TCGA-ER-A3ET      TCGA-GN-A261      TCGA-GN-A264 
  "PLCB4 MUTATED"   "PLCB4 MUTATED" "PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
     TCGA-GN-A26A      TCGA-GN-A26D 
"PLCB4 WILD-TYPE" "PLCB4 WILD-TYPE" 
[1] "hr=" "2"  
D5V2, continuous
                 vv
clus              DISTANT METASTASIS
  PLCB4 MUTATED                    0
  PLCB4 WILD-TYPE                  3
                 vv
clus              REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)
  PLCB4 MUTATED                                                                                          1
  PLCB4 WILD-TYPE                                                                                        5
                 vv
clus              REGIONAL LYMPH NODE
  PLCB4 MUTATED                     3
  PLCB4 WILD-TYPE                  10
D5V3, multiclass
                                                                                          clus
vv                                                                                         PLCB4 MUTATED
  DISTANT METASTASIS                                                                                   0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)             1
  REGIONAL LYMPH NODE                                                                                  3
                                                                                          clus
vv                                                                                         PLCB4 WILD-TYPE
  DISTANT METASTASIS                                                                                     3
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE (INCLUDES SATELLITE AND IN-TRANSIT METASTASIS)               5
  REGIONAL LYMPH NODE                                                                                   10
D5V4, binary
                 cls
clus               0  1
  PLCB4 MUTATED    1  3
  PLCB4 WILD-TYPE 10  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PLCB4 MUTATED      1    3
  PLCB4 WILD-TYPE   10    8
        clus
vv       PLCB4 MUTATED PLCB4 WILD-TYPE
  FEMALE             1              10
  MALE               3               8
                 vv
clus              N0 N1 N1A N1B N2B N3
  PLCB4 MUTATED    1  0   1   1   0  1
  PLCB4 WILD-TYPE  9  1   1   2   2  1
D5V5, multiclass
D5V6, continuous
                 vv
clus              STAGE I STAGE IA STAGE II STAGE IIB STAGE IIC STAGE III
  PLCB4 MUTATED         1        0        0         0         0         0
  PLCB4 WILD-TYPE       2        1        1         2         3         1
                 vv
clus              STAGE IIIA STAGE IIIB STAGE IIIC
  PLCB4 MUTATED            1          0          2
  PLCB4 WILD-TYPE          1          2          2
D5V7, 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")
