[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTPCPG-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PCPG-TP/11541607/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/10685824/transformed.cor.cli.txt"

nPatients in clinical file=132, in cluster file=178, common to both=132
[1] "Reduce the number of clustering variables from 9 to 6."
[1]   6 132
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
            14            118 
  HRAS MUTATED HRAS WILD-TYPE 
            14            118 
[1] "EPAS1 MUTATION ANALYSIS"
[1] 3
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              7             125 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              7             125 
[1] "NF1 MUTATION ANALYSIS"
[1] 3
  NF1 MUTATED NF1 WILD-TYPE 
           13           119 
  NF1 MUTATED NF1 WILD-TYPE 
           13           119 
[1] "RET MUTATION ANALYSIS"
[1] 3
  RET MUTATED RET WILD-TYPE 
            6           126 
  RET MUTATED RET WILD-TYPE 
            6           126 
[1] "CSDE1 MUTATION ANALYSIS"
[1] 3
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             128 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             128 
[1] "AMMECR1 MUTATION ANALYSIS"
[1] 3
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               129 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               129 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 132 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
         818          957          883           69           29          179 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK 
         240         2485          852           38         1102          211 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
          55           22          766           70          134           24 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
          29         1178           28         2957         1249          246 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 
        2643          604           89          216         1013          724 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
          32           26          405           37          356          397 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
         242          191         2214          457           21          134 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
          54           NA           18          611          730          800 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
         715          441          346          909          912          601 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
         527          324          358          185          240          371 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI 
        3180         3087         2149         2040         1857         2983 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
         274         3013           43            3         1558         1656 
TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
        2020         2222         3247         3362         3269           NA 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
         750          345         1509          132          765          242 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
         317          770          432          522           36          604 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY 
         366          380          505          538          779          324 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P 
         840          678          136          144          128         9219 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
        3880          887           NA         1000          182          531 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
         992          795          234          371           24         1131 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
         730          737         1294           34           57          595 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
         652         1406          395           NA           49          357 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
         288         2161         1719           41         2822          210 
Variable 1:'AGE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=119,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"       "GENDER"    "RACE"      "ETHNICITY"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 132 columns, 1 survival variables, and 4 non-survival variables.
AGE, nv=57, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = HRAS MUTATION ANALYSIS
D1V1, survival
                sevent
clus2              0   1
  HRAS MUTATED    14   0
  HRAS WILD-TYPE 114   4
  HRAS MUTATED HRAS WILD-TYPE 
            14            118 
  HRAS MUTATED HRAS WILD-TYPE 
             0              4 
$`HRAS MUTATED`
TCGA-P8-A5KD TCGA-PR-A5PG TCGA-S7-A7WN TCGA-S7-A7WR TCGA-SP-A6QF TCGA-SP-A6QJ 
        2.27        81.70        26.30        29.88        70.65         9.01 
TCGA-SR-A6MQ TCGA-SR-A6MY TCGA-W2-A7HC TCGA-W2-A7HD TCGA-WB-A80N TCGA-WB-A80O 
       54.44        24.66        12.03        12.49         4.73         4.21 
TCGA-WB-A81R TCGA-WB-A81T 
        1.61         9.47 

$`HRAS WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
       26.89        31.46        29.03         0.95         5.88         7.89 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
        0.59        20.09        24.00        23.51        14.50        11.38 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QH 
        7.89        12.20       104.55       101.49        67.07        61.05 
TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MR 
       98.07        99.06         1.41         0.10        51.22        66.41 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ 
       73.05       106.75       110.53       107.47         3.12        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HE TCGA-W2-A7HF 
       14.20        17.16         1.18        19.86        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P 
       25.61        10.65        27.62        22.29         4.47       303.09 
TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      127.56        29.16        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81V 
       21.44        46.22        12.99        24.82        11.74        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

  HRAS MUTATED HRAS WILD-TYPE 
          1.61           0.10 
  HRAS MUTATED HRAS WILD-TYPE 
         81.70         303.09 
  HRAS MUTATED HRAS WILD-TYPE 
        12.260         17.245 
[1] "1.6 - 81.7 (12.3)"  "0.1 - 303.1 (17.2)"
[1] "hr="     "7.9e+07"
D1V2, continuous
D1V3, binary
                cls
clus              0  1
  HRAS MUTATED    9  5
  HRAS WILD-TYPE 66 52
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      9    5
  HRAS WILD-TYPE   66   52
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            9             66
  MALE              5             52
[1] 2 2
[1] FALSE
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HRAS MUTATED                                  0     2
  HRAS WILD-TYPE                                1     3
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED                           0    12
  HRAS WILD-TYPE                         9   102
D1V4, multiclass
                                  clus
vv                                 HRAS MUTATED HRAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       2              3
  BLACK OR AFRICAN AMERICAN                   0              9
  WHITE                                      12            102
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus              0  1
  HRAS MUTATED    0 14
  HRAS WILD-TYPE  3 87
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      0   14
  HRAS WILD-TYPE    3   87
                        clus
vv                       HRAS MUTATED HRAS WILD-TYPE
  HISPANIC OR LATINO                0              3
  NOT HISPANIC OR LATINO           14             87
[1] 2 2
[1] FALSE

Clustering(2) Variable = EPAS1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2               0   1
  EPAS1 MUTATED     7   0
  EPAS1 WILD-TYPE 121   4
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              7             125 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
              0               4 
$`EPAS1 MUTATED`
TCGA-QT-A5XL TCGA-QT-A7U0 TCGA-RW-A68D TCGA-S7-A7X0 TCGA-SR-A6MV TCGA-WB-A814 
        1.81         0.95        72.79         6.08       107.47        32.88 
TCGA-WB-A821 
        1.35 

$`EPAS1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27         0.95         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK 
        7.89        81.70        28.01         1.25        36.23         6.94 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RM-A68T 
        0.72        25.18         2.30         4.41         0.79        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       15.02         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       61.05        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
       51.22        54.44        66.41        73.05       106.75       110.53 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
        3.12        24.66        11.34        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        7.96        10.42        25.32        14.20        17.16         1.18 
TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
       19.86        12.03        12.49        16.60        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        27.62        22.29         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 
      303.09       127.56        29.16        19.59         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52        92.78         6.90 

  EPAS1 MUTATED EPAS1 WILD-TYPE 
           0.95            0.10 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
         107.47          303.09 
  EPAS1 MUTATED EPAS1 WILD-TYPE 
           6.08           17.16 
[1] "0.9 - 107.5 (6.1)"  "0.1 - 303.1 (17.2)"
[1] "hr="     "2.6e+07"
D2V2, continuous
D2V3, binary
                 cls
clus               0  1
  EPAS1 MUTATED    5  2
  EPAS1 WILD-TYPE 70 55
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      5    2
  EPAS1 WILD-TYPE   70   55
        clus
vv       EPAS1 MUTATED EPAS1 WILD-TYPE
  FEMALE             5              70
  MALE               2              55
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EPAS1 MUTATED                                  0     1
  EPAS1 WILD-TYPE                                1     4
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  EPAS1 MUTATED                           1     5
  EPAS1 WILD-TYPE                         8   109
D2V4, multiclass
                                  clus
vv                                 EPAS1 MUTATED EPAS1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1               4
  BLACK OR AFRICAN AMERICAN                    1               8
  WHITE                                        5             109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                 cls
clus               0  1
  EPAS1 MUTATED    0  5
  EPAS1 WILD-TYPE  3 96
[1] "tbl2"
                 cls
clus              [,1] [,2]
  EPAS1 MUTATED      0    5
  EPAS1 WILD-TYPE    3   96
                        clus
vv                       EPAS1 MUTATED EPAS1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             5              96
[1] 2 2
[1] FALSE

Clustering(3) Variable = NF1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2             0   1
  NF1 MUTATED    13   0
  NF1 WILD-TYPE 115   4
  NF1 MUTATED NF1 WILD-TYPE 
           13           119 
  NF1 MUTATED NF1 WILD-TYPE 
            0             4 
$`NF1 MUTATED`
TCGA-QR-A6GS TCGA-RT-A6YA TCGA-RW-A67Y TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 
        1.25        41.06         7.10         0.85         1.22        11.70 
TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-SQ-A6I6 TCGA-WB-A818 TCGA-WB-A81P 
        1.78        20.09        24.00         0.10        26.14        12.99 
TCGA-WB-A81V 
       71.05 

$`NF1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27         0.95         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        7.89        81.70        28.01        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
       38.73         0.92        97.22         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68A 
        2.93        33.30        23.80         1.05        13.32        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02         0.69         4.41 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
        2.89         0.59        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       67.07        61.05        98.07         9.01        99.06         1.41 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
       51.22        54.44        66.41        73.05       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        25.32        14.20        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
        1.18        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       127.56        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
        5.98        17.46        32.61         7.69        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       19.56        21.44        46.22        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        56.52         1.35        92.78         6.90 

  NF1 MUTATED NF1 WILD-TYPE 
         0.10          0.59 
  NF1 MUTATED NF1 WILD-TYPE 
        71.05        303.09 
  NF1 MUTATED NF1 WILD-TYPE 
        11.70         17.33 
[1] "0.1 - 71.0 (11.7)"  "0.6 - 303.1 (17.3)"
[1] "hr="     "7.4e+07"
D3V2, continuous
D3V3, binary
               cls
clus             0  1
  NF1 MUTATED    7  6
  NF1 WILD-TYPE 68 51
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      7    6
  NF1 WILD-TYPE   68   51
        clus
vv       NF1 MUTATED NF1 WILD-TYPE
  FEMALE           7            68
  MALE             6            51
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  NF1 MUTATED                                  0     0
  NF1 WILD-TYPE                                1     5
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  NF1 MUTATED                           0    13
  NF1 WILD-TYPE                         9   101
D3V4, multiclass
                                  clus
vv                                 NF1 MUTATED NF1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                      0             5
  BLACK OR AFRICAN AMERICAN                  0             9
  WHITE                                     13           101
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
               cls
clus             0  1
  NF1 MUTATED    0  7
  NF1 WILD-TYPE  3 94
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF1 MUTATED      0    7
  NF1 WILD-TYPE    3   94
                        clus
vv                       NF1 MUTATED NF1 WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           7            94
[1] 2 2
[1] FALSE

Clustering(4) Variable = RET MUTATION ANALYSIS
D4V1, survival
               sevent
clus2             0   1
  RET MUTATED     6   0
  RET WILD-TYPE 122   4
  RET MUTATED RET WILD-TYPE 
            6           126 
  RET MUTATED RET WILD-TYPE 
            0             4 
$`RET MUTATED`
TCGA-QT-A5XK TCGA-QT-A5XM TCGA-SP-A6QK TCGA-W2-A7HA TCGA-WB-A80V TCGA-WB-A819 
        6.94         0.72        99.06         1.18        29.16         7.69 

$`RET WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27         0.95         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XL 
        7.89        81.70        28.01         1.25        36.23         1.81 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
        2.93         7.10        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SQ-A6I4 
       70.65        67.07        61.05        98.07         9.01         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MS TCGA-SR-A6MT 
        0.10        51.22        54.44        66.41        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       107.47         3.12        24.66        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
        4.34        25.15         7.96        10.42        25.32        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE TCGA-W2-A7HF 
       17.16        19.86        12.03        12.49        16.60        17.69 
TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N 
       25.61        10.65        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
        4.21       303.09       127.56        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       17.46        32.61        26.14        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S 
       21.44        46.22        12.99        24.82         1.61        11.74 
TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        9.47        71.05        56.52         1.35        92.78         6.90 

  RET MUTATED RET WILD-TYPE 
         0.72          0.10 
  RET MUTATED RET WILD-TYPE 
        99.06        303.09 
  RET MUTATED RET WILD-TYPE 
        7.315        17.245 
[1] "0.7 - 99.1 (7.3)"   "0.1 - 303.1 (17.2)"
[1] "hr="     "2.6e+07"
D4V2, continuous
D4V3, binary
               cls
clus             0  1
  RET MUTATED    4  2
  RET WILD-TYPE 71 55
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      4    2
  RET WILD-TYPE   71   55
        clus
vv       RET MUTATED RET WILD-TYPE
  FEMALE           4            71
  MALE             2            55
[1] 2 2
[1] FALSE
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RET MUTATED                                  1     1
  RET WILD-TYPE                                0     4
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RET MUTATED                           1     3
  RET WILD-TYPE                         8   111
D4V4, multiclass
                                  clus
vv                                 RET MUTATED RET WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1             4
  BLACK OR AFRICAN AMERICAN                  1             8
  WHITE                                      3           111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
               cls
clus             0  1
  RET MUTATED    0  4
  RET WILD-TYPE  3 97
[1] "tbl2"
               cls
clus            [,1] [,2]
  RET MUTATED      0    4
  RET WILD-TYPE    3   97
                        clus
vv                       RET MUTATED RET WILD-TYPE
  HISPANIC OR LATINO               0             3
  NOT HISPANIC OR LATINO           4            97
[1] 2 2
[1] FALSE

Clustering(5) Variable = CSDE1 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  CSDE1 MUTATED     4   0
  CSDE1 WILD-TYPE 124   4
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              4             128 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
              0               4 
$`CSDE1 MUTATED`
TCGA-RW-A681 TCGA-S7-A7WT TCGA-WB-A80M TCGA-WB-A81M 
       23.80        29.98         4.47        21.44 

$`CSDE1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY 
       26.89        31.46        29.03         2.27         0.95         5.88 
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK 
        7.89        81.70        28.01         1.25        36.23         6.94 
TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q 
        1.81         0.72        25.18         2.30         4.41         0.79 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
        0.95        38.73         0.92        97.22        41.06         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 
       86.89        19.86         2.93         7.10        33.30         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
        0.85        13.32         1.22        11.70        13.05         7.96 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        6.28        72.79        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       14.50        11.38        29.88        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
       70.65        67.07        61.05        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MS 
        1.41         0.10        51.22        54.44        66.41        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       14.20        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        27.62        22.29 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       32.88         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.12         1.87        19.56        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        11.74         9.47        71.05        56.52         1.35 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  CSDE1 MUTATED CSDE1 WILD-TYPE 
           4.47            0.10 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
          29.98          303.09 
  CSDE1 MUTATED CSDE1 WILD-TYPE 
          22.62           15.81 
[1] "4.5 - 30.0 (22.6)"  "0.1 - 303.1 (15.8)"
[1] "hr="     "2.6e+07"
D5V2, continuous
D5V3, binary
                 cls
clus               0  1
  CSDE1 MUTATED    1  3
  CSDE1 WILD-TYPE 74 54
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSDE1 MUTATED      1    3
  CSDE1 WILD-TYPE   74   54
        clus
vv       CSDE1 MUTATED CSDE1 WILD-TYPE
  FEMALE             1              74
  MALE               3              54
[1] 2 2
[1] FALSE
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CSDE1 MUTATED                                  0     0
  CSDE1 WILD-TYPE                                1     5
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  CSDE1 MUTATED                           0     4
  CSDE1 WILD-TYPE                         9   110
D5V4, multiclass
                                  clus
vv                                 CSDE1 MUTATED CSDE1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        0               5
  BLACK OR AFRICAN AMERICAN                    0               9
  WHITE                                        4             110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                 cls
clus               0  1
  CSDE1 MUTATED    0  2
  CSDE1 WILD-TYPE  3 99
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CSDE1 MUTATED      0    2
  CSDE1 WILD-TYPE    3   99
                        clus
vv                       CSDE1 MUTATED CSDE1 WILD-TYPE
  HISPANIC OR LATINO                 0               3
  NOT HISPANIC OR LATINO             2              99
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMMECR1 MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  AMMECR1 MUTATED     3   0
  AMMECR1 WILD-TYPE 125   4
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                3               129 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
                0                 4 
$`AMMECR1 MUTATED`
TCGA-P8-A6RX TCGA-RW-A688 TCGA-WB-A814 
        0.95         1.22        32.88 

$`AMMECR1 WILD-TYPE`
TCGA-P7-A5NX TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF 
       26.89        31.46        29.03         2.27         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        0.72        25.18         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
       19.86         2.93         7.10        33.30        23.80         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
        0.85        13.32        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QH TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
       70.65        67.07        61.05        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MR TCGA-SR-A6MS 
        1.41         0.10        51.22        54.44        66.41        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       14.20        17.16         1.18        19.86        12.03        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L 
       16.60        17.69        25.61        10.65        27.62        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       127.56        29.16 
TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       19.59         5.98        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
             0.95              0.10 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
            32.88            303.09 
  AMMECR1 MUTATED AMMECR1 WILD-TYPE 
             1.22             17.16 
[1] "0.9 - 32.9 (1.2)"   "0.1 - 303.1 (17.2)"
[1] "hr="     "9100000"
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  AMMECR1 MUTATED    2  1
  AMMECR1 WILD-TYPE 73 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      2    1
  AMMECR1 WILD-TYPE   73   56
        clus
vv       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  FEMALE               2                73
  MALE                 1                56
[1] 2 2
[1] FALSE
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMMECR1 MUTATED                                  0     0
  AMMECR1 WILD-TYPE                                1     5
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  AMMECR1 MUTATED                           1     2
  AMMECR1 WILD-TYPE                         8   112
D6V4, multiclass
                                  clus
vv                                 AMMECR1 MUTATED AMMECR1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 1
  ASIAN                                          0                 5
  BLACK OR AFRICAN AMERICAN                      1                 8
  WHITE                                          2               112
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                   cls
clus                 0  1
  AMMECR1 MUTATED    0  2
  AMMECR1 WILD-TYPE  3 99
[1] "tbl2"
                   cls
clus                [,1] [,2]
  AMMECR1 MUTATED      0    2
  AMMECR1 WILD-TYPE    3   99
                        clus
vv                       AMMECR1 MUTATED AMMECR1 WILD-TYPE
  HISPANIC OR LATINO                   0                 3
  NOT HISPANIC OR LATINO               2                99
[1] 2 2
[1] FALSE
