[1] "ofn"        "-oTDLBC-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/22506396/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/22541055/DLBC-TP.mergedcluster.txt"

nPatients in clinical file=48, in cluster file=48, common to both=48
[1] 10 48
[1] "CN_CNMF"
[1] 3
 1  2  3 
20  7 21 
 1  2  3 
20  7 21 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4 
 9 13 19  7 
 1  2  3  4 
 9 13 19  7 
[1] "RPPA_CNMF"
[1] 3
1 2 3 4 5 6 
6 5 5 6 6 5 
1 2 3 4 5 6 
6 5 5 6 6 5 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
 6 15 12 
 1  2  3 
 6 15 12 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5  6 
10 12  9  3  8  6 
 1  2  3  4  5  6 
10 12  9  3  8  6 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
22 11  7  8 
 1  2  3  4 
22 11  7  8 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
16 16 15 
 1  2  3 
16 16 15 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
 9 12  8 12  6 
 1  2  3  4  5 
 9 12  8 12  6 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
 9 10  9 14 
 1  2  3  4 
 9 10  9 14 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
 8 15  5 14 
 1  2  3  4 
 8 15  5 14 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "NUMBER_OF_LYMPH_NODES"               
[15] "RACE"                                
[16] "ETHNICITY"                           

Input Data has 16 rows and 48 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=37,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGIC_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NUMBER_OF_LYMPH_NODES is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 48 columns, 1 survival variables, and 7 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "TUMOR_TISSUE_SITE" "GENDER"           
[4] "RADIATION_THERAPY" "HISTOLOGICAL_TYPE" "RACE"             
[7] "ETHNICITY"        
YEARS_TO_BIRTH, nv=34, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=13, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 14  5
  subtype2  5  2
  subtype3 19  2
subtype1 subtype2 subtype3 
      19        7       21 
subtype1 subtype2 subtype3 
       5        2        2 
$subtype1
TCGA-FA-8693 TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8062 TCGA-FF-A7CX 
        4.34         8.15        35.54        24.69        22.32        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6906 TCGA-G8-6909 TCGA-GR-7351 
       31.96        41.16        51.98       211.23       116.81       150.51 
TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TW TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A6JB 
       42.71        57.17        53.16        25.15        12.85         0.03 
TCGA-RQ-AAAT 
        0.56 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7353 
        4.34         1.91        70.06        19.56       196.60        98.07 
TCGA-GS-A9TV 
       24.00 

$subtype3
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8042 
       23.28        24.62        23.64        14.04        18.18        31.10 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
       31.73         4.14        27.35         9.80        10.29        26.01 
TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TX 
       51.98        43.86        32.28        38.24       128.12        45.14 
TCGA-GS-A9TY TCGA-GS-A9U3 TCGA-RQ-A68N 
      109.58       111.58        25.91 

subtype1 subtype2 subtype3 
    0.03     1.91     4.14 
subtype1 subtype2 subtype3 
  211.23   196.60   128.12 
subtype1 subtype2 subtype3 
   31.96    24.00    27.35 
[1] "0.0 - 211.2 (32.0)" "1.9 - 196.6 (24.0)" "4.1 - 128.1 (27.4)"
D1V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       1                  1    2     1      0     1     0
  subtype2       0                  1    0     0      0     0     1
  subtype3       1                  0    2     2      1     1     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  subtype1                     1             0               0
  subtype2                     0             0               0
  subtype3                     0             1               3
          vv
clus       SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  subtype1                                             1       2       2
  subtype2                                             0       0       0
  subtype3                                             0       0       0
D1V3, multiclass
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
      12        2       11 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype3" "subtype3" "subtype1" "subtype1"
[13] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[19] "subtype3" "subtype3" "subtype1" "subtype1" "subtype1"
                                               clus
vv                                              subtype1 subtype3
  ADRENAL                                              1        1
  ASCITES/PERITONEUM                                   1        0
  BONE                                                 2        2
  BRAIN                                                1        2
  BREAST                                               0        1
  COLON                                                1        1
  OTHER EXTRANODAL SITE                                1        0
  PAROTID GLAND                                        0        1
  SMALL INTESTINE                                      0        3
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        1        0
  STOMACH                                              2        0
  THYROID                                              2        0
[1] 12  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V4, binary
          cls
clus        0  1
  subtype1 12  8
  subtype2  2  5
  subtype3 12  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    8
  subtype2    2    5
  subtype3   12    9
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12        2       12
  MALE          8        5        9
[1] 2 3
[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
  subtype1 16  3
  subtype2  6  1
  subtype3 18  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    3
  subtype2    6    1
  subtype3   18    3
     clus
vv    subtype1 subtype2 subtype3
  NO        16        6       18
  YES        3        1        3
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                15
  subtype2                                                                                 6
  subtype3                                                                                20
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        2                                  3
  subtype2                        0                                  1
  subtype3                        1                                  0
D1V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       15
  PRIMARY DLBCL OF THE CNS                                                                 2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       3
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        6
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       20
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         1    14
  subtype2     1                         0     6
  subtype3    12                         0     9
D1V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            5        1       12
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                           14        6        9
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus        0  1
  subtype1  4 16
  subtype2  1  6
  subtype3  7 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   16
  subtype2    1    6
  subtype3    7   14
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        7
  NOT HISPANIC OR LATINO       16        6       14
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1  7  2
  subtype2 11  2
  subtype3 14  4
  subtype4  6  1
subtype1 subtype2 subtype3 subtype4 
       9       13       18        7 
subtype1 subtype2 subtype3 subtype4 
       2        2        4        1 
$subtype1
TCGA-FA-8693 TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8062 TCGA-G8-6909 TCGA-GR-7351 
        4.34         1.91        35.54        22.32       116.81       150.51 
TCGA-GR-7353 TCGA-GS-A9TW TCGA-GS-A9TZ 
       98.07        53.16        25.15 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-A7CW TCGA-G8-6324 TCGA-G8-6325 
        4.34        24.62        18.18        26.01        41.16        51.98 
TCGA-G8-6326 TCGA-GR-A4D5 TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX TCGA-GS-A9U3 
       70.06        42.71       128.12        24.00        45.14       111.58 
TCGA-GS-A9U4 
       12.85 

$subtype3
TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8047 
       23.28        23.64         8.15        14.04        31.10         4.14 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6906 TCGA-GR-A4D9 
        9.80        10.29        12.66        31.96       211.23        57.17 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9TY TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       32.28        38.24       109.58        25.91         0.03         0.56 

$subtype4
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-A4D4 
       31.73        24.69        27.35        19.56       196.60        51.98 
TCGA-GR-A4D6 
       43.86 

subtype1 subtype2 subtype3 subtype4 
    1.91     4.34     0.03    19.56 
subtype1 subtype2 subtype3 subtype4 
  150.51   128.12   211.23   196.60 
subtype1 subtype2 subtype3 subtype4 
   35.54    41.16    23.46    31.73 
[1] "1.9 - 150.5 (35.5)"  "4.3 - 128.1 (41.2)"  "0.0 - 211.2 (23.5)" 
[4] "19.6 - 196.6 (31.7)"
D2V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  0    0     0      0     0     0
  subtype2       0                  2    1     0      0     0     1
  subtype3       2                  0    2     3      1     1     0
  subtype4       0                  0    1     0      0     1     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  subtype1                     0             0               0
  subtype2                     0             1               0
  subtype3                     1             0               2
  subtype4                     0             0               1
          vv
clus       SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  subtype1                                             0       1       2
  subtype2                                             0       0       0
  subtype3                                             1       1       0
  subtype4                                             0       0       0
D2V3, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADRENAL                                              0        0        2
  ASCITES/PERITONEUM                                   0        2        0
  BONE                                                 0        1        2
  BRAIN                                                0        0        3
  BREAST                                               0        0        1
  COLON                                                0        0        1
  LIVER                                                0        1        0
  OTHER EXTRANODAL SITE                                0        0        1
  PAROTID GLAND                                        0        1        0
  SMALL INTESTINE                                      0        0        2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        0        0        1
  STOMACH                                              1        0        1
  THYROID                                              2        0        0
                                               clus
vv                                              subtype4
  ADRENAL                                              0
  ASCITES/PERITONEUM                                   0
  BONE                                                 1
  BRAIN                                                0
  BREAST                                               0
  COLON                                                1
  LIVER                                                0
  OTHER EXTRANODAL SITE                                0
  PAROTID GLAND                                        0
  SMALL INTESTINE                                      1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        0
  STOMACH                                              0
  THYROID                                              0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V4, binary
          cls
clus        0  1
  subtype1  4  5
  subtype2  7  6
  subtype3 11  8
  subtype4  4  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    5
  subtype2    7    6
  subtype3   11    8
  subtype4    4    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4        7       11        4
  MALE          5        6        8        3
[1] 2 4
[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
  subtype1  6  3
  subtype2 10  3
  subtype3 17  1
  subtype4  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    3
  subtype2   10    3
  subtype3   17    1
  subtype4    7    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6       10       17        7
  YES        3        3        1        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                 6
  subtype2                                                                                12
  subtype3                                                                                16
  subtype4                                                                                 7
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        0                                  3
  subtype2                        0                                  1
  subtype3                        3                                  0
  subtype4                        0                                  0
D2V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        6
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       3
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       12
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       16
  PRIMARY DLBCL OF THE CNS                                                                 3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype4
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        7
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         0     6
  subtype2     2                         1    10
  subtype3     9                         0    10
  subtype4     4                         0     3
D2V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        2        9        4
  BLACK OR AFRICAN AMERICAN        0        1        0        0
  WHITE                            6       10       10        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus        0  1
  subtype1  2  7
  subtype2  5  8
  subtype3  5 14
  subtype4  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    5    8
  subtype3    5   14
  subtype4    0    7
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        5        5        0
  NOT HISPANIC OR LATINO        7        8       14        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2      0 1
  subtype1 4 1
  subtype2 3 2
  subtype3 4 1
  subtype4 6 0
  subtype5 5 1
  subtype6 4 1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       5        5        5        6        6        5 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        2        1        0        1        1 
$subtype1
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8043 
        4.34         4.34        23.28        14.04        31.73 

$subtype2
TCGA-FA-A6HN TCGA-FA-A86F TCGA-FF-A7CR TCGA-GS-A9TV TCGA-GS-A9TX 
        1.91        18.18        10.29        24.00        45.14 

$subtype3
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CW 
       24.62         8.15         4.14        22.32        26.01 

$subtype4
TCGA-FA-A7DS TCGA-FF-8042 TCGA-FF-8046 TCGA-G8-6914 TCGA-GS-A9TT TCGA-GS-A9TW 
       23.64        31.10        24.69       196.60        38.24        53.16 

$subtype5
TCGA-FF-8041 TCGA-FF-8061 TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6906 TCGA-GS-A9TZ 
       35.54        27.35        31.96        51.98       211.23        25.15 

$subtype6
TCGA-FF-A7CX TCGA-G8-6326 TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB 
       12.66        70.06        12.85        25.91         0.03 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    4.34     1.91     4.14    23.64    25.15     0.03 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   31.73    45.14    26.01   196.60   211.23    70.06 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   14.04    18.18    22.32    34.67    33.75    12.85 
[1] "4.3 - 31.7 (14.0)"   "1.9 - 45.1 (18.2)"   "4.1 - 26.0 (22.3)"  
[4] "23.6 - 196.6 (34.7)" "25.1 - 211.2 (33.8)" "0.0 - 70.1 (12.8)"  
D3V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  0    0     0      0     1     1
  subtype2       0                  0    0     1      0     0     0
  subtype3       0                  0    0     0      0     0     0
  subtype4       0                  0    1     0      1     0     0
  subtype5       0                  0    0     0      0     1     0
  subtype6       1                  1    1     1      0     0     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE STOMACH THYROID
  subtype1                     0             0               2       2       0
  subtype2                     0             0               0       0       0
  subtype3                     0             1               0       0       1
  subtype4                     0             0               0       0       0
  subtype5                     1             0               1       0       0
  subtype6                     0             0               0       0       0
D3V3, multiclass
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        1        2        2        3        4 
 [1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype5"
 [7] "subtype6" "subtype5" "subtype6" "subtype5" "subtype6" "subtype6"
[13] "subtype1"
                       clus
vv                      subtype1 subtype5 subtype6
  ADRENAL                      0        0        1
  ASCITES/PERITONEUM           0        0        1
  BONE                         0        0        1
  BRAIN                        0        0        1
  COLON                        1        1        0
  LIVER                        1        0        0
  OTHER EXTRANODAL SITE        0        1        0
  SMALL INTESTINE              2        1        0
  STOMACH                      2        0        0
[1] 9 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V4, binary
          cls
clus       0 1
  subtype1 2 4
  subtype2 2 3
  subtype3 4 1
  subtype4 3 3
  subtype5 2 4
  subtype6 2 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    4
  subtype2    2    3
  subtype3    4    1
  subtype4    3    3
  subtype5    2    4
  subtype6    2    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        2        2        4        3        2        2
  MALE          4        3        1        3        4        3
[1] 2 6
[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
  subtype1 6 0
  subtype2 3 2
  subtype3 5 0
  subtype4 4 2
  subtype5 5 1
  subtype6 4 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    0
  subtype2    3    2
  subtype3    5    0
  subtype4    4    2
  subtype5    5    1
  subtype6    4    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         6        3        5        4        5        4
  YES        0        2        0        2        1        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                 6
  subtype2                                                                                 4
  subtype3                                                                                 5
  subtype4                                                                                 5
  subtype5                                                                                 4
  subtype6                                                                                 3
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        0                                  0
  subtype2                        0                                  1
  subtype3                        0                                  0
  subtype4                        0                                  1
  subtype5                        0                                  2
  subtype6                        2                                  0
D3V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        6
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        4
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        5
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype4
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        5
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype5
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        4
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       2
                                                                                   clus
vv                                                                                  subtype6
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        3
  PRIMARY DLBCL OF THE CNS                                                                 2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN WHITE
  subtype1     3     3
  subtype2     2     3
  subtype3     5     0
  subtype4     3     3
  subtype5     2     4
  subtype6     1     4
D3V7, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  ASIAN        3        2        5        3        2        1
  WHITE        3        3        0        3        4        4
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus       0 1
  subtype1 0 6
  subtype2 2 3
  subtype3 0 5
  subtype4 2 4
  subtype5 1 5
  subtype6 2 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    6
  subtype2    2    3
  subtype3    0    5
  subtype4    2    4
  subtype5    1    5
  subtype6    2    3
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        2        0        2        1        2
  NOT HISPANIC OR LATINO        6        3        5        4        5        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1  5  1
  subtype2 12  2
  subtype3  9  3
subtype1 subtype2 subtype3 
       6       14       12 
subtype1 subtype2 subtype3 
       1        2        3 
$subtype1
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A82F TCGA-G8-6326 TCGA-GS-A9U4 TCGA-RQ-A6JB 
        4.34         4.34        14.04        70.06        12.85         0.03 

$subtype2
TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
       23.28        23.64        35.54        31.10        31.73        24.69 
TCGA-FF-8061 TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6906 TCGA-GS-A9TT 
       27.35        12.66        31.96        51.98       211.23        38.24 
TCGA-GS-A9TW TCGA-GS-A9TZ 
       53.16        25.15 

$subtype3
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8047 TCGA-FF-8062 
        1.91        24.62         8.15        18.18         4.14        22.32 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-G8-6914 TCGA-GS-A9TV TCGA-GS-A9TX TCGA-RQ-A68N 
       10.29        26.01       196.60        24.00        45.14        25.91 

subtype1 subtype2 subtype3 
    0.03    12.66     1.91 
subtype1 subtype2 subtype3 
   70.06   211.23   196.60 
subtype1 subtype2 subtype3 
   8.595   31.415   23.160 
[1] "0.0 - 70.1 (8.6)"    "12.7 - 211.2 (31.4)" "1.9 - 196.6 (23.2)" 
D4V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  1    1     0      0     0     1
  subtype2       1                  0    1     0      1     2     0
  subtype3       0                  0    0     2      0     0     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE STOMACH THYROID
  subtype1                     0             0               1       1       0
  subtype2                     1             0               2       1       0
  subtype3                     0             1               0       0       1
D4V3, multiclass
                       clus
vv                      subtype1 subtype2 subtype3
  ADRENAL                      0        1        0
  ASCITES/PERITONEUM           1        0        0
  BONE                         1        1        0
  BRAIN                        0        0        2
  BREAST                       0        1        0
  COLON                        0        2        0
  LIVER                        1        0        0
  OTHER EXTRANODAL SITE        0        1        0
  PAROTID GLAND                0        0        1
  SMALL INTESTINE              1        2        0
  STOMACH                      1        1        0
  THYROID                      0        0        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V4, binary
          cls
clus       0 1
  subtype1 3 3
  subtype2 6 9
  subtype3 6 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    6    9
  subtype3    6    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        6        6
  MALE          3        9        6
[1] 2 3
[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
  subtype1  5  0
  subtype2 12  3
  subtype3 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   12    3
  subtype3   10    2
     clus
vv    subtype1 subtype2 subtype3
  NO         5       12       10
  YES        0        3        2
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                 5
  subtype2                                                                                12
  subtype3                                                                                10
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        1                                  0
  subtype2                        0                                  3
  subtype3                        1                                  1
D4V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        5
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       12
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       3
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       10
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN WHITE
  subtype1     1     5
  subtype2     8     7
  subtype3     7     5
D4V7, multiclass
       clus
vv      subtype1 subtype2 subtype3
  ASIAN        1        8        7
  WHITE        5        7        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
          cls
clus        0  1
  subtype1  1  5
  subtype2  3 12
  subtype3  3  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    5
  subtype2    3   12
  subtype3    3    9
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        3
  NOT HISPANIC OR LATINO        5       12        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1  7  2
  subtype2 10  2
  subtype3  8  1
  subtype4  2  1
  subtype5  6  2
  subtype6  5  1
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       9       12        9        3        8        6 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       2        2        1        1        2        1 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6906 
        4.34        23.28        31.10        27.35        22.32       211.23 
TCGA-G8-6914 TCGA-GR-7351 TCGA-RQ-A6JB 
      196.60       150.51         0.03 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8046 TCGA-FF-A7CW 
        4.34         1.91        24.62        18.18        24.69        26.01 
TCGA-G8-6324 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9U3 
       41.16        42.71        43.86       128.12        45.14       111.58 

$subtype3
TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8047 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX 
       23.64        14.04         4.14         9.80        10.29        12.66 
TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-RQ-A68N 
       57.17        38.24        25.91 

$subtype4
TCGA-FA-A7Q1 TCGA-GR-A4D4 TCGA-GS-A9TQ 
        8.15        51.98        32.28 

$subtype5
TCGA-FF-8041 TCGA-FF-8043 TCGA-FM-8000 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7353 
       35.54        31.73        31.96        19.56       116.81        98.07 
TCGA-GS-A9TY TCGA-RQ-AAAT 
      109.58         0.56 

$subtype6
TCGA-G8-6325 TCGA-G8-6326 TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TZ TCGA-GS-A9U4 
       51.98        70.06        24.00        53.16        25.15        12.85 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.03     1.91     4.14     8.15     0.56    12.85 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  211.23   128.12    57.17    51.98   116.81    70.06 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  27.350   33.585   14.040   32.280   33.750   38.565 
[1] "0.0 - 211.2 (27.4)" "1.9 - 128.1 (33.6)" "4.1 - 57.2 (14.0)" 
[4] "8.2 - 52.0 (32.3)"  "0.6 - 116.8 (33.8)" "12.8 - 70.1 (38.6)"
D5V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  0    1     0      0     0     0
  subtype2       0                  1    1     0      0     0     1
  subtype3       2                  0    1     2      1     0     0
  subtype4       0                  0    1     0      0     0     0
  subtype5       0                  0    0     1      0     2     0
  subtype6       0                  1    0     0      0     0     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  subtype1                     1             0               2
  subtype2                     0             1               0
  subtype3                     0             0               1
  subtype4                     0             0               0
  subtype5                     0             0               0
  subtype6                     0             0               0
          vv
clus       SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  subtype1                                             0       2       2
  subtype2                                             0       0       0
  subtype3                                             1       0       0
  subtype4                                             0       0       0
  subtype5                                             0       0       0
  subtype6                                             0       0       0
D5V3, multiclass
[1] "Remove cluster labels:" "subtype4"               "subtype6"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       8        4        8        1        3        1 
 [1] "subtype1" "subtype2" "subtype1" "subtype3" "subtype3" "subtype5"
 [7] "subtype1" "subtype1" "subtype3" "subtype3" "subtype2" "subtype3"
[13] "subtype5" "subtype2" "subtype1" "subtype1" "subtype2" "subtype3"
[19] "subtype3" "subtype3" "subtype1" "subtype5" "subtype1"
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADRENAL                                              0        0        2
  ASCITES/PERITONEUM                                   0        1        0
  BONE                                                 1        1        1
  BRAIN                                                0        0        2
  BREAST                                               0        0        1
  COLON                                                0        0        0
  LIVER                                                0        1        0
  OTHER EXTRANODAL SITE                                1        0        0
  PAROTID GLAND                                        0        1        0
  SMALL INTESTINE                                      2        0        1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        0        0        1
  STOMACH                                              2        0        0
  THYROID                                              2        0        0
                                               clus
vv                                              subtype5
  ADRENAL                                              0
  ASCITES/PERITONEUM                                   0
  BONE                                                 0
  BRAIN                                                1
  BREAST                                               0
  COLON                                                2
  LIVER                                                0
  OTHER EXTRANODAL SITE                                0
  PAROTID GLAND                                        0
  SMALL INTESTINE                                      0
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        0
  STOMACH                                              0
  THYROID                                              0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V4, binary
          cls
clus       0 1
  subtype1 4 6
  subtype2 6 6
  subtype3 4 5
  subtype4 3 0
  subtype5 6 2
  subtype6 3 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4    6
  subtype2    6    6
  subtype3    4    5
  subtype4    3    0
  subtype5    6    2
  subtype6    3    3
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        4        6        4        3        6        3
  MALE          6        6        5        0        2        3
[1] 2 6
[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
  subtype1  8  1
  subtype2 10  2
  subtype3  8  1
  subtype4  3  0
  subtype5  8  0
  subtype6  3  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    1
  subtype2   10    2
  subtype3    8    1
  subtype4    3    0
  subtype5    8    0
  subtype6    3    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         8       10        8        3        8        3
  YES        1        2        1        0        0        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                 9
  subtype2                                                                                12
  subtype3                                                                                 8
  subtype4                                                                                 3
  subtype5                                                                                 6
  subtype6                                                                                 3
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        1                                  0
  subtype2                        0                                  0
  subtype3                        1                                  0
  subtype4                        0                                  0
  subtype5                        1                                  1
  subtype6                        0                                  3
D5V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        9
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       12
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        8
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype4
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        3
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype5
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        6
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype6
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        3
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       3
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         0     6
  subtype2     5                         1     6
  subtype3     6                         0     3
  subtype4     1                         0     2
  subtype5     2                         0     6
  subtype6     0                         0     6
D5V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            4        5        6        1        2
  BLACK OR AFRICAN AMERICAN        0        1        0        0        0
  WHITE                            6        6        3        2        6
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        0
  WHITE                            6
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1  0 10
  subtype2  3  9
  subtype3  2  7
  subtype4  1  2
  subtype5  2  6
  subtype6  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   10
  subtype2    3    9
  subtype3    2    7
  subtype4    1    2
  subtype5    2    6
  subtype6    4    2
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        3        2        1        2        4
  NOT HISPANIC OR LATINO       10        9        7        2        6        2
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 18  3
  subtype2  9  2
  subtype3  5  2
  subtype4  6  2
subtype1 subtype2 subtype3 subtype4 
      21       11        7        8 
subtype1 subtype2 subtype3 subtype4 
       3        2        2        2 
$subtype1
TCGA-FA-8693 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        4.34        14.04        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6326 
        4.14        27.35        22.32        31.96        51.98        70.06 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       116.81       196.60       150.51        98.07 
TCGA-GS-A9TY TCGA-RQ-A68N TCGA-RQ-AAAT 
      109.58        25.91         0.56 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-A7CW TCGA-G8-6324 
        4.34         1.91        24.62        18.18        26.01        41.16 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9U3 
       42.71        43.86       128.12        45.14       111.58 

$subtype3
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FF-A7CX TCGA-GR-A4D4 TCGA-GS-A9TQ TCGA-GS-A9TT 
       23.28         8.15        12.66        51.98        32.28        38.24 
TCGA-RQ-A6JB 
        0.03 

$subtype4
TCGA-FA-A7DS TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-GR-A4D9 TCGA-GS-A9TV TCGA-GS-A9TW 
       23.64         9.80        10.29        57.17        24.00        53.16 
TCGA-GS-A9TZ TCGA-GS-A9U4 
       25.15        12.85 

subtype1 subtype2 subtype3 subtype4 
    0.56     1.91     0.03     9.80 
subtype1 subtype2 subtype3 subtype4 
  211.23   128.12    51.98    57.17 
subtype1 subtype2 subtype3 subtype4 
   31.73    41.16    23.28    23.82 
[1] "0.6 - 211.2 (31.7)" "1.9 - 128.1 (41.2)" "0.0 - 52.0 (23.3)" 
[4] "9.8 - 57.2 (23.8)" 
D6V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  1    0     2      0     2     0
  subtype2       0                  1    1     0      0     0     1
  subtype3       1                  0    3     0      0     0     0
  subtype4       1                  0    0     1      1     0     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  subtype1                     1             0               2
  subtype2                     0             1               0
  subtype3                     0             0               1
  subtype4                     0             0               0
          vv
clus       SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  subtype1                                             0       2       2
  subtype2                                             0       0       0
  subtype3                                             0       0       0
  subtype4                                             1       0       0
D6V3, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADRENAL                                              0        0        1
  ASCITES/PERITONEUM                                   1        1        0
  BONE                                                 0        1        3
  BRAIN                                                2        0        0
  BREAST                                               0        0        0
  COLON                                                2        0        0
  LIVER                                                0        1        0
  OTHER EXTRANODAL SITE                                1        0        0
  PAROTID GLAND                                        0        1        0
  SMALL INTESTINE                                      2        0        1
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        0        0        0
  STOMACH                                              2        0        0
  THYROID                                              2        0        0
                                               clus
vv                                              subtype4
  ADRENAL                                              1
  ASCITES/PERITONEUM                                   0
  BONE                                                 0
  BRAIN                                                1
  BREAST                                               1
  COLON                                                0
  LIVER                                                0
  OTHER EXTRANODAL SITE                                0
  PAROTID GLAND                                        0
  SMALL INTESTINE                                      0
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        1
  STOMACH                                              0
  THYROID                                              0
[1] 13  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V4, binary
          cls
clus        0  1
  subtype1 11 11
  subtype2  6  5
  subtype3  4  3
  subtype4  5  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   11
  subtype2    6    5
  subtype3    4    3
  subtype4    5    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       11        6        4        5
  MALE         11        5        3        3
[1] 2 4
[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
  subtype1 21  1
  subtype2  9  2
  subtype3  5  1
  subtype4  5  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    1
  subtype2    9    2
  subtype3    5    1
  subtype4    5    3
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21        9        5        5
  YES        1        2        1        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                19
  subtype2                                                                                11
  subtype3                                                                                 6
  subtype4                                                                                 5
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        2                                  1
  subtype2                        0                                  0
  subtype3                        1                                  0
  subtype4                        0                                  3
D6V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       19
  PRIMARY DLBCL OF THE CNS                                                                 2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       11
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        6
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype4
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        5
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     8                         0    14
  subtype2     4                         1     6
  subtype3     3                         0     4
  subtype4     3                         0     5
D6V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            8        4        3        3
  BLACK OR AFRICAN AMERICAN        0        1        0        0
  WHITE                           14        6        4        5
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1  3 19
  subtype2  3  8
  subtype3  2  5
  subtype4  4  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   19
  subtype2    3    8
  subtype3    2    5
  subtype4    4    4
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        3        2        4
  NOT HISPANIC OR LATINO       19        8        5        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 12  3
  subtype2 12  4
  subtype3 13  2
subtype1 subtype2 subtype3 
      15       16       15 
subtype1 subtype2 subtype3 
       3        4        2 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8061 
        4.34        23.28         8.15        14.04        31.10        27.35 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6914 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TW 
       70.06       211.23       196.60        57.17        38.24        53.16 
TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       25.91         0.03         0.56 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        4.34         1.91        35.54        31.73        24.69         4.14 
TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6907 TCGA-G8-6909 
       22.32        31.96        41.16        51.98        19.56       116.81 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GS-A9TY 
       98.07        51.98        43.86       109.58 

$subtype3
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A86F TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
       24.62        23.64        18.18         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-GR-A4D5 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TX 
       12.66        42.71        32.28       128.12        24.00        45.14 
TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       25.15       111.58        12.85 

subtype1 subtype2 subtype3 
    0.03     1.91     9.80 
subtype1 subtype2 subtype3 
  211.23   116.81   128.12 
subtype1 subtype2 subtype3 
   27.35    33.75    24.62 
[1] "0.0 - 211.2 (27.4)" "1.9 - 116.8 (33.8)" "9.8 - 128.1 (24.6)"
D7V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  1    2     2      0     0     0
  subtype2       0                  1    1     0      0     2     1
  subtype3       2                  0    1     1      1     0     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  subtype1                     1             0               3
  subtype2                     0             0               0
  subtype3                     0             1               0
          vv
clus       SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  subtype1                                             1       2       0
  subtype2                                             0       0       1
  subtype3                                             0       0       0
D7V3, multiclass
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADRENAL                                              0        0        2
  ASCITES/PERITONEUM                                   1        1        0
  BONE                                                 2        1        1
  BRAIN                                                2        0        1
  BREAST                                               0        0        1
  COLON                                                0        2        0
  LIVER                                                0        1        0
  OTHER EXTRANODAL SITE                                1        0        0
  PAROTID GLAND                                        0        0        1
  SMALL INTESTINE                                      3        0        0
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        1        0        0
  STOMACH                                              2        0        0
  THYROID                                              0        1        0
[1] 13  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V4, binary
          cls
clus        0  1
  subtype1  7  9
  subtype2 10  6
  subtype3  8  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    9
  subtype2   10    6
  subtype3    8    7
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       10        8
  MALE          9        6        7
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
          cls
clus        0  1
  subtype1 13  2
  subtype2 16  0
  subtype3 11  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    2
  subtype2   16    0
  subtype3   11    4
     clus
vv    subtype1 subtype2 subtype3
  NO        13       16       11
  YES        2        0        4
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                12
  subtype2                                                                                15
  subtype3                                                                                13
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        3                                  1
  subtype2                        0                                  1
  subtype3                        0                                  2
D7V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       12
  PRIMARY DLBCL OF THE CNS                                                                 3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       15
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       13
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     5                         0    11
  subtype2     7                         1     8
  subtype3     6                         0     9
D7V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            5        7        6
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                           11        8        9
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1  4 12
  subtype2  1 15
  subtype3  7  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   12
  subtype2    1   15
  subtype3    7    8
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        7
  NOT HISPANIC OR LATINO       12       15        8
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1  8  1
  subtype2  9  3
  subtype3  5  2
  subtype4 10  2
  subtype5  5  1
subtype1 subtype2 subtype3 subtype4 subtype5 
       9       12        7       12        6 
subtype1 subtype2 subtype3 subtype4 subtype5 
       1        3        2        2        1 
$subtype1
TCGA-FA-8693 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-A7CX TCGA-G8-6325 
        4.34        31.10        24.69        27.35        12.66        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-GR-A4D4 
       70.06       211.23        51.98 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8062 TCGA-G8-6324 
        4.34         1.91        24.62        18.18        22.32        41.16 
TCGA-G8-6909 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TV TCGA-GS-A9TY TCGA-GS-A9TZ 
      116.81        42.71        43.86        24.00       109.58        25.15 

$subtype3
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-G8-6914 TCGA-RQ-A68N TCGA-RQ-A6JB 
       23.28         8.15        14.04       196.60        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

$subtype4
TCGA-FA-A7DS TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-GR-A4D9 TCGA-GS-A9TQ 
       23.64         9.80        10.29        26.01        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-GS-A9U4 
       38.24       128.12        53.16        45.14       111.58        12.85 

$subtype5
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 TCGA-FM-8000 TCGA-G8-6907 TCGA-GR-7353 
       35.54        31.73         4.14        31.96        19.56        98.07 

subtype1 subtype2 subtype3 subtype4 subtype5 
    4.34     1.91     0.03     9.80     4.14 
subtype1 subtype2 subtype3 subtype4 subtype5 
  211.23   116.81   196.60   128.12    98.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  31.100   24.885   14.040   35.260   31.845 
[1] "4.3 - 211.2 (31.1)" "1.9 - 116.8 (24.9)" "0.0 - 196.6 (14.0)"
[4] "9.8 - 128.1 (35.3)" "4.1 - 98.1 (31.8)" 
D8V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       1                  1    1     0      0     0     0
  subtype2       0                  1    1     0      0     0     1
  subtype3       0                  0    1     2      0     0     0
  subtype4       1                  0    1     1      1     0     0
  subtype5       0                  0    0     0      0     2     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE
  subtype1                     1             0               1
  subtype2                     0             0               0
  subtype3                     0             0               2
  subtype4                     0             1               0
  subtype5                     0             0               0
          vv
clus       SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS) STOMACH THYROID
  subtype1                                             0       1       0
  subtype2                                             0       0       1
  subtype3                                             0       1       0
  subtype4                                             1       0       0
  subtype5                                             0       0       0
D8V3, multiclass
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       6        4        6        6        2 
 [1] "subtype1" "subtype2" "subtype3" "subtype4" "subtype3" "subtype1"
 [7] "subtype2" "subtype4" "subtype4" "subtype4" "subtype1" "subtype2"
[13] "subtype1" "subtype1" "subtype1" "subtype2" "subtype4" "subtype4"
[19] "subtype3" "subtype3" "subtype3" "subtype3"
                                               clus
vv                                              subtype1 subtype2 subtype3
  ADRENAL                                              1        0        0
  ASCITES/PERITONEUM                                   1        1        0
  BONE                                                 1        1        1
  BRAIN                                                0        0        2
  BREAST                                               0        0        0
  LIVER                                                0        1        0
  OTHER EXTRANODAL SITE                                1        0        0
  PAROTID GLAND                                        0        0        0
  SMALL INTESTINE                                      1        0        2
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        0        0        0
  STOMACH                                              1        0        1
  THYROID                                              0        1        0
                                               clus
vv                                              subtype4
  ADRENAL                                              1
  ASCITES/PERITONEUM                                   0
  BONE                                                 1
  BRAIN                                                1
  BREAST                                               1
  LIVER                                                0
  OTHER EXTRANODAL SITE                                0
  PAROTID GLAND                                        1
  SMALL INTESTINE                                      0
  SOFT TISSUE (MUSCLE  LIGAMENTS  SUBCUTANEOUS)        1
  STOMACH                                              0
  THYROID                                              0
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V4, binary
          cls
clus       0 1
  subtype1 2 7
  subtype2 8 4
  subtype3 4 4
  subtype4 6 6
  subtype5 5 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    8    4
  subtype3    4    4
  subtype4    6    6
  subtype5    5    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        2        8        4        6        5
  MALE          7        4        4        6        1
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1  9  0
  subtype2 10  2
  subtype3  7  0
  subtype4  8  4
  subtype5  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    0
  subtype2   10    2
  subtype3    7    0
  subtype4    8    4
  subtype5    6    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         9       10        7        8        6
  YES        0        2        0        4        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                 9
  subtype2                                                                                10
  subtype3                                                                                 5
  subtype4                                                                                11
  subtype5                                                                                 5
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        0                                  0
  subtype2                        0                                  2
  subtype3                        3                                  0
  subtype4                        0                                  1
  subtype5                        0                                  1
D8V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        9
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       10
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       2
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        5
  PRIMARY DLBCL OF THE CNS                                                                 3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype4
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       11
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype5
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        5
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         0     5
  subtype2     4                         1     7
  subtype3     3                         0     5
  subtype4     4                         0     8
  subtype5     3                         0     3
D8V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            4        4        3        4        3
  BLACK OR AFRICAN AMERICAN        0        1        0        0        0
  WHITE                            5        7        5        8        3
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus       0 1
  subtype1 0 9
  subtype2 3 9
  subtype3 2 6
  subtype4 7 5
  subtype5 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    9
  subtype2    3    9
  subtype3    2    6
  subtype4    7    5
  subtype5    0    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        3        2        7        0
  NOT HISPANIC OR LATINO        9        9        6        5        6
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1  7  1
  subtype2  8  2
  subtype3  7  2
  subtype4 10  4
subtype1 subtype2 subtype3 subtype4 
       8       10        9       14 
subtype1 subtype2 subtype3 subtype4 
       1        2        2        4 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8046 TCGA-G8-6914 TCGA-RQ-A68N 
        4.34        23.28        14.04        24.69       196.60        25.91 
TCGA-RQ-A6JB TCGA-RQ-AAAT 
        0.03         0.56 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A86F TCGA-G8-6325 TCGA-G8-6326 TCGA-GR-A4D5 
        4.34         1.91        18.18        51.98        70.06        42.71 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        53.16       111.58        12.85 

$subtype3
TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GS-A9TQ 
       23.64         8.15        10.29        26.01        12.66        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TX 
       38.24       128.12        45.14 

$subtype4
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73         4.14        27.35        22.32 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7353 
       31.96        41.16       211.23        19.56       116.81        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       51.98        43.86 

subtype1 subtype2 subtype3 subtype4 
    0.03     1.91     8.15     4.14 
subtype1 subtype2 subtype3 subtype4 
  196.60   111.58   128.12   211.23 
subtype1 subtype2 subtype3 subtype4 
  18.660   33.355   26.010   33.750 
[1] "0.0 - 196.6 (18.7)" "1.9 - 111.6 (33.4)" "8.2 - 128.1 (26.0)"
[4] "4.1 - 211.2 (33.8)"
D9V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  0    1     2      0     0     0
  subtype2       0                  1    1     0      0     0     1
  subtype3       1                  0    1     1      1     0     0
  subtype4       0                  1    1     0      0     2     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE STOMACH THYROID
  subtype1                     0             0               2       2       0
  subtype2                     0             0               0       0       0
  subtype3                     0             1               0       0       0
  subtype4                     1             0               1       0       1
D9V3, multiclass
                       clus
vv                      subtype1 subtype2 subtype3 subtype4
  ADRENAL                      0        0        1        0
  ASCITES/PERITONEUM           0        1        0        1
  BONE                         1        1        1        1
  BRAIN                        2        0        1        0
  BREAST                       0        0        1        0
  COLON                        0        0        0        2
  LIVER                        0        1        0        0
  OTHER EXTRANODAL SITE        0        0        0        1
  PAROTID GLAND                0        0        1        0
  SMALL INTESTINE              2        0        0        1
  STOMACH                      2        0        0        0
  THYROID                      0        0        0        1
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V4, binary
          cls
clus        0  1
  subtype1  3  6
  subtype2  6  4
  subtype3  3  6
  subtype4 10  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    6
  subtype2    6    4
  subtype3    3    6
  subtype4   10    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        6        3       10
  MALE          6        4        6        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
          cls
clus        0  1
  subtype1  8  0
  subtype2  8  2
  subtype3  6  3
  subtype4 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    0
  subtype2    8    2
  subtype3    6    3
  subtype4   14    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         8        8        6       14
  YES        0        2        3        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                 6
  subtype2                                                                                 8
  subtype3                                                                                 9
  subtype4                                                                                13
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        3                                  0
  subtype2                        0                                  2
  subtype3                        0                                  0
  subtype4                        0                                  1
D9V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        6
  PRIMARY DLBCL OF THE CNS                                                                 3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        8
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       2
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        9
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype4
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       13
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         0     6
  subtype2     1                         0     9
  subtype3     5                         0     4
  subtype4     7                         1     6
D9V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        1        5        7
  BLACK OR AFRICAN AMERICAN        0        0        0        1
  WHITE                            6        9        4        6
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus        0  1
  subtype1  2  7
  subtype2  4  6
  subtype3  4  5
  subtype4  0 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    4    6
  subtype3    4    5
  subtype4    0   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4        4        0
  NOT HISPANIC OR LATINO        7        6        5       14
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1  6  1
  subtype2 11  4
  subtype3  4  1
  subtype4 11  3
subtype1 subtype2 subtype3 subtype4 
       7       15        5       14 
subtype1 subtype2 subtype3 subtype4 
       1        4        1        3 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A82F TCGA-FF-8062 TCGA-G8-6914 TCGA-RQ-A68N 
        4.34        23.28        14.04        22.32       196.60        25.91 
TCGA-RQ-AAAT 
        0.56 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A86F TCGA-FF-8041 TCGA-G8-6324 TCGA-G8-6325 
        4.34         1.91        18.18        35.54        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6909 TCGA-GR-A4D5 TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW 
       70.06       116.81        42.71       128.12        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9U3 TCGA-GS-A9U4 
       45.14       111.58        12.85 

$subtype3
TCGA-FA-A7DS TCGA-FF-A7CR TCGA-FF-A7CW TCGA-GS-A9TQ TCGA-GS-A9TT 
       23.64        10.29        26.01        32.28        38.24 

$subtype4
TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
        8.15        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6906 TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D4 
       12.66        31.96       211.23        19.56        98.07        51.98 
TCGA-GR-A4D6 TCGA-RQ-A6JB 
       43.86         0.03 

subtype1 subtype2 subtype3 subtype4 
    0.56     1.91    10.29     0.03 
subtype1 subtype2 subtype3 subtype4 
  196.60   128.12    38.24   211.23 
subtype1 subtype2 subtype3 subtype4 
  22.320   42.710   26.010   29.225 
[1] "0.6 - 196.6 (22.3)" "1.9 - 128.1 (42.7)" "10.3 - 38.2 (26.0)"
[4] "0.0 - 211.2 (29.2)"
D10V2, continuous
          vv
clus       ADRENAL ASCITES/PERITONEUM BONE BRAIN BREAST COLON LIVER
  subtype1       0                  0    0     2      0     0     0
  subtype2       0                  2    1     0      0     0     1
  subtype3       0                  0    1     1      1     0     0
  subtype4       1                  0    2     0      0     2     0
          vv
clus       OTHER EXTRANODAL SITE PAROTID GLAND SMALL INTESTINE STOMACH THYROID
  subtype1                     0             0               2       2       1
  subtype2                     0             0               0       0       0
  subtype3                     0             1               0       0       0
  subtype4                     1             0               1       0       0
D10V3, multiclass
                       clus
vv                      subtype1 subtype2 subtype3 subtype4
  ADRENAL                      0        0        0        1
  ASCITES/PERITONEUM           0        2        0        0
  BONE                         0        1        1        2
  BRAIN                        2        0        1        0
  BREAST                       0        0        1        0
  COLON                        0        0        0        2
  LIVER                        0        1        0        0
  OTHER EXTRANODAL SITE        0        0        0        1
  PAROTID GLAND                0        0        1        0
  SMALL INTESTINE              2        0        0        1
  STOMACH                      2        0        0        0
  THYROID                      1        0        0        0
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V4, binary
          cls
clus       0 1
  subtype1 3 5
  subtype2 8 7
  subtype3 2 3
  subtype4 9 5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    5
  subtype2    8    7
  subtype3    2    3
  subtype4    9    5
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        8        2        9
  MALE          5        7        3        5
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
          cls
clus        0  1
  subtype1  8  0
  subtype2 11  4
  subtype3  4  1
  subtype4 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    0
  subtype2   11    4
  subtype3    4    1
  subtype4   13    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         8       11        4       13
  YES        0        4        1        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                 6
  subtype2                                                                                12
  subtype3                                                                                 5
  subtype4                                                                                13
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        2                                  0
  subtype2                        0                                  3
  subtype3                        0                                  0
  subtype4                        1                                  0
D10V6, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        6
  PRIMARY DLBCL OF THE CNS                                                                 2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       12
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       3
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        5
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype4
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       13
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         0     5
  subtype2     2                         1    12
  subtype3     3                         0     2
  subtype4     8                         0     6
D10V7, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            3        2        3        8
  BLACK OR AFRICAN AMERICAN        0        1        0        0
  WHITE                            5       12        2        6
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus        0  1
  subtype1  2  6
  subtype2  6  9
  subtype3  2  3
  subtype4  0 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    6
  subtype2    6    9
  subtype3    2    3
  subtype4    0   14
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        6        2        0
  NOT HISPANIC OR LATINO        6        9        3       14
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
