[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/19775131/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/DLBC-TP/20125263/DLBC-TP.mergedcluster.txt"

nPatients in clinical file=47, in cluster file=48, common to both=47
[1] 10 47
[1] "CN_CNMF"
[1] 3
 1  2 
29 18 
 1  2 
29 18 
[1] "METHLYATION_CNMF"
[1] 3
 1  2 
24 23 
 1  2 
24 23 
[1] "RPPA_CNMF"
[1] 3
 1  2 
17 15 
 1  2 
17 15 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
 6 14 12 
 1  2  3 
 6 14 12 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2 
15 13 
 1  2 
15 13 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
13 10  5 
 1  2  3 
13 10  5 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4 
13 11 10 12 
 1  2  3  4 
13 11 10 12 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
 9 12  7 12  6 
 1  2  3  4  5 
 9 12  7 12  6 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2 
18 23 
 1  2 
18 23 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
1 2 3 4 5 6 7 8 9 
3 5 6 6 8 3 5 2 3 
1 2 3 4 5 6 7 9 
3 5 6 6 8 3 5 3 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "PATHOLOGIC_STAGE"                    
 [6] "PATHOLOGY_T_STAGE"                   
 [7] "PATHOLOGY_N_STAGE"                   
 [8] "PATHOLOGY_M_STAGE"                   
 [9] "GENDER"                              
[10] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[11] "RADIATION_THERAPY"                   
[12] "HISTOLOGICAL_TYPE"                   
[13] "RACE"                                
[14] "ETHNICITY"                           

Input Data has 14 rows and 47 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=33,	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=40,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'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 6:'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 7:'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 8:'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 9:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'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 11:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'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 47 columns, 1 survival variables, and 6 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH"    "GENDER"            "RADIATION_THERAPY"
[4] "HISTOLOGICAL_TYPE" "RACE"              "ETHNICITY"        
YEARS_TO_BIRTH, nv=33, binary=FALSE, numeric=TRUE
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 22  7
  subtype2 16  2
subtype1 subtype2 
      29       18 
subtype1 subtype2 
       7        2 
$subtype1
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A86F TCGA-FF-8041 
        4.34         4.34         1.91        23.64        18.18        35.54 
TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX 
       24.69        27.35        22.32         9.80        10.29        12.66 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        70.06       211.23        19.56       116.81 
TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-GS-A9TT TCGA-GS-A9TV TCGA-GS-A9TW 
      150.51        42.71        57.17        38.24        24.00        53.16 
TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 TCGA-RQ-A6JB 
       45.14        25.15       111.58        12.85         0.03 

$subtype2
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 
       23.28        24.62         8.15        14.04        31.10        31.73 
TCGA-FF-8047 TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 
        4.14        26.01        31.96       196.60        98.07        51.98 
TCGA-GR-A4D6 TCGA-GS-A9TQ TCGA-GS-A9TU TCGA-GS-A9TY TCGA-RQ-A68N TCGA-RQ-AAAT 
       43.86        32.28       128.12       109.58        25.91         0.56 

subtype1 subtype2 
    0.03     0.56 
subtype1 subtype2 
  211.23   196.60 
subtype1 subtype2 
  25.150   31.415 
[1] "0.0 - 211.2 (25.1)" "0.6 - 196.6 (31.4)"
[1] "hr=" "2"  
D1V2, continuous
D1V3, binary
          cls
clus        0  1
  subtype1 14 15
  subtype2 12  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   15
  subtype2   12    6
        clus
vv       subtype1 subtype2
  FEMALE       14       12
  MALE         15        6
[1] 2 2
[1] FALSE
D1V4, binary
          cls
clus        0  1
  subtype1 22  6
  subtype2 17  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22    6
  subtype2   17    1
     clus
vv    subtype1 subtype2
  NO        22       17
  YES        6        1
[1] 2 2
[1] FALSE
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                24
  subtype2                                                                                16
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        1                                  4
  subtype2                        2                                  0
D1V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       24
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       4
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       16
  PRIMARY DLBCL OF THE CNS                                                                 2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     9                         1    19
  subtype2     9                         0     9
D1V6, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            9        9
  BLACK OR AFRICAN AMERICAN        1        0
  WHITE                           19        9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1  7 22
  subtype2  5 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   22
  subtype2    5   13
                        clus
vv                       subtype1 subtype2
  HISPANIC OR LATINO            7        5
  NOT HISPANIC OR LATINO       22       13
[1] 2 2
[1] FALSE

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 21  3
  subtype2 17  6
subtype1 subtype2 
      24       23 
subtype1 subtype2 
       3        6 
$subtype1
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A86F TCGA-FF-8046 
        4.34         4.34         1.91        24.62        18.18        24.69 
TCGA-FF-8062 TCGA-FF-A7CW TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6914 
       22.32        26.01        41.16        51.98        70.06       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TU 
      150.51        98.07        51.98        42.71        43.86       128.12 
TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9TZ TCGA-GS-A9U3 TCGA-GS-A9U4 
       24.00        53.16        45.14        25.15       111.58        12.85 

$subtype2
TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 
       23.28        23.64         8.15        14.04        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX 
       31.73         4.14        27.35         9.80        10.29        12.66 
TCGA-FM-8000 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-A4D9 TCGA-GS-A9TQ 
       31.96       211.23        19.56       116.81        57.17        32.28 
TCGA-GS-A9TT TCGA-GS-A9TY TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       38.24       109.58        25.91         0.03         0.56 

subtype1 subtype2 
    1.91     0.03 
subtype1 subtype2 
  196.60   211.23 
subtype1 subtype2 
  41.935   25.910 
[1] "1.9 - 196.6 (41.9)" "0.0 - 211.2 (25.9)"
[1] "hr=" "2.3"
D2V2, continuous
D2V3, binary
          cls
clus        0  1
  subtype1 12 12
  subtype2 14  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   12
  subtype2   14    9
        clus
vv       subtype1 subtype2
  FEMALE       12       14
  MALE         12        9
[1] 2 2
[1] FALSE
D2V4, binary
          cls
clus        0  1
  subtype1 18  6
  subtype2 21  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    6
  subtype2   21    1
     clus
vv    subtype1 subtype2
  NO        18       21
  YES        6        1
[1] 2 2
[1] FALSE
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                21
  subtype2                                                                                19
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        0                                  3
  subtype2                        3                                  1
D2V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       21
  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)       19
  PRIMARY DLBCL OF THE CNS                                                                 3
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         1    17
  subtype2    12                         0    11
D2V6, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            6       12
  BLACK OR AFRICAN AMERICAN        1        0
  WHITE                           17       11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  7 17
  subtype2  5 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   17
  subtype2    5   18
                        clus
vv                       subtype1 subtype2
  HISPANIC OR LATINO            7        5
  NOT HISPANIC OR LATINO       17       18
[1] 2 2
[1] FALSE

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 15  2
  subtype2 11  4
subtype1 subtype2 
      17       15 
subtype1 subtype2 
       2        4 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 
        4.34        23.28        23.64        14.04        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6325 
       31.73        24.69        27.35        12.66        31.96        51.98 
TCGA-G8-6906 TCGA-G8-6914 TCGA-GS-A9TT TCGA-GS-A9TW TCGA-RQ-A6JB 
      211.23       196.60        38.24        53.16         0.03 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A86F TCGA-FF-8047 
        4.34         1.91        24.62         8.15        18.18         4.14 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CW TCGA-G8-6326 TCGA-GS-A9TV TCGA-GS-A9TX 
       22.32        10.29        26.01        70.06        24.00        45.14 
TCGA-GS-A9TZ TCGA-GS-A9U4 TCGA-RQ-A68N 
       25.15        12.85        25.91 

subtype1 subtype2 
    0.03     1.91 
subtype1 subtype2 
  211.23    70.06 
subtype1 subtype2 
   31.10    22.32 
[1] "0.0 - 211.2 (31.1)" "1.9 - 70.1 (22.3)" 
[1] "hr=" "5.5"
D3V2, continuous
D3V3, binary
          cls
clus       0 1
  subtype1 8 9
  subtype2 7 8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8    9
  subtype2    7    8
        clus
vv       subtype1 subtype2
  FEMALE        8        7
  MALE          9        8
[1] 2 2
[1] FALSE
D3V4, binary
          cls
clus        0  1
  subtype1 14  2
  subtype2 12  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14    2
  subtype2   12    3
     clus
vv    subtype1 subtype2
  NO        14       12
  YES        2        3
[1] 2 2
[1] FALSE
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                14
  subtype2                                                                                12
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        1                                  2
  subtype2                        1                                  2
D3V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       14
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       2
                                                                                   clus
vv                                                                                  subtype2
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       12
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN WHITE
  subtype1     9     8
  subtype2     7     8
D3V6, multiclass
       clus
vv      subtype1 subtype2
  ASIAN        9        7
  WHITE        8        8
[1] 2 2
[1] FALSE
D3V7, binary
          cls
clus        0  1
  subtype1  2 15
  subtype2  5 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   15
  subtype2    5   10
                        clus
vv                       subtype1 subtype2
  HISPANIC OR LATINO            2        5
  NOT HISPANIC OR LATINO       15       10
[1] 2 2
[1] FALSE

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
D4V3, binary
          cls
clus       0 1
  subtype1 3 3
  subtype2 6 8
  subtype3 6 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    3
  subtype2    6    8
  subtype3    6    6
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        3        6        6
  MALE          3        8        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"
D4V4, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2 11  3
  subtype3 10  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2   11    3
  subtype3   10    2
     clus
vv    subtype1 subtype2 subtype3
  NO         5       11       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                                                                                11
  subtype3                                                                                10
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        1                                  0
  subtype2                        0                                  3
  subtype3                        1                                  1
D4V5, 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)       11
  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     6
  subtype3     7     5
D4V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  ASIAN        1        8        7
  WHITE        5        6        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"
D4V7, binary
          cls
clus        0  1
  subtype1  1  5
  subtype2  3 11
  subtype3  3  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    5
  subtype2    3   11
  subtype3    3    9
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        3
  NOT HISPANIC OR LATINO        5       11        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 12  3
  subtype2 10  3
subtype1 subtype2 
      15       13 
subtype1 subtype2 
       3        3 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 TCGA-G8-6325 
        4.34        23.28        31.10        31.73        27.35        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 
       70.06       211.23       116.81       196.60       150.51        51.98 
TCGA-GR-A4D9 TCGA-RQ-A68N TCGA-RQ-A6JB 
       57.17        25.91         0.03 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8047 
        4.34         1.91        24.62        35.54        24.69         4.14 
TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D5 
       22.32        31.96        41.16        19.56        98.07        42.71 
TCGA-GR-A4D6 
       43.86 

subtype1 subtype2 
    0.03     1.91 
subtype1 subtype2 
  211.23    98.07 
subtype1 subtype2 
   51.98    24.69 
[1] "0.0 - 211.2 (52.0)" "1.9 - 98.1 (24.7)" 
[1] "hr=" "4.4"
D5V2, continuous
D5V3, binary
          cls
clus       0 1
  subtype1 6 9
  subtype2 9 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    9
  subtype2    9    4
        clus
vv       subtype1 subtype2
  FEMALE        6        9
  MALE          9        4
[1] 2 2
[1] FALSE
D5V4, binary
          cls
clus        0  1
  subtype1 13  1
  subtype2 13  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    1
  subtype2   13    0
     clus
vv    subtype1 subtype2
  NO        13       13
  YES        1        0
[1] 2 2
[1] FALSE
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                13
  subtype2                                                                                12
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        2                                  0
  subtype2                        0                                  1
D5V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       13
  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                                                       1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         0    11
  subtype2     7                         1     5
D5V6, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            4        7
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                           11        5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  1 14
  subtype2  0 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   14
  subtype2    0   13
                        clus
vv                       subtype1 subtype2
  HISPANIC OR LATINO            1        0
  NOT HISPANIC OR LATINO       14       13
[1] 2 2
[1] FALSE

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 11  2
  subtype2  7  3
  subtype3  4  1
subtype1 subtype2 subtype3 
      13       10        5 
subtype1 subtype2 subtype3 
       2        3        1 
$subtype1
TCGA-FA-8693 TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 
        4.34        35.54        31.10        31.73        27.35        22.32 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       51.98        70.06       211.23       116.81       196.60       150.51 
TCGA-RQ-A68N 
       25.91 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8046 TCGA-FF-8047 TCGA-FM-8000 
        4.34         1.91        24.62        24.69         4.14        31.96 
TCGA-G8-6324 TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D6 
       41.16        19.56        98.07        43.86 

$subtype3
TCGA-FA-A4XK TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A6JB 
       23.28        51.98        42.71        57.17         0.03 

subtype1 subtype2 subtype3 
    4.34     1.91     0.03 
subtype1 subtype2 subtype3 
  211.23    98.07    57.17 
subtype1 subtype2 subtype3 
  35.540   24.655   42.710 
[1] "4.3 - 211.2 (35.5)" "1.9 - 98.1 (24.7)"  "0.0 - 57.2 (42.7)" 
D6V2, continuous
D6V3, binary
          cls
clus       0 1
  subtype1 5 8
  subtype2 6 4
  subtype3 4 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    8
  subtype2    6    4
  subtype3    4    1
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        5        6        4
  MALE          8        4        1
[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"
D6V4, binary
          cls
clus        0  1
  subtype1 12  1
  subtype2 10  0
  subtype3  4  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    1
  subtype2   10    0
  subtype3    4    0
     clus
vv    subtype1 subtype2 subtype3
  NO        12       10        4
  YES        1        0        0
[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                                                                                11
  subtype2                                                                                10
  subtype3                                                                                 4
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        1                                  1
  subtype2                        0                                  0
  subtype3                        1                                  0
D6V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       11
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   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                                                       0
                                                                                   clus
vv                                                                                  subtype3
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        4
  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                         0     8
  subtype2     5                         1     4
  subtype3     1                         0     4
D6V6, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            5        5        1
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                            8        4        4
[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"
D6V7, binary
          cls
clus        0  1
  subtype1  1 12
  subtype2  0 10
  subtype3  0  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   12
  subtype2    0   10
  subtype3    0    5
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO       12       10        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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 10  3
  subtype2  9  2
  subtype3  8  2
  subtype4 10  2
subtype1 subtype2 subtype3 subtype4 
      13       11       10       12 
subtype1 subtype2 subtype3 subtype4 
       3        2        2        2 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8046 
        4.34        23.28         8.15        14.04        31.10        24.69 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6914 TCGA-GR-A4D9 TCGA-RQ-A68N TCGA-RQ-A6JB 
       70.06       211.23       196.60        57.17        25.91         0.03 
TCGA-RQ-AAAT 
        0.56 

$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-GR-A4D5 TCGA-GR-A4D6 TCGA-GS-A9TV TCGA-GS-A9TZ TCGA-GS-A9U3 
       42.71        43.86        24.00        25.15       111.58 

$subtype3
TCGA-FA-A7DS TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GS-A9TQ 
       23.64         9.80        10.29        26.01        12.66        32.28 
TCGA-GS-A9TT TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9U4 
       38.24       128.12        45.14        12.85 

$subtype4
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FM-8000 TCGA-G8-6325 
       35.54        31.73         4.14        27.35        31.96        51.98 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GS-A9TW TCGA-GS-A9TY 
       19.56       116.81        98.07        51.98        53.16       109.58 

subtype1 subtype2 subtype3 subtype4 
    0.03     1.91     9.80     4.14 
subtype1 subtype2 subtype3 subtype4 
  211.23   111.58   128.12   116.81 
subtype1 subtype2 subtype3 subtype4 
  24.690   24.620   24.825   43.760 
[1] "0.0 - 211.2 (24.7)" "1.9 - 111.6 (24.6)" "9.8 - 128.1 (24.8)"
[4] "4.1 - 116.8 (43.8)"
D7V2, continuous
D7V3, binary
          cls
clus       0 1
  subtype1 6 7
  subtype2 8 3
  subtype3 3 7
  subtype4 8 4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    7
  subtype2    8    3
  subtype3    3    7
  subtype4    8    4
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6        8        3        8
  MALE          7        3        7        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"
D7V4, binary
          cls
clus        0  1
  subtype1 12  0
  subtype2  9  2
  subtype3  7  3
  subtype4 11  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12    0
  subtype2    9    2
  subtype3    7    3
  subtype4   11    1
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        12        9        7       11
  YES        0        2        3        1
[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                                                                                10
  subtype2                                                                                 9
  subtype3                                                                                10
  subtype4                                                                                10
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        3                                  0
  subtype2                        0                                  2
  subtype3                        0                                  0
  subtype4                        0                                  2
D7V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       10
  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)        9
  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)       10
  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)       10
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       2
[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     5                         0     8
  subtype2     4                         1     6
  subtype3     5                         0     5
  subtype4     4                         0     8
D7V6, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            5        4        5        4
  BLACK OR AFRICAN AMERICAN        0        1        0        0
  WHITE                            8        6        5        8
[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"
D7V7, binary
          cls
clus        0  1
  subtype1  2 11
  subtype2  3  8
  subtype3  5  5
  subtype4  2 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   11
  subtype2    3    8
  subtype3    5    5
  subtype4    2   10
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        3        5        2
  NOT HISPANIC OR LATINO       11        8        5       10
[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(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
D8V3, binary
          cls
clus       0 1
  subtype1 2 7
  subtype2 8 4
  subtype3 4 3
  subtype4 6 6
  subtype5 5 1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    7
  subtype2    8    4
  subtype3    4    3
  subtype4    6    6
  subtype5    5    1
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        2        8        4        6        5
  MALE          7        4        3        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"
D8V4, binary
          cls
clus        0  1
  subtype1  9  0
  subtype2 10  2
  subtype3  6  0
  subtype4  8  4
  subtype5  6  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    0
  subtype2   10    2
  subtype3    6    0
  subtype4    8    4
  subtype5    6    0
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         9       10        6        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                                                                                 4
  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
D8V5, 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)        4
  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     4
  subtype4     4                         0     8
  subtype5     3                         0     3
D8V6, 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        4        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"
D8V7, binary
          cls
clus       0 1
  subtype1 0 9
  subtype2 3 9
  subtype3 2 5
  subtype4 7 5
  subtype5 0 6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    9
  subtype2    3    9
  subtype3    2    5
  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        5        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 14  4
  subtype2 18  5
subtype1 subtype2 
      18       23 
subtype1 subtype2 
       4        5 
$subtype1
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8042 
        4.34        23.28        23.64         8.15        14.04        31.10 
TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6906 TCGA-G8-6914 
       24.69        27.35        26.01        12.66       211.23       196.60 
TCGA-GS-A9TQ TCGA-GS-A9TT TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-A6JB TCGA-RQ-AAAT 
       32.28        38.24        12.85        25.91         0.03         0.56 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 
        4.34         1.91        18.18        35.54        31.73         4.14 
TCGA-FF-8062 TCGA-FF-A7CR TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       22.32        10.29        31.96        41.16        51.98        70.06 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
       19.56       116.81        98.07        51.98        42.71        43.86 
TCGA-GS-A9TU TCGA-GS-A9TV TCGA-GS-A9TW TCGA-GS-A9TX TCGA-GS-A9U3 
      128.12        24.00        53.16        45.14       111.58 

subtype1 subtype2 
    0.03     1.91 
subtype1 subtype2 
  211.23   128.12 
subtype1 subtype2 
  24.165   41.160 
[1] "0.0 - 211.2 (24.2)" "1.9 - 128.1 (41.2)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
          cls
clus        0  1
  subtype1  8 10
  subtype2 14  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   10
  subtype2   14    9
        clus
vv       subtype1 subtype2
  FEMALE        8       14
  MALE         10        9
[1] 2 2
[1] FALSE
D9V4, binary
          cls
clus        0  1
  subtype1 16  1
  subtype2 19  4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16    1
  subtype2   19    4
     clus
vv    subtype1 subtype2
  NO        16       19
  YES        1        4
[1] 2 2
[1] FALSE
          vv
clus       DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)
  subtype1                                                                                15
  subtype2                                                                                20
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        3                                  0
  subtype2                        0                                  3
D9V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)       15
  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)       20
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     9                         0     9
  subtype2     7                         1    15
D9V6, multiclass
                           clus
vv                          subtype1 subtype2
  ASIAN                            9        7
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            9       15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1  5 13
  subtype2  5 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   13
  subtype2    5   18
                        clus
vv                       subtype1 subtype2
  HISPANIC OR LATINO            5        5
  NOT HISPANIC OR LATINO       13       18
[1] 2 2
[1] FALSE

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2      0 1
  subtype1 3 0
  subtype2 4 1
  subtype3 4 2
  subtype4 5 1
  subtype5 6 2
  subtype6 2 1
  subtype7 4 1
  subtype9 3 0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype9 
       3        5        6        6        8        3        5        3 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype9 
       0        1        2        1        2        1        1        0 
$subtype1
TCGA-FA-8693 TCGA-FA-A82F TCGA-FF-8062 
        4.34        14.04        22.32 

$subtype2
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A86F TCGA-GR-A4D5 TCGA-GS-A9TV 
        4.34         1.91        18.18        42.71        24.00 

$subtype3
TCGA-FA-A4XK TCGA-G8-6914 TCGA-GS-A9TW TCGA-GS-A9U4 TCGA-RQ-A68N TCGA-RQ-AAAT 
       23.28       196.60        53.16        12.85        25.91         0.56 

$subtype4
TCGA-FA-A7DS TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-GS-A9TQ TCGA-GS-A9TT 
       23.64        10.29        26.01        12.66        32.28        38.24 

$subtype5
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-G8-6906 TCGA-GR-7353 
      211.23        98.07 

$subtype6
TCGA-FF-8041 TCGA-G8-6325 TCGA-G8-6909 
       35.54        51.98       116.81 

$subtype7
TCGA-FM-8000 TCGA-G8-6907 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-RQ-A6JB 
       31.96        19.56        51.98        43.86         0.03 

$subtype9
TCGA-GS-A9TU TCGA-GS-A9TX TCGA-GS-A9U3 
      128.12        45.14       111.58 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype9 
    4.34     1.91     0.56    10.29     4.14    35.54     0.03    45.14 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype9 
   22.32    42.71   196.60    38.24   211.23   116.81    51.98   128.12 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype9 
  14.040   18.180   24.595   24.825   29.225   51.980   31.960  111.580 
[1] "4.3 - 22.3 (14.0)"    "1.9 - 42.7 (18.2)"    "0.6 - 196.6 (24.6)"  
[4] "10.3 - 38.2 (24.8)"   "4.1 - 211.2 (29.2)"   "35.5 - 116.8 (52.0)" 
[7] "0.0 - 52.0 (32.0)"    "45.1 - 128.1 (111.6)"
D10V2, continuous
D10V3, binary
          cls
clus       0 1
  subtype1 2 1
  subtype2 3 2
  subtype3 3 3
  subtype4 2 4
  subtype5 4 4
  subtype6 1 2
  subtype7 5 0
  subtype9 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2    1
  subtype2    3    2
  subtype3    3    3
  subtype4    2    4
  subtype5    4    4
  subtype6    1    2
  subtype7    5    0
  subtype9    1    2
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        2        3        3        2        4        1        5
  MALE          1        2        3        4        4        2        0
        clus
vv       subtype9
  FEMALE        1
  MALE          2
[1] 2 8
[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 0
  subtype2 4 1
  subtype3 5 1
  subtype4 5 1
  subtype5 8 0
  subtype6 3 0
  subtype7 4 0
  subtype9 1 2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    0
  subtype2    4    1
  subtype3    5    1
  subtype4    5    1
  subtype5    8    0
  subtype6    3    0
  subtype7    4    0
  subtype9    1    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype9
  NO         3        4        5        5        8        3        4        1
  YES        0        1        1        1        0        0        0        2
[1] 2 8
[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                                                                                 3
  subtype2                                                                                 4
  subtype3                                                                                 3
  subtype4                                                                                 6
  subtype5                                                                                 8
  subtype6                                                                                 2
  subtype7                                                                                 4
  subtype9                                                                                 3
          vv
clus       PRIMARY DLBCL OF THE CNS PRIMARY MEDIASTINAL (THYMIC) DLBCL
  subtype1                        0                                  0
  subtype2                        0                                  1
  subtype3                        2                                  1
  subtype4                        0                                  0
  subtype5                        0                                  0
  subtype6                        0                                  1
  subtype7                        1                                  0
  subtype9                        0                                  0
D10V5, multiclass
                                                                                   clus
vv                                                                                  subtype1
  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                                                                                  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)        3
  PRIMARY DLBCL OF THE CNS                                                                 2
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype4
  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                                                                                  subtype5
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        8
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype6
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        2
  PRIMARY DLBCL OF THE CNS                                                                 0
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       1
                                                                                   clus
vv                                                                                  subtype7
  DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) NOS (ANY ANATOMIC SITE NODAL OR EXTRANODAL)        4
  PRIMARY DLBCL OF THE CNS                                                                 1
  PRIMARY MEDIASTINAL (THYMIC) DLBCL                                                       0
                                                                                   clus
vv                                                                                  subtype9
  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
[1] 3 8
[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     2     1
  subtype2     1     4
  subtype3     1     5
  subtype4     4     2
  subtype5     6     2
  subtype6     1     2
  subtype7     1     4
  subtype9     0     3
D10V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype9
  ASIAN        2        1        1        4        6        1        1        0
  WHITE        1        4        5        2        2        2        4        3
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus       0 1
  subtype1 0 3
  subtype2 1 4
  subtype3 4 2
  subtype4 2 4
  subtype5 0 8
  subtype6 0 3
  subtype7 0 5
  subtype9 3 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    3
  subtype2    1    4
  subtype3    4    2
  subtype4    2    4
  subtype5    0    8
  subtype6    0    3
  subtype7    0    5
  subtype9    3    0
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        4        2        0        0
  NOT HISPANIC OR LATINO        3        4        2        4        8        3
                        clus
vv                       subtype7 subtype9
  HISPANIC OR LATINO            0        3
  NOT HISPANIC OR LATINO        5        0
[1] 2 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
