Testicular Germ Cell Tumors

A document describing the TCGA cancer code

Details

> experiments( TGCT )
ExperimentList class object of length 11:
 [1] TGCT_CNASNP-20160128: RaggedExperiment with 137968 rows and 271 columns
 [2] TGCT_CNVSNP-20160128: RaggedExperiment with 25479 rows and 271 columns
 [3] TGCT_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
 [4] TGCT_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 48 rows and 134 columns
 [5] TGCT_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 134 columns
 [6] TGCT_Mutation-20160128: RaggedExperiment with 14672 rows and 138 columns
 [7] TGCT_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 139 columns
 [8] TGCT_RPPAArray-20160128: SummarizedExperiment with 192 rows and 107 columns
 [9] TGCT_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 139 columns
 [10] TGCT_RNASeq2GeneNorm-20160128: SummarizedExperiment with 19036 rows and 139 columns
 [11] TGCT_Methylation-20160128: SummarizedExperiment with 485577 rows and 139 columns

> rownames( TGCT )
CharacterList of length 11
[["TGCT_CNASNP-20160128"]] character(0)
[["TGCT_CNVSNP-20160128"]] character(0)
[["TGCT_GISTIC_AllByGene-20160128"]] character(0)
[["TGCT_GISTIC_Peaks-20160128"]] 17 18 1 19 2 20 21 ... 44 45 47 46 48 15 16
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["TGCT_Mutation-20160128"]] character(0)
[["TGCT_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["TGCT_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["TGCT_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["TGCT_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>

> colnames( TGCT )
CharacterList of length 11
[["TGCT_CNASNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_CNVSNP-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_AllByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_Peaks-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_GISTIC_ThresholdedByGene-20160128"]] TCGA-2G-AAEW-01A-11D-A42X-01 ...
[["TGCT_Mutation-20160128"]] TCGA-2G-AAEW-01A-11D-A42Y-10 ...
[["TGCT_RNASeq2Gene-20160128"]] TCGA-2G-AAEW-01A-11R-A430-07 ...
[["TGCT_RPPAArray-20160128"]] TCGA-2G-AAEW-01A-21-A45P-20 ...
[["TGCT_miRNASeqGene-20160128"]] TCGA-2G-AAEW-01A-11R-A439-13 ...
[["TGCT_RNASeq2GeneNorm-20160128"]] TCGA-2G-AAEW-01 ... TCGA-ZM-AA0N-01
...
<1 more element>

Sizes of each ExperimentList element:

                                    assay size.Mb
1                    TGCT_CNASNP-20160128  3.8 Mb
2                    TGCT_CNVSNP-20160128  0.8 Mb
3          TGCT_GISTIC_AllByGene-20160128 28.8 Mb
4              TGCT_GISTIC_Peaks-20160128  0.1 Mb
5  TGCT_GISTIC_ThresholdedByGene-20160128 28.7 Mb
6                  TGCT_Mutation-20160128   10 Mb
7               TGCT_RNASeq2Gene-20160128 24.3 Mb
8                 TGCT_RPPAArray-20160128  0.2 Mb
9              TGCT_miRNASeqGene-20160128  1.3 Mb
10          TGCT_RNASeq2GeneNorm-20160128 22.6 Mb
11              TGCT_Methylation-20160128   75 Mb

---------------------------
Overall survival time-to-event summary (in years):
---------------------------

Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
    -1)

   130 observations deleted due to missingness
     n events median 0.95LCL 0.95UCL
[1,] 4      4   1.55  0.0466      NA


---------------------------
Available sample meta-data:
---------------------------

years_to_birth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
  14.00   26.00   31.00   31.99   37.00   67.00

vital_status:
  0   1
130   4

days_to_death:
  17  513  618 6972 NA's
   1    1    1    1  130

days_to_last_followup:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
    3.0   688.2  1265.5  2092.7  2826.2  7437.0       4

tumor_tissue_site:
testes
   134


pathology_T_stage:
t1 t2 t3 tx
76 51  6  1

pathology_N_stage:
  n0   n1   n2   nx NA's
  46   11    2   65   10

pathology_M_stage:
  m0   m1  m1a  m1b NA's
 115    2    1    1   15

gender:
male
 134

date_of_initial_pathologic_diagnosis:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.
   1992    2006    2009    2008    2012    2013

radiation_therapy:
  no  yes NA's
 111   21    2

karnofsky_performance_score:
  80   90  100 NA's
   5   41   56   32

race:
                    asian black or african american                     white
                        4                         6                       119
                     NA's
                        5

ethnicity:
    hispanic or latino not hispanic or latino                   NA's
                    12                    111                     11

Including an additional 762 columns