Skin Cutaneous Melanoma

A document describing the TCGA cancer code
Details


> experiments( SKCM )
ExperimentList class object of length 11:
 [1] SKCM_CNASeq-20160128: RaggedExperiment with 31416 rows and 238 columns
 [2] SKCM_CNASNP-20160128: RaggedExperiment with 452114 rows and 938 columns
 [3] SKCM_CNVSNP-20160128: RaggedExperiment with 108084 rows and 937 columns
 [4] SKCM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
 [5] SKCM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 53 rows and 367 columns
 [6] SKCM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 367 columns
 [7] SKCM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 452 columns
 [8] SKCM_Mutation-20160128: RaggedExperiment with 290322 rows and 345 columns
 [9] SKCM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 473 columns
 [10] SKCM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 355 columns
 [11] SKCM_Methylation-20160128: SummarizedExperiment with 485577 rows and 475 columns

> rownames( SKCM )
CharacterList of length 11
[["SKCM_CNASeq-20160128"]] character(0)
[["SKCM_CNASNP-20160128"]] character(0)
[["SKCM_CNVSNP-20160128"]] character(0)
[["SKCM_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["SKCM_GISTIC_Peaks-20160128"]] chr1:1-6847369 ... chr22:41468899-41849552
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["SKCM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SKCM_Mutation-20160128"]] character(0)
[["SKCM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["SKCM_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<1 more element>

> colnames( SKCM )
CharacterList of length 11
[["SKCM_CNASeq-20160128"]] TCGA-BF-A1PU-01A-11D-A18Z-02 ...
[["SKCM_CNASNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_CNVSNP-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_AllByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_Peaks-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3N-A9WB-06A-11D-A38F-01 ...
[["SKCM_miRNASeqGene-20160128"]] TCGA-3N-A9WC-06A-11R-A38N-13 ...
[["SKCM_Mutation-20160128"]] TCGA-BF-A1PU-01A-11D-A19A-08 ...
[["SKCM_RNASeq2GeneNorm-20160128"]] TCGA-3N-A9WB-06A-11R-A38C-07 ...
[["SKCM_RPPAArray-20160128"]] TCGA-3N-A9WC-06A-21-A444-20 ...
...
<1 more element>

Sizes of each ExperimentList element:

                                    assay  size.Mb
1                    SKCM_CNASeq-20160128   0.9 Mb
2                    SKCM_CNASNP-20160128  12.3 Mb
3                    SKCM_CNVSNP-20160128   3.2 Mb
4          SKCM_GISTIC_AllByGene-20160128   4.9 Mb
5              SKCM_GISTIC_Peaks-20160128   0.1 Mb
6  SKCM_GISTIC_ThresholdedByGene-20160128   4.9 Mb
7              SKCM_miRNASeqGene-20160128   0.1 Mb
8                  SKCM_Mutation-20160128 299.6 Mb
9           SKCM_RNASeq2GeneNorm-20160128   1.3 Mb
10                SKCM_RPPAArray-20160128     0 Mb
11              SKCM_Methylation-20160128  75.1 Mb

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

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

   249 observations deleted due to missingness
      n  events  median 0.95LCL 0.95UCL
 221.00  221.00    2.99    2.40    3.90


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

years_to_birth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
  15.00   48.00   58.00   58.24   71.00   90.00       8

vital_status:
  0   1
247 223

days_to_death:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
     79     518    1093    1789    2073   10870     249

days_to_last_followup:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
   -2.0   477.5  1146.0  1885.3  2658.8 11252.0     230

days_to_submitted_specimen_dx:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
     -2       0     344    1017    1372   10847      14





melanoma_ulceration:
  no  yes NA's
 146  167  157

melanoma_primary_known:
 no yes
 47 423

Breslow_thickness:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
  0.000   1.300   3.000   5.585   6.950  75.000     111

gender:
female   male
   180    290

date_of_initial_pathologic_diagnosis:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's
   1978    2003    2008    2006    2011    2013      11

radiation_therapy:
  no  yes NA's
 420   49    1

race:
                    asian black or african american                     white
                       12                         1                       447
                     NA's
                       10

ethnicity:
    hispanic or latino not hispanic or latino                   NA's
                    11                    446                     13

Including an additional 1517 columns
Details

See also
