SKCM-v2.0.1: Skin Cutaneous Melanoma

In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Skin Cutaneous Melanoma

Description

A document describing the TCGA cancer code

Details

> experiments( SKCM )
ExperimentList class object of length 12:
 [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_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 473 columns
 [10] SKCM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 473 columns
 [11] SKCM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 355 columns
 [12] SKCM_Methylation-20160128: SummarizedExperiment with 485577 rows and 475 columns

> rownames( SKCM )
CharacterList of length 12
[["SKCM_CNASeq-20160128"]] character(0)
[["SKCM_CNASNP-20160128"]] character(0)
[["SKCM_CNVSNP-20160128"]] character(0)
[["SKCM_GISTIC_AllByGene-20160128"]] character(0)
[["SKCM_GISTIC_Peaks-20160128"]] 21 22 1 2 3 23 24 4 ... 50 51 52 18 53 19 20
[["SKCM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["SKCM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SKCM_Mutation-20160128"]] character(0)
[["SKCM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["SKCM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<2 more elements>

> colnames( SKCM )
CharacterList of length 12
[["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_RNASeq2Gene-20160128"]] TCGA-3N-A9WB-06A-11R-A38C-07 ...
[["SKCM_RNASeq2GeneNorm-20160128"]] TCGA-3N-A9WB-06A-11R-A38C-07 ...
...
<2 more elements>

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    73 Mb
5              SKCM_GISTIC_Peaks-20160128   0.3 Mb
6  SKCM_GISTIC_ThresholdedByGene-20160128  72.8 Mb
7              SKCM_miRNASeqGene-20160128   3.8 Mb
8                  SKCM_Mutation-20160128 299.6 Mb
9               SKCM_RNASeq2Gene-20160128  76.6 Mb
10          SKCM_RNASeq2GeneNorm-20160128  76.6 Mb
11                SKCM_RPPAArray-20160128   0.7 Mb
12              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

waldronlab/curatedTCGAData documentation built on Feb. 7, 2024, 1:12 p.m.