Stomach adenocarcinoma
STAD-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( STAD )
ExperimentList class object of length 14:
[1] STAD_CNASeq-20160128: RaggedExperiment with 31824 rows and 214 columns
[2] STAD_CNASNP-20160128: RaggedExperiment with 443042 rows and 906 columns
[3] STAD_CNVSNP-20160128: RaggedExperiment with 118389 rows and 904 columns
[4] STAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[5] STAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 84 rows and 441 columns
[6] STAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 441 columns
[7] STAD_Mutation-20160128: RaggedExperiment with 148520 rows and 289 columns
[8] STAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 450 columns
[9] STAD_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 271 columns
[10] STAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 357 columns
[11] STAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 430 columns
[12] STAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18664 rows and 450 columns
[13] STAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 73 columns
[14] STAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 397 columns
> rownames( STAD )
CharacterList of length 14
[["STAD_CNASeq-20160128"]] character(0)
[["STAD_CNASNP-20160128"]] character(0)
[["STAD_CNVSNP-20160128"]] character(0)
[["STAD_GISTIC_AllByGene-20160128"]] character(0)
[["STAD_GISTIC_Peaks-20160128"]] 1 37 38 2 3 39 40 ... 81 34 82 35 83 84 85
[["STAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["STAD_Mutation-20160128"]] character(0)
[["STAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["STAD_RNASeqGene-20160128"]] AADACL3 AADACL4 AB007962 ... VCY XKRY ZFY
[["STAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<4 more elements>
> colnames( STAD )
CharacterList of length 14
[["STAD_CNASeq-20160128"]] TCGA-B7-5816-01A-21D-1598-02 ...
[["STAD_CNASNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_CNVSNP-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_AllByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_Peaks-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3M-AB46-01A-11D-A40Z-01 ...
[["STAD_Mutation-20160128"]] TCGA-B7-5816-01A-21D-1600-08 ...
[["STAD_RNASeq2Gene-20160128"]] TCGA-3M-AB46-01A-11R-A414-31 ...
[["STAD_RNASeqGene-20160128"]] TCGA-B7-5816-01A-21R-1602-13 ...
[["STAD_RPPAArray-20160128"]] TCGA-3M-AB47-01A-11-A43D-20 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 STAD_CNASeq-20160128 0.9 Mb
2 STAD_CNASNP-20160128 12.1 Mb
3 STAD_CNVSNP-20160128 3.4 Mb
4 STAD_GISTIC_AllByGene-20160128 87 Mb
5 STAD_GISTIC_Peaks-20160128 0.4 Mb
6 STAD_GISTIC_ThresholdedByGene-20160128 86.8 Mb
7 STAD_Mutation-20160128 161.5 Mb
8 STAD_RNASeq2Gene-20160128 73 Mb
9 STAD_RNASeqGene-20160128 57.4 Mb
10 STAD_RPPAArray-20160128 0.6 Mb
11 STAD_miRNASeqGene-20160128 3.7 Mb
12 STAD_RNASeq2GeneNorm-20160128 66.5 Mb
13 STAD_Methylation_methyl27-20160128 4.9 Mb
14 STAD_Methylation_methyl450-20160128 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)
273 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 170 170 0.948 0.792 1.08
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 58.00 67.00 65.73 73.00 90.00 9
vital_status:
0 1
268 175
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 194.0 346.0 423.7 553.5 2197.0 273
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 335.5 547.5 673.7 912.0 3720.0 177
tumor_tissue_site:
stomach
443
pathology_M_stage:
m0 m1 mx
391 30 22
gender:
female male
158 285
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1996 2010 2011 2010 2012 2013 6
radiation_therapy:
no yes NA's
323 77 43
residual_tumor:
r0 r1 r2 rx NA's
350 18 19 25 31
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 3.000 5.635 8.000 57.000 51
race:
asian
89
black or african american
13
native hawaiian or other pacific islander
1
white
278
NA's
62
ethnicity:
hispanic or latino not hispanic or latino NA's
5 318 120
Including an additional 1390 columns