Sarcoma
SARC.RdA document describing the TCGA cancer code
Details
> experiments( SARC )
ExperimentList class object of length 10:
[1] SARC_CNASNP-20160128: RaggedExperiment with 337377 rows and 516 columns
[2] SARC_CNVSNP-20160128: RaggedExperiment with 106739 rows and 513 columns
[3] SARC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[4] SARC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 64 rows and 257 columns
[5] SARC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 257 columns
[6] SARC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 263 columns
[7] SARC_Mutation-20160128: RaggedExperiment with 20376 rows and 247 columns
[8] SARC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 265 columns
[9] SARC_RPPAArray-20160128: SummarizedExperiment with 192 rows and 226 columns
[10] SARC_Methylation-20160128: SummarizedExperiment with 485577 rows and 269 columns
> rownames( SARC )
CharacterList of length 10
[["SARC_CNASNP-20160128"]] character(0)
[["SARC_CNVSNP-20160128"]] character(0)
[["SARC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["SARC_GISTIC_Peaks-20160128"]] chr1:1-5923787 ... chr22:45095899-51304566
[["SARC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["SARC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["SARC_Mutation-20160128"]] character(0)
[["SARC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["SARC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["SARC_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( SARC )
CharacterList of length 10
[["SARC_CNASNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_CNVSNP-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_AllByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_Peaks-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3B-A9HI-01A-11D-A386-01 ...
[["SARC_miRNASeqGene-20160128"]] TCGA-3B-A9HI-01A-11R-A38N-13 ...
[["SARC_Mutation-20160128"]] TCGA-3B-A9HI-01A-11D-A387-09 ...
[["SARC_RNASeq2GeneNorm-20160128"]] TCGA-3B-A9HI-01A-11R-A38C-07 ...
[["SARC_RPPAArray-20160128"]] TCGA-3B-A9HI-01A-21-A456-20 ...
[["SARC_Methylation-20160128"]] TCGA-3B-A9HI-01A-11D-A388-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 SARC_CNASNP-20160128 9.2 Mb
2 SARC_CNVSNP-20160128 3 Mb
3 SARC_GISTIC_AllByGene-20160128 4.9 Mb
4 SARC_GISTIC_Peaks-20160128 0.1 Mb
5 SARC_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 SARC_miRNASeqGene-20160128 0.1 Mb
7 SARC_Mutation-20160128 19.5 Mb
8 SARC_RNASeq2GeneNorm-20160128 1.3 Mb
9 SARC_RPPAArray-20160128 0 Mb
10 SARC_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)
162 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
99.00 99.00 1.78 1.51 2.46
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 53.00 61.00 60.88 71.00 90.00 1
vital_status:
0 1
162 99
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.0 322.5 648.0 863.6 1169.5 2694.0 162
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
15.0 585.8 1092.0 1391.1 1891.8 5723.0 99
gender:
female male
142 119
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1994 2007 2010 2009 2012 2013 4
radiation_therapy:
no yes NA's
181 74 6
residual_tumor:
r0 r1 r2 rx NA's
155 70 9 26 1
race:
asian black or african american white
6 18 228
NA's
9
ethnicity:
hispanic or latino not hispanic or latino NA's
5 223 33
Including an additional 1413 columns