SARC | R Documentation |
A document describing the TCGA cancer code
> 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
SARC-v2.0.1
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.