BRCA | R Documentation |
A document describing the TCGA cancer code
> experiments( BRCA ) ExperimentList class object of length 14: [1] BRCA_CNASeq-20160128: RaggedExperiment with 5298 rows and 38 columns [2] BRCA_CNASNP-20160128: RaggedExperiment with 1132786 rows and 2209 columns [3] BRCA_CNVSNP-20160128: RaggedExperiment with 284458 rows and 2199 columns [4] BRCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns [5] BRCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 1080 columns [6] BRCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns [7] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849 columns [8] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590 columns [9] BRCA_Mutation-20160128: RaggedExperiment with 90490 rows and 993 columns [10] BRCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 1212 columns [11] BRCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 878 columns [12] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns [13] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 343 columns [14] BRCA_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 885 columns > rownames( BRCA ) CharacterList of length 14 [["BRCA_CNASeq-20160128"]] character(0) [["BRCA_CNASNP-20160128"]] character(0) [["BRCA_CNVSNP-20160128"]] character(0) [["BRCA_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7 [["BRCA_GISTIC_Peaks-20160128"]] chr1:12675879-21133098 ... [["BRCA_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ... [["BRCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["BRCA_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC [["BRCA_Mutation-20160128"]] character(0) [["BRCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR ... <4 more elements> > colnames( BRCA ) CharacterList of length 14 [["BRCA_CNASeq-20160128"]] TCGA-A2-A0EU-01A-22D-A060-02 ... [["BRCA_CNASNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ... [["BRCA_CNVSNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ... [["BRCA_GISTIC_AllByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ... [["BRCA_GISTIC_Peaks-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ... [["BRCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ... [["BRCA_miRNASeqGene-20160128"]] TCGA-3C-AAAU-01A-11R-A41G-13 ... [["BRCA_mRNAArray-20160128"]] TCGA-A1-A0SD-01A-11R-A115-07 ... [["BRCA_Mutation-20160128"]] TCGA-A1-A0SB-01A-11D-A142-09 ... [["BRCA_RNASeq2GeneNorm-20160128"]] TCGA-3C-AAAU-01A-11R-A41B-07 ... ... <4 more elements> Sizes of each ExperimentList element: assay size.Mb 1 BRCA_CNASeq-20160128 0.2 Mb 2 BRCA_CNASNP-20160128 30.9 Mb 3 BRCA_CNVSNP-20160128 8.2 Mb 4 BRCA_GISTIC_AllByGene-20160128 5 Mb 5 BRCA_GISTIC_Peaks-20160128 0.2 Mb 6 BRCA_GISTIC_ThresholdedByGene-20160128 5 Mb 7 BRCA_miRNASeqGene-20160128 0.1 Mb 8 BRCA_mRNAArray-20160128 1.2 Mb 9 BRCA_Mutation-20160128 67.4 Mb 10 BRCA_RNASeq2GeneNorm-20160128 1.4 Mb 11 BRCA_RNASeqGene-20160128 1.4 Mb 12 BRCA_RPPAArray-20160128 0.1 Mb 13 BRCA_Methylation_methyl27-20160128 4.9 Mb 14 BRCA_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) 947 observations deleted due to missingness n events median 0.95LCL 0.95UCL 151.00 151.00 3.48 2.83 4.50 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 26.0 49.0 59.0 58.6 68.0 90.0 16 vital_status: 0 1 NA's 945 152 1 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 116.0 700.5 1272.0 1644.7 2367.0 7455.0 947 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's -7 440 761 1183 1572 8605 153 tumor_tissue_site: breast NA's 1097 1 pathology_M_stage: cm0 (i+) m0 m1 mx NA's 6 906 22 163 1 gender: female male NA's 1085 12 1 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1988 2007 2009 2008 2010 2013 3 days_to_last_known_alive: 735 2576 NA's 1 1 1096 radiation_therapy: no yes NA's 446 556 96 number_of_lymph_nodes: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.000 0.000 1.000 2.363 2.000 35.000 169 race: american indian or alaska native asian 1 61 black or african american white 183 757 NA's 96 ethnicity: hispanic or latino not hispanic or latino NA's 39 884 175 Including an additional 2667 columns
BRCA-v2.0.1
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