CHOL-v2.1.0 | R Documentation |
A document describing the TCGA cancer code
> experiments( CHOL ) ExperimentList class object of length 11: [1] CHOL_CNASNP-20160128: RaggedExperiment with 39698 rows and 85 columns [2] CHOL_CNVSNP-20160128: RaggedExperiment with 7570 rows and 85 columns [3] CHOL_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns [4] CHOL_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 19 rows and 36 columns [5] CHOL_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 36 columns [6] CHOL_Mutation-20160128: RaggedExperiment with 6755 rows and 35 columns [7] CHOL_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 45 columns [8] CHOL_RPPAArray-20160128: SummarizedExperiment with 192 rows and 30 columns [9] CHOL_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 45 columns [10] CHOL_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18002 rows and 45 columns [11] CHOL_Methylation-20160128: SummarizedExperiment with 485577 rows and 45 columns > rownames( CHOL ) CharacterList of length 11 [["CHOL_CNASNP-20160128"]] character(0) [["CHOL_CNVSNP-20160128"]] character(0) [["CHOL_GISTIC_AllByGene-20160128"]] character(0) [["CHOL_GISTIC_Peaks-20160128"]] 4 1 5 6 7 8 9 10 ... 13 3 14 15 18 16 17 20 [["CHOL_GISTIC_ThresholdedByGene-20160128"]] character(0) [["CHOL_Mutation-20160128"]] character(0) [["CHOL_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR [["CHOL_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363 [["CHOL_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["CHOL_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR ... <1 more element> > colnames( CHOL ) CharacterList of length 11 [["CHOL_CNASNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ... [["CHOL_CNVSNP-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ... [["CHOL_GISTIC_AllByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ... [["CHOL_GISTIC_Peaks-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ... [["CHOL_GISTIC_ThresholdedByGene-20160128"]] TCGA-3X-AAV9-01A-72D-A416-01 ... [["CHOL_Mutation-20160128"]] TCGA-3X-AAV9-01A-72D-A417-09 ... [["CHOL_RNASeq2Gene-20160128"]] TCGA-3X-AAV9-01A-72R-A41I-07 ... [["CHOL_RPPAArray-20160128"]] TCGA-3X-AAV9-01A-81-A45N-20 ... [["CHOL_miRNASeqGene-20160128"]] TCGA-3X-AAV9-01A-72R-A41D-13 ... [["CHOL_RNASeq2GeneNorm-20160128"]] TCGA-3X-AAV9-01 ... TCGA-ZU-A8S4-01 ... <1 more element> Sizes of each ExperimentList element: assay size.Mb 1 CHOL_CNASNP-20160128 1.1 Mb 2 CHOL_CNVSNP-20160128 0.2 Mb 3 CHOL_GISTIC_AllByGene-20160128 10.2 Mb 4 CHOL_GISTIC_Peaks-20160128 0 Mb 5 CHOL_GISTIC_ThresholdedByGene-20160128 10.1 Mb 6 CHOL_Mutation-20160128 4.6 Mb 7 CHOL_RNASeq2Gene-20160128 9.6 Mb 8 CHOL_RPPAArray-20160128 0.1 Mb 9 CHOL_miRNASeqGene-20160128 0.5 Mb 10 CHOL_RNASeq2GeneNorm-20160128 8.4 Mb 11 CHOL_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) 18 observations deleted due to missingness n events median 0.95LCL 0.95UCL [1,] 18 18 1.37 0.742 2.53 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. 29.00 56.50 66.50 63.03 72.00 82.00 vital_status: 0 1 18 18 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 21.0 195.2 500.0 592.9 731.0 1939.0 18 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 10.0 539.8 942.5 936.6 1394.0 1976.0 18 tumor_tissue_site: bile duct 36 pathology_T_stage: t1 t2 t2a t2b t3 19 6 2 4 5 pathology_N_stage: n0 n1 nx 26 5 5 pathology_M_stage: m0 m1 mx 28 5 3 gender: female male 20 16 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. 2005 2010 2011 2010 2012 2013 radiation_therapy: no NA's 35 1 histological_type: cholangiocarcinoma; distal cholangiocarcinoma; hilar/perihilar 2 4 cholangiocarcinoma; intrahepatic 30 residual_tumor: r0 r1 rx 28 5 3 race: asian black or african american white 3 2 31 ethnicity: hispanic or latino not hispanic or latino NA's 2 33 1 Including an additional 622 columns
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