ESCA-v2.1.0 | R Documentation |
A document describing the TCGA cancer code
> experiments( ESCA ) ExperimentList class object of length 13: [1] ESCA_CNASeq-20160128: RaggedExperiment with 17059 rows and 104 columns [2] ESCA_CNASNP-20160128: RaggedExperiment with 203186 rows and 373 columns [3] ESCA_CNVSNP-20160128: RaggedExperiment with 60803 rows and 373 columns [4] ESCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns [5] ESCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 77 rows and 184 columns [6] ESCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns [7] ESCA_Mutation-20160128: RaggedExperiment with 58602 rows and 185 columns [8] ESCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 196 columns [9] ESCA_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 198 columns [10] ESCA_RPPAArray-20160128: SummarizedExperiment with 192 rows and 126 columns [11] ESCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 198 columns [12] ESCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18730 rows and 196 columns [13] ESCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 202 columns > rownames( ESCA ) CharacterList of length 13 [["ESCA_CNASeq-20160128"]] character(0) [["ESCA_CNASNP-20160128"]] character(0) [["ESCA_CNVSNP-20160128"]] character(0) [["ESCA_GISTIC_AllByGene-20160128"]] character(0) [["ESCA_GISTIC_Peaks-20160128"]] 31 1 32 2 3 33 4 34 ... 73 74 29 75 76 77 78 [["ESCA_GISTIC_ThresholdedByGene-20160128"]] character(0) [["ESCA_Mutation-20160128"]] character(0) [["ESCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR [["ESCA_RNASeqGene-20160128"]] AADACL3 AADACL4 AB007962 ... VCY XKRY ZFY [["ESCA_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363 ... <3 more elements> > colnames( ESCA ) CharacterList of length 13 [["ESCA_CNASeq-20160128"]] TCGA-IG-A3I8-01A-11D-A248-26 ... [["ESCA_CNASNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ... [["ESCA_CNVSNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ... [["ESCA_GISTIC_AllByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ... [["ESCA_GISTIC_Peaks-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ... [["ESCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ... [["ESCA_Mutation-20160128"]] TCGA-2H-A9GF-01A-11D-A37C-09 ... [["ESCA_RNASeq2Gene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ... [["ESCA_RNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ... [["ESCA_RPPAArray-20160128"]] TCGA-2H-A9GF-01A-21-A41Y-20 ... ... <3 more elements> Sizes of each ExperimentList element: assay size.Mb 1 ESCA_CNASeq-20160128 0.5 Mb 2 ESCA_CNASNP-20160128 5.5 Mb 3 ESCA_CNVSNP-20160128 1.7 Mb 4 ESCA_GISTIC_AllByGene-20160128 38.3 Mb 5 ESCA_GISTIC_Peaks-20160128 0.2 Mb 6 ESCA_GISTIC_ThresholdedByGene-20160128 38.1 Mb 7 ESCA_Mutation-20160128 45 Mb 8 ESCA_RNASeq2Gene-20160128 33.2 Mb 9 ESCA_RNASeqGene-20160128 42.8 Mb 10 ESCA_RPPAArray-20160128 0.2 Mb 11 ESCA_miRNASeqGene-20160128 1.8 Mb 12 ESCA_RNASeq2GeneNorm-20160128 30.4 Mb 13 ESCA_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) 108 observations deleted due to missingness n events median 0.95LCL 0.95UCL [1,] 77 77 0.962 0.677 1.35 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. 27.00 54.00 61.00 62.46 72.00 90.00 vital_status: 0 1 108 77 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 9.0 180.0 351.0 495.2 650.0 2532.0 108 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 4.0 336.5 402.5 570.1 696.8 3714.0 77 tumor_tissue_site: esophagus 185 pathology_M_stage: m0 m1 m1a mx NA's 136 4 5 18 22 gender: female male 27 158 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1998 2007 2011 2009 2012 2013 7 radiation_therapy: no yes NA's 124 43 18 karnofsky_performance_score: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 20.00 60.00 80.00 73.82 90.00 100.00 117 histological_type: esophagus adenocarcinoma, nos esophagus squamous cell carcinoma 89 96 number_pack_years_smoked: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1.00 17.62 30.00 34.48 47.25 102.00 87 residual_tumor: r0 r1 r2 rx NA's 137 13 2 7 26 number_of_lymph_nodes: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.000 0.000 1.000 2.526 4.000 21.000 50 race: asian black or african american white 46 5 114 NA's 20 ethnicity: hispanic or latino not hispanic or latino NA's 6 88 91 Including an additional 940 columns
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