LIHC-v2.1.0 | R Documentation |
A document describing the TCGA cancer code
> experiments( LIHC ) ExperimentList class object of length 12: [1] LIHC_CNASNP-20160128: RaggedExperiment with 363628 rows and 760 columns [2] LIHC_CNVSNP-20160128: RaggedExperiment with 93328 rows and 760 columns [3] LIHC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns [4] LIHC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 59 rows and 370 columns [5] LIHC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 370 columns [6] LIHC_Mutation-20160128: RaggedExperiment with 27892 rows and 198 columns [7] LIHC_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 423 columns [8] LIHC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 26 columns [9] LIHC_RPPAArray-20160128: SummarizedExperiment with 219 rows and 184 columns [10] LIHC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 424 columns [11] LIHC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17690 rows and 423 columns [12] LIHC_Methylation-20160128: SummarizedExperiment with 485577 rows and 429 columns > rownames( LIHC ) CharacterList of length 12 [["LIHC_CNASNP-20160128"]] character(0) [["LIHC_CNVSNP-20160128"]] character(0) [["LIHC_GISTIC_AllByGene-20160128"]] character(0) [["LIHC_GISTIC_Peaks-20160128"]] 28 29 1 2 3 30 4 31 ... 23 24 58 25 26 59 60 [["LIHC_GISTIC_ThresholdedByGene-20160128"]] character(0) [["LIHC_Mutation-20160128"]] character(0) [["LIHC_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR [["LIHC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR [["LIHC_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363 [["LIHC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b ... <2 more elements> > colnames( LIHC ) CharacterList of length 12 [["LIHC_CNASNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ... [["LIHC_CNVSNP-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ... [["LIHC_GISTIC_AllByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ... [["LIHC_GISTIC_Peaks-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ... [["LIHC_GISTIC_ThresholdedByGene-20160128"]] TCGA-2V-A95S-01A-11D-A36W-01 ... [["LIHC_Mutation-20160128"]] TCGA-BC-4073-01B-02D-A12Z-10 ... [["LIHC_RNASeq2Gene-20160128"]] TCGA-2V-A95S-01A-11R-A37K-07 ... [["LIHC_RNASeqGene-20160128"]] TCGA-BC-4073-01B-02R-A131-07 ... [["LIHC_RPPAArray-20160128"]] TCGA-BC-4072-01B-21-A40L-20 ... [["LIHC_miRNASeqGene-20160128"]] TCGA-2V-A95S-01A-11R-A37G-13 ... ... <2 more elements> Sizes of each ExperimentList element: assay size.Mb 1 LIHC_CNASNP-20160128 9.9 Mb 2 LIHC_CNVSNP-20160128 2.7 Mb 3 LIHC_GISTIC_AllByGene-20160128 73.5 Mb 4 LIHC_GISTIC_Peaks-20160128 0.3 Mb 5 LIHC_GISTIC_ThresholdedByGene-20160128 73.3 Mb 6 LIHC_Mutation-20160128 16.8 Mb 7 LIHC_RNASeq2Gene-20160128 68.8 Mb 8 LIHC_RNASeqGene-20160128 6.6 Mb 9 LIHC_RPPAArray-20160128 0.4 Mb 10 LIHC_miRNASeqGene-20160128 3.6 Mb 11 LIHC_RNASeq2GeneNorm-20160128 59.3 Mb 12 LIHC_Methylation-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) 245 observations deleted due to missingness n events median 0.95LCL 0.95UCL [1,] 132 132 1.14 0.956 1.63 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 16.00 51.00 61.00 59.27 69.00 87.00 4 vital_status: 0 1 245 132 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 9.0 194.8 417.5 672.1 837.0 3258.0 245 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.0 395.8 649.5 885.8 1222.0 3675.0 133 tumor_tissue_site: liver 377 pathology_N_stage: n0 n1 nx NA's 257 4 115 1 pathology_M_stage: m0 m1 mx 272 4 101 gender: female male 122 255 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1995 2008 2011 2010 2012 2013 3 radiation_therapy: no yes NA's 345 9 23 histological_type: fibrolamellar carcinoma hepatocellular carcinoma 3 367 hepatocholangiocarcinoma (mixed) 7 residual_tumor: r0 r1 r2 rx NA's 330 17 1 22 7 race: american indian or alaska native asian 2 161 black or african american white 17 187 NA's 10 ethnicity: hispanic or latino not hispanic or latino NA's 18 340 19 Including an additional 1218 columns
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