GBM | R Documentation |
A document describing the TCGA cancer code
> experiments( GBM ) ExperimentList class object of length 18: [1] GBM_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 81512 rows and 438 columns [2] GBM_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 57975 rows and 338 columns [3] GBM_CNASNP-20160128: RaggedExperiment with 602338 rows and 1104 columns [4] GBM_CNVSNP-20160128: RaggedExperiment with 146852 rows and 1104 columns [5] GBM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns [6] GBM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 68 rows and 577 columns [7] GBM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 577 columns [8] GBM_miRNAArray-20160128: SummarizedExperiment with 534 rows and 565 columns [9] GBM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 0 columns [10] GBM_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 431 columns [11] GBM_mRNAArray_TX_g4502a_1-20160128: SummarizedExperiment with 17814 rows and 401 columns [12] GBM_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 101 columns [13] GBM_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 528 columns [14] GBM_Mutation-20160128: RaggedExperiment with 22073 rows and 290 columns [15] GBM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 166 columns [16] GBM_RPPAArray-20160128: SummarizedExperiment with 208 rows and 244 columns [17] GBM_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 285 columns [18] GBM_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 154 columns > rownames( GBM ) CharacterList of length 18 [["GBM_CNACGH_CGH_hg_244a-20160128"]] character(0) [["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0) [["GBM_CNASNP-20160128"]] character(0) [["GBM_CNVSNP-20160128"]] character(0) [["GBM_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7 [["GBM_GISTIC_Peaks-20160128"]] chr1:3394251-6475685 ... [["GBM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ... [["GBM_miRNAArray-20160128"]] ebv-miR-BART1-3p ... kshv-miR-K12-9* [["GBM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["GBM_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7 ... <8 more elements> > colnames( GBM ) CharacterList of length 18 [["GBM_CNACGH_CGH_hg_244a-20160128"]] TCGA-02-0001-01C-01D-0185-02 ... [["GBM_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-02-2466-01A-01D-0787-02 ... [["GBM_CNASNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ... [["GBM_CNVSNP-20160128"]] TCGA-02-0001-01C-01D-0182-01 ... [["GBM_GISTIC_AllByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ... [["GBM_GISTIC_Peaks-20160128"]] TCGA-02-0001-01C-01D-0182-01 ... [["GBM_GISTIC_ThresholdedByGene-20160128"]] TCGA-02-0001-01C-01D-0182-01 ... [["GBM_miRNAArray-20160128"]] TCGA-02-0001-01C-01T-0179-07 ... [["GBM_miRNASeqGene-20160128"]] character(0) [["GBM_mRNAArray_huex-20160128"]] TCGA-02-0001-01C-01R-0178-03 ... ... <8 more elements> Sizes of each ExperimentList element: assay size.Mb 1 GBM_CNACGH_CGH_hg_244a-20160128 2.3 Mb 2 GBM_CNACGH_CGH_hg_415k_g4124a-20160128 1.7 Mb 3 GBM_CNASNP-20160128 16.4 Mb 4 GBM_CNVSNP-20160128 4.2 Mb 5 GBM_GISTIC_AllByGene-20160128 4.9 Mb 6 GBM_GISTIC_Peaks-20160128 0.1 Mb 7 GBM_GISTIC_ThresholdedByGene-20160128 4.9 Mb 8 GBM_miRNAArray-20160128 0.1 Mb 9 GBM_miRNASeqGene-20160128 0.1 Mb 10 GBM_mRNAArray_huex-20160128 1.2 Mb 11 GBM_mRNAArray_TX_g4502a_1-20160128 1.1 Mb 12 GBM_mRNAArray_TX_g4502a-20160128 1.1 Mb 13 GBM_mRNAArray_TX_ht_hg_u133a-20160128 0.8 Mb 14 GBM_Mutation-20160128 31 Mb 15 GBM_RNASeq2GeneNorm-20160128 1.3 Mb 16 GBM_RPPAArray-20160128 0 Mb 17 GBM_Methylation_methyl27-20160128 4.9 Mb 18 GBM_Methylation_methyl450-20160128 75 Mb --------------------------- Overall survival time-to-event summary (in years): --------------------------- Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~ -1) 109 observations deleted due to missingness n events median 0.95LCL 0.95UCL 490.000 490.000 1.047 0.981 1.156 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 10.00 50.00 59.00 57.82 68.00 89.00 4 vital_status: 0 1 NA's 104 491 4 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 3.0 170.5 382.0 504.5 609.2 3881.0 109 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.0 156.2 261.0 479.4 628.0 2818.0 497 tumor_tissue_site: brain NA's 595 4 gender: female male NA's 230 365 4 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1989 2002 2006 2005 2009 2013 4 radiation_therapy: no yes NA's 78 489 32 karnofsky_performance_score: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.00 70.00 80.00 77.04 80.00 100.00 157 histological_type: glioblastoma multiforme (gbm) treated primary gbm 31 20 untreated primary (de novo) gbm NA's 544 4 race: asian black or african american white 13 51 506 NA's 29 ethnicity: hispanic or latino not hispanic or latino NA's 13 489 97 Including an additional 4368 columns
GBM-v2.0.1
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