PCPG | R Documentation |
A document describing the TCGA cancer code
> experiments( PCPG ) ExperimentList class object of length 10: [1] PCPG_CNASNP-20160128: RaggedExperiment with 297329 rows and 360 columns [2] PCPG_CNVSNP-20160128: RaggedExperiment with 31256 rows and 346 columns [3] PCPG_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns [4] PCPG_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 27 rows and 162 columns [5] PCPG_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 162 columns [6] PCPG_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 187 columns [7] PCPG_Mutation-20160128: RaggedExperiment with 4662 rows and 184 columns [8] PCPG_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 187 columns [9] PCPG_RPPAArray-20160128: SummarizedExperiment with 192 rows and 82 columns [10] PCPG_Methylation-20160128: SummarizedExperiment with 485577 rows and 187 columns > rownames( PCPG ) CharacterList of length 10 [["PCPG_CNASNP-20160128"]] character(0) [["PCPG_CNVSNP-20160128"]] character(0) [["PCPG_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7 [["PCPG_GISTIC_Peaks-20160128"]] chr1:117751737-118152240 ... [["PCPG_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ... [["PCPG_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["PCPG_Mutation-20160128"]] character(0) [["PCPG_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR [["PCPG_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363 [["PCPG_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873 > colnames( PCPG ) CharacterList of length 10 [["PCPG_CNASNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ... [["PCPG_CNVSNP-20160128"]] TCGA-P7-A5NX-10A-01D-A35A-01 ... [["PCPG_GISTIC_AllByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ... [["PCPG_GISTIC_Peaks-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ... [["PCPG_GISTIC_ThresholdedByGene-20160128"]] TCGA-P7-A5NY-01A-12D-A35C-01 ... [["PCPG_miRNASeqGene-20160128"]] TCGA-P7-A5NX-01A-11R-A35M-13 ... [["PCPG_Mutation-20160128"]] TCGA-P7-A5NX-01A-11D-A35D-08 ... [["PCPG_RNASeq2GeneNorm-20160128"]] TCGA-P7-A5NX-01A-11R-A35K-07 ... [["PCPG_RPPAArray-20160128"]] TCGA-P7-A5NX-01A-21-A43B-20 ... [["PCPG_Methylation-20160128"]] TCGA-P7-A5NX-01A-11D-A35E-05 ... Sizes of each ExperimentList element: assay size.Mb 1 PCPG_CNASNP-20160128 8.1 Mb 2 PCPG_CNVSNP-20160128 0.9 Mb 3 PCPG_GISTIC_AllByGene-20160128 4.9 Mb 4 PCPG_GISTIC_Peaks-20160128 0 Mb 5 PCPG_GISTIC_ThresholdedByGene-20160128 4.9 Mb 6 PCPG_miRNASeqGene-20160128 0.1 Mb 7 PCPG_Mutation-20160128 8.4 Mb 8 PCPG_RNASeq2GeneNorm-20160128 1.3 Mb 9 PCPG_RPPAArray-20160128 0 Mb 10 PCPG_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) 173 observations deleted due to missingness n events median 0.95LCL 0.95UCL 6.00 6.00 1.24 0.26 NA --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. 19.00 35.00 46.00 47.33 58.50 83.00 vital_status: 0 1 173 6 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 88.0 148.5 452.5 901.0 715.2 3563.0 173 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 2 352 766 1071 1301 9634 6 tumor_tissue_site: adrenal gland extra-adrenal site 147 32 gender: female male 101 78 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. 1988 2009 2011 2010 2012 2013 radiation_therapy: no yes NA's 172 5 2 karnofsky_performance_score: 70 80 90 100 NA's 1 2 13 46 117 histological_type: paraganglioma 18 paraganglioma; extra-adrenal pheochromocytoma 13 pheochromocytoma 148 number_of_lymph_nodes: 0 1 2 13 NA's 16 3 1 1 158 race: american indian or alaska native asian 1 6 black or african american white 20 148 NA's 4 ethnicity: hispanic or latino not hispanic or latino NA's 5 138 36 Including an additional 894 columns
PCPG-v2.0.1
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