UVM | R Documentation |
A document describing the TCGA cancer code
> experiments( UVM ) ExperimentList class object of length 11: [1] UVM_CNASeq-20160128: RaggedExperiment with 6496 rows and 102 columns [2] UVM_CNASNP-20160128: RaggedExperiment with 69487 rows and 160 columns [3] UVM_CNVSNP-20160128: RaggedExperiment with 12973 rows and 160 columns [4] UVM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns [5] UVM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 80 columns [6] UVM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns [7] UVM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns [8] UVM_Mutation-20160128: RaggedExperiment with 2174 rows and 80 columns [9] UVM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 80 columns [10] UVM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 12 columns [11] UVM_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns > rownames( UVM ) CharacterList of length 11 [["UVM_CNASeq-20160128"]] character(0) [["UVM_CNASNP-20160128"]] character(0) [["UVM_CNVSNP-20160128"]] character(0) [["UVM_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7 [["UVM_GISTIC_Peaks-20160128"]] chr1:19073360-24108626 ... [["UVM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ... [["UVM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["UVM_Mutation-20160128"]] character(0) [["UVM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR [["UVM_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363 ... <1 more element> > colnames( UVM ) CharacterList of length 11 [["UVM_CNASeq-20160128"]] TCGA-RZ-AB0B-01A-11D-A40D-26 ... [["UVM_CNASNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ... [["UVM_CNVSNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ... [["UVM_GISTIC_AllByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ... [["UVM_GISTIC_Peaks-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ... [["UVM_GISTIC_ThresholdedByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ... [["UVM_miRNASeqGene-20160128"]] TCGA-RZ-AB0B-01A-11R-A40B-13 ... [["UVM_Mutation-20160128"]] TCGA-RZ-AB0B-01A-11D-A39W-08 ... [["UVM_RNASeq2GeneNorm-20160128"]] TCGA-RZ-AB0B-01A-11R-A405-07 ... [["UVM_RPPAArray-20160128"]] TCGA-V3-A9ZX-01A-21-A41Z-20 ... ... <1 more element> Sizes of each ExperimentList element: assay size.Mb 1 UVM_CNASeq-20160128 0.2 Mb 2 UVM_CNASNP-20160128 1.9 Mb 3 UVM_CNVSNP-20160128 0.4 Mb 4 UVM_GISTIC_AllByGene-20160128 4.9 Mb 5 UVM_GISTIC_Peaks-20160128 0 Mb 6 UVM_GISTIC_ThresholdedByGene-20160128 4.9 Mb 7 UVM_miRNASeqGene-20160128 0.1 Mb 8 UVM_Mutation-20160128 12.3 Mb 9 UVM_RNASeq2GeneNorm-20160128 1.3 Mb 10 UVM_RPPAArray-20160128 0 Mb 11 UVM_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) 57 observations deleted due to missingness n events median 0.95LCL 0.95UCL 23.00 23.00 1.66 1.14 3.05 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. 22.00 51.00 61.50 61.65 74.25 86.00 vital_status: 0 1 57 23 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 40.0 393.5 606.0 693.9 1029.0 1581.0 57 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 4.0 495.0 821.0 861.9 1184.0 2600.0 23 tumor_tissue_site: choroid 80 pathology_N_stage: n0 nx NA's 52 27 1 pathology_M_stage: m0 m1 m1b mx NA's 51 2 2 23 2 gender: female male 35 45 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. 2007 2011 2012 2012 2013 2013 radiation_therapy: no yes NA's 76 3 1 race: white NA's 55 25 ethnicity: hispanic or latino not hispanic or latino NA's 1 52 27 Including an additional 448 columns
UVM-v2.0.1
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