LAML-v2.1.0 | R Documentation |
A document describing the TCGA cancer code
> experiments( LAML ) ExperimentList class object of length 11: [1] LAML_CNASNP-20160128: RaggedExperiment with 874897 rows and 392 columns [2] LAML_CNVSNP-20160128: RaggedExperiment with 28324 rows and 380 columns [3] LAML_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns [4] LAML_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 191 columns [5] LAML_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 191 columns [6] LAML_Mutation-20160128: RaggedExperiment with 2585 rows and 197 columns [7] LAML_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 173 columns [8] LAML_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 179 columns [9] LAML_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17258 rows and 173 columns [10] LAML_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 194 columns [11] LAML_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 194 columns > rownames( LAML ) CharacterList of length 11 [["LAML_CNASNP-20160128"]] character(0) [["LAML_CNVSNP-20160128"]] character(0) [["LAML_GISTIC_AllByGene-20160128"]] character(0) [["LAML_GISTIC_Peaks-20160128"]] 1 5 6 7 8 9 2 10 11 12 13 14 15 3 16 4 [["LAML_GISTIC_ThresholdedByGene-20160128"]] character(0) [["LAML_Mutation-20160128"]] character(0) [["LAML_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR [["LAML_RNASeqGene-20160128"]] AADACL3 AADACL4 ABCA4 ... XGPY2 XKRY2 ZFY [["LAML_RNASeq2GeneNorm-20160128"]] A1BG A2LD1 A2ML1 ... ZZZ3 psiTPTE22 tAKR [["LAML_Methylation_methyl27-20160128"]] cg00000292 cg00002426 ... cg27665659 ... <1 more element> > colnames( LAML ) CharacterList of length 11 [["LAML_CNASNP-20160128"]] TCGA-AB-2802-03A-01D-0756-21 ... [["LAML_CNVSNP-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ... [["LAML_GISTIC_AllByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ... [["LAML_GISTIC_Peaks-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ... [["LAML_GISTIC_ThresholdedByGene-20160128"]] TCGA-AB-2803-03A-01D-0756-21 ... [["LAML_Mutation-20160128"]] TCGA-AB-2802-03B-01W-0728-08 ... [["LAML_RNASeq2Gene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ... [["LAML_RNASeqGene-20160128"]] TCGA-AB-2803-03A-01T-0734-13 ... [["LAML_RNASeq2GeneNorm-20160128"]] TCGA-AB-2803-03 ... TCGA-AB-3012-03 [["LAML_Methylation_methyl27-20160128"]] TCGA-AB-2802-03A-01D-0741-05 ... ... <1 more element> Sizes of each ExperimentList element: assay size.Mb 1 LAML_CNASNP-20160128 23.5 Mb 2 LAML_CNVSNP-20160128 0.9 Mb 3 LAML_GISTIC_AllByGene-20160128 39.5 Mb 4 LAML_GISTIC_Peaks-20160128 0.1 Mb 5 LAML_GISTIC_ThresholdedByGene-20160128 39.5 Mb 6 LAML_Mutation-20160128 2.8 Mb 7 LAML_RNASeq2Gene-20160128 29.6 Mb 8 LAML_RNASeqGene-20160128 29.8 Mb 9 LAML_RNASeq2GeneNorm-20160128 24.9 Mb 10 LAML_Methylation_methyl27-20160128 4.9 Mb 11 LAML_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) 80 observations deleted due to missingness n events median 0.95LCL 0.95UCL [1,] 120 120 0.748 0.586 0.918 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. 18.00 44.75 57.00 55.02 67.00 88.00 vital_status: 0 1 67 133 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.0 91.5 273.0 355.7 489.0 1706.0 80 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.0 296.2 699.0 913.5 1506.8 2861.0 132 tumor_tissue_site: bone marrow NA's 199 1 gender: female male 91 109 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. 2001 2004 2006 2006 2008 2010 race: asian black or african american white 2 15 181 NA's 2 ethnicity: hispanic or latino not hispanic or latino NA's 3 194 3 Including an additional 478 columns
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