KICH-v2.0.1 | R Documentation |
A document describing the TCGA cancer code
> experiments( KICH ) ExperimentList class object of length 11: [1] KICH_CNASNP-20160128: RaggedExperiment with 57729 rows and 132 columns [2] KICH_CNVSNP-20160128: RaggedExperiment with 10164 rows and 132 columns [3] KICH_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns [4] KICH_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 2 rows and 66 columns [5] KICH_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 66 columns [6] KICH_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 91 columns [7] KICH_Mutation-20160128: RaggedExperiment with 7559 rows and 66 columns [8] KICH_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 91 columns [9] KICH_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 91 columns [10] KICH_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns [11] KICH_Methylation-20160128: SummarizedExperiment with 485577 rows and 66 columns > rownames( KICH ) CharacterList of length 11 [["KICH_CNASNP-20160128"]] character(0) [["KICH_CNVSNP-20160128"]] character(0) [["KICH_GISTIC_AllByGene-20160128"]] character(0) [["KICH_GISTIC_Peaks-20160128"]] 1 2 [["KICH_GISTIC_ThresholdedByGene-20160128"]] character(0) [["KICH_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["KICH_Mutation-20160128"]] character(0) [["KICH_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR [["KICH_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR [["KICH_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363 ... <1 more element> > colnames( KICH ) CharacterList of length 11 [["KICH_CNASNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ... [["KICH_CNVSNP-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ... [["KICH_GISTIC_AllByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ... [["KICH_GISTIC_Peaks-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ... [["KICH_GISTIC_ThresholdedByGene-20160128"]] TCGA-KL-8323-01A-21D-2308-01 ... [["KICH_miRNASeqGene-20160128"]] TCGA-KL-8323-01A-21R-2314-13 ... [["KICH_Mutation-20160128"]] TCGA-KL-8323-01A-21D-2310-10 ... [["KICH_RNASeq2Gene-20160128"]] TCGA-KL-8323-01A-21R-2315-07 ... [["KICH_RNASeq2GeneNorm-20160128"]] TCGA-KL-8323-01A-21R-2315-07 ... [["KICH_RPPAArray-20160128"]] TCGA-KL-8324-01A-21-A421-20 ... ... <1 more element> Sizes of each ExperimentList element: assay size.Mb 1 KICH_CNASNP-20160128 1.6 Mb 2 KICH_CNVSNP-20160128 0.3 Mb 3 KICH_GISTIC_AllByGene-20160128 15.9 Mb 4 KICH_GISTIC_Peaks-20160128 0 Mb 5 KICH_GISTIC_ThresholdedByGene-20160128 15.8 Mb 6 KICH_miRNASeqGene-20160128 0.9 Mb 7 KICH_Mutation-20160128 2.6 Mb 8 KICH_RNASeq2Gene-20160128 16.8 Mb 9 KICH_RNASeq2GeneNorm-20160128 16.8 Mb 10 KICH_RPPAArray-20160128 0.1 Mb 11 KICH_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 9.00 9.00 2.34 1.99 NA --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. 17.00 42.00 50.00 51.52 61.75 86.00 vital_status: 0 1 56 10 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 325 725 855 1001 1158 2172 57 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 30 1366 2713 2320 3138 4676 10 tumor_tissue_site: kidney 66 pathologic_stage: stage i stage ii stage iii stage iv 21 25 14 6 pathology_N_stage: n0 n1 n2 nx 40 3 2 21 pathology_M_stage: m0 m1 mx NA's 34 2 9 21 gender: female male 27 39 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. 2000 2004 2005 2005 2007 2011 radiation_therapy: no 66 karnofsky_performance_score: 90 100 NA's 3 10 53 histological_type: kidney chromophobe 66 number_pack_years_smoked: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1.00 8.00 24.00 25.09 31.00 75.00 55 year_of_tobacco_smoking_onset: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1949 1964 1974 1974 1984 1997 58 race: asian black or african american white 2 4 58 NA's 2 ethnicity: hispanic or latino not hispanic or latino NA's 4 32 30 Including an additional 718 columns
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