KIRC | R Documentation |
A document describing the TCGA cancer code
> experiments( KIRC ) ExperimentList class object of length 13: [1] KIRC_CNASNP-20160128: RaggedExperiment with 488691 rows and 1059 columns [2] KIRC_CNVSNP-20160128: RaggedExperiment with 85036 rows and 1059 columns [3] KIRC_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns [4] KIRC_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 26 rows and 528 columns [5] KIRC_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 528 columns [6] KIRC_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns [7] KIRC_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 72 columns [8] KIRC_Mutation-20160128: RaggedExperiment with 26369 rows and 437 columns [9] KIRC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 606 columns [10] KIRC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 537 columns [11] KIRC_RPPAArray-20160128: SummarizedExperiment with 217 rows and 478 columns [12] KIRC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 418 columns [13] KIRC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 480 columns > rownames( KIRC ) CharacterList of length 13 [["KIRC_CNASNP-20160128"]] character(0) [["KIRC_CNVSNP-20160128"]] character(0) [["KIRC_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7 [["KIRC_GISTIC_Peaks-20160128"]] chr1:1-31345223 ... chr14:56181301-107349540 [["KIRC_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ... [["KIRC_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["KIRC_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC [["KIRC_Mutation-20160128"]] character(0) [["KIRC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR [["KIRC_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR ... <3 more elements> > colnames( KIRC ) CharacterList of length 13 [["KIRC_CNASNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ... [["KIRC_CNVSNP-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ... [["KIRC_GISTIC_AllByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ... [["KIRC_GISTIC_Peaks-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ... [["KIRC_GISTIC_ThresholdedByGene-20160128"]] TCGA-3Z-A93Z-01A-11D-A36W-01 ... [["KIRC_miRNASeqGene-20160128"]] TCGA-3Z-A93Z-01A-11R-A37P-13 ... [["KIRC_mRNAArray-20160128"]] TCGA-A3-3306-01A-01R-0864-07 ... [["KIRC_Mutation-20160128"]] TCGA-A3-3308-01A-01D-0966-08 ... [["KIRC_RNASeq2GeneNorm-20160128"]] TCGA-3Z-A93Z-01A-11R-A37O-07 ... [["KIRC_RNASeqGene-20160128"]] TCGA-A3-3306-01A-01R-0864-07 ... ... <3 more elements> Sizes of each ExperimentList element: assay size.Mb 1 KIRC_CNASNP-20160128 13.4 Mb 2 KIRC_CNVSNP-20160128 2.6 Mb 3 KIRC_GISTIC_AllByGene-20160128 4.9 Mb 4 KIRC_GISTIC_Peaks-20160128 0.1 Mb 5 KIRC_GISTIC_ThresholdedByGene-20160128 4.9 Mb 6 KIRC_miRNASeqGene-20160128 0.1 Mb 7 KIRC_mRNAArray-20160128 1.1 Mb 8 KIRC_Mutation-20160128 8.2 Mb 9 KIRC_RNASeq2GeneNorm-20160128 1.3 Mb 10 KIRC_RNASeqGene-20160128 1.3 Mb 11 KIRC_RPPAArray-20160128 0.1 Mb 12 KIRC_Methylation_methyl27-20160128 4.9 Mb 13 KIRC_Methylation_methyl450-20160128 75.1 Mb --------------------------- Overall survival time-to-event summary (in years): --------------------------- Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~ -1) 360 observations deleted due to missingness n events median 0.95LCL 0.95UCL 177.00 177.00 2.24 1.77 2.61 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 26.00 52.00 61.00 60.57 70.00 90.00 1 vital_status: 0 1 360 177 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 2.0 333.0 819.0 961.2 1432.0 3615.0 360 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.0 710.5 1454.5 1536.9 2172.0 4537.0 177 tumor_tissue_site: kidney 537 pathologic_stage: stage i stage ii stage iii stage iv NA's 269 57 125 84 2 pathology_N_stage: n0 n1 nx 240 17 280 pathology_M_stage: m0 m1 mx NA's 426 79 30 2 gender: female male 191 346 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. 1998 2004 2006 2006 2007 2013 days_to_last_known_alive: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0 191 1172 1117 1887 2799 510 radiation_therapy: no yes NA's 142 2 393 karnofsky_performance_score: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.00 90.00 90.00 85.56 100.00 100.00 483 histological_type: kidney clear cell renal carcinoma 537 number_pack_years_smoked: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 7.00 14.00 30.00 28.33 40.00 65.00 516 year_of_tobacco_smoking_onset: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1946 1966 1978 1979 1996 2001 525 race: asian black or african american white 8 56 466 NA's 7 ethnicity: hispanic or latino not hispanic or latino NA's 26 359 152 Including an additional 2250 columns
KIRC-v2.0.1
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.