KIRP | R Documentation |
A document describing the TCGA cancer code
> experiments( KIRP ) ExperimentList class object of length 13: [1] KIRP_CNASNP-20160128: RaggedExperiment with 300681 rows and 593 columns [2] KIRP_CNVSNP-20160128: RaggedExperiment with 46914 rows and 590 columns [3] KIRP_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns [4] KIRP_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 28 rows and 288 columns [5] KIRP_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 288 columns [6] KIRP_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 326 columns [7] KIRP_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 16 columns [8] KIRP_Mutation-20160128: RaggedExperiment with 15585 rows and 161 columns [9] KIRP_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 323 columns [10] KIRP_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 14 columns [11] KIRP_RPPAArray-20160128: SummarizedExperiment with 195 rows and 216 columns [12] KIRP_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 21 columns [13] KIRP_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 321 columns > rownames( KIRP ) CharacterList of length 13 [["KIRP_CNASNP-20160128"]] character(0) [["KIRP_CNVSNP-20160128"]] character(0) [["KIRP_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7 [["KIRP_GISTIC_Peaks-20160128"]] chr1:1-29472434 ... chr22:29969457-30128393 [["KIRP_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ... [["KIRP_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b [["KIRP_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC [["KIRP_Mutation-20160128"]] character(0) [["KIRP_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR [["KIRP_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR ... <3 more elements> > colnames( KIRP ) CharacterList of length 13 [["KIRP_CNASNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ... [["KIRP_CNVSNP-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ... [["KIRP_GISTIC_AllByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ... [["KIRP_GISTIC_Peaks-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ... [["KIRP_GISTIC_ThresholdedByGene-20160128"]] TCGA-2K-A9WE-01A-11D-A381-01 ... [["KIRP_miRNASeqGene-20160128"]] TCGA-2K-A9WE-01A-11R-A38N-13 ... [["KIRP_mRNAArray-20160128"]] TCGA-AL-3466-01A-01R-1193-07 ... [["KIRP_Mutation-20160128"]] TCGA-A4-7286-01A-11D-2136-08 ... [["KIRP_RNASeq2GeneNorm-20160128"]] TCGA-2K-A9WE-01A-11R-A38C-07 ... [["KIRP_RNASeqGene-20160128"]] TCGA-AL-3466-01A-02R-1351-07 ... ... <3 more elements> Sizes of each ExperimentList element: assay size.Mb 1 KIRP_CNASNP-20160128 8.2 Mb 2 KIRP_CNVSNP-20160128 1.4 Mb 3 KIRP_GISTIC_AllByGene-20160128 4.9 Mb 4 KIRP_GISTIC_Peaks-20160128 0.1 Mb 5 KIRP_GISTIC_ThresholdedByGene-20160128 4.9 Mb 6 KIRP_miRNASeqGene-20160128 0.1 Mb 7 KIRP_mRNAArray-20160128 1.1 Mb 8 KIRP_Mutation-20160128 10.6 Mb 9 KIRP_RNASeq2GeneNorm-20160128 1.3 Mb 10 KIRP_RNASeqGene-20160128 1.3 Mb 11 KIRP_RPPAArray-20160128 0 Mb 12 KIRP_Methylation_methyl27-20160128 4.9 Mb 13 KIRP_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) 247 observations deleted due to missingness n events median 0.95LCL 0.95UCL 44.00 44.00 1.76 1.35 3.60 --------------------------- Available sample meta-data: --------------------------- years_to_birth: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 28.00 53.25 61.50 61.52 71.00 88.00 5 vital_status: 0 1 247 44 days_to_death: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 122.0 341.2 641.0 989.8 1498.5 2941.0 247 days_to_last_followup: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.0 438.2 774.5 1070.2 1513.0 5925.0 45 tumor_tissue_site: kidney 291 pathologic_stage: stage i stage ii stage iii stage iv NA's 173 21 52 15 30 pathology_N_stage: n0 n1 n2 nx NA's 50 24 4 212 1 pathology_M_stage: m0 m1 mx NA's 95 9 172 15 gender: female male 77 214 date_of_initial_pathologic_diagnosis: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1996 2008 2011 2010 2012 2013 25 days_to_last_known_alive: 34 NA's 1 290 radiation_therapy: no yes NA's 209 1 81 karnofsky_performance_score: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 0.00 90.00 90.00 87.66 100.00 100.00 214 histological_type: kidney papillary renal cell carcinoma 291 number_pack_years_smoked: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 3.00 15.00 24.50 31.73 41.25 185.00 215 year_of_tobacco_smoking_onset: Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1941 1961 1970 1972 1984 2010 235 race: american indian or alaska native asian 2 6 black or african american white 61 207 NA's 15 ethnicity: hispanic or latino not hispanic or latino NA's 12 243 36 Including an additional 1686 columns
KIRP-v2.0.1
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.