Kidney renal papillary cell carcinoma
KIRP.RdA document describing the TCGA cancer code
Details
> 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