Kidney renal clear cell carcinoma
KIRC-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( KIRC )
ExperimentList class object of length 14:
[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_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 606 columns
[10] KIRC_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 606 columns
[11] KIRC_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 537 columns
[12] KIRC_RPPAArray-20160128: SummarizedExperiment with 217 rows and 478 columns
[13] KIRC_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 418 columns
[14] KIRC_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 480 columns
> rownames( KIRC )
CharacterList of length 14
[["KIRC_CNASNP-20160128"]] character(0)
[["KIRC_CNVSNP-20160128"]] character(0)
[["KIRC_GISTIC_AllByGene-20160128"]] character(0)
[["KIRC_GISTIC_Peaks-20160128"]] 11 12 1 2 13 14 15 16 ... 7 25 26 8 27 28 29
[["KIRC_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["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_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["KIRC_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( KIRC )
CharacterList of length 14
[["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_RNASeq2Gene-20160128"]] TCGA-3Z-A93Z-01A-11R-A37O-07 ...
[["KIRC_RNASeq2GeneNorm-20160128"]] TCGA-3Z-A93Z-01A-11R-A37O-07 ...
...
<4 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 103.4 Mb
4 KIRC_GISTIC_Peaks-20160128 0.2 Mb
5 KIRC_GISTIC_ThresholdedByGene-20160128 103.2 Mb
6 KIRC_miRNASeqGene-20160128 2.8 Mb
7 KIRC_mRNAArray-20160128 12 Mb
8 KIRC_Mutation-20160128 8.2 Mb
9 KIRC_RNASeq2Gene-20160128 97.4 Mb
10 KIRC_RNASeq2GeneNorm-20160128 97.4 Mb
11 KIRC_RNASeqGene-20160128 86.6 Mb
12 KIRC_RPPAArray-20160128 0.9 Mb
13 KIRC_Methylation_methyl27-20160128 4.9 Mb
14 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