Kidney Chromophobe
KICH.RdA document describing the TCGA cancer code
Details
> experiments( KICH )
ExperimentList class object of length 10:
[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_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 91 columns
[9] KICH_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[10] KICH_Methylation-20160128: SummarizedExperiment with 485577 rows and 66 columns
> rownames( KICH )
CharacterList of length 10
[["KICH_CNASNP-20160128"]] character(0)
[["KICH_CNVSNP-20160128"]] character(0)
[["KICH_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["KICH_GISTIC_Peaks-20160128"]] chr8:116272008-117149163 chr15:1-66482794
[["KICH_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["KICH_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["KICH_Mutation-20160128"]] character(0)
[["KICH_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["KICH_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["KICH_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( KICH )
CharacterList of length 10
[["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_RNASeq2GeneNorm-20160128"]] TCGA-KL-8323-01A-21R-2315-07 ...
[["KICH_RPPAArray-20160128"]] TCGA-KL-8324-01A-21-A421-20 ...
[["KICH_Methylation-20160128"]] TCGA-KL-8323-01A-21D-2312-05 ...
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 4.9 Mb
4 KICH_GISTIC_Peaks-20160128 0 Mb
5 KICH_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 KICH_miRNASeqGene-20160128 0.1 Mb
7 KICH_Mutation-20160128 2.6 Mb
8 KICH_RNASeq2GeneNorm-20160128 1.3 Mb
9 KICH_RPPAArray-20160128 0 Mb
10 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