Bladder Urothelial Carcinoma
BLCA-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( BLCA )
ExperimentList class object of length 13:
[1] BLCA_CNASeq-20160128: RaggedExperiment with 35692 rows and 232 columns
[2] BLCA_CNASNP-20160128: RaggedExperiment with 479978 rows and 806 columns
[3] BLCA_CNVSNP-20160128: RaggedExperiment with 104349 rows and 797 columns
[4] BLCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[5] BLCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 71 rows and 408 columns
[6] BLCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 408 columns
[7] BLCA_Mutation-20160128: RaggedExperiment with 39312 rows and 130 columns
[8] BLCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 427 columns
[9] BLCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 67 columns
[10] BLCA_RPPAArray-20160128: SummarizedExperiment with 208 rows and 344 columns
[11] BLCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 429 columns
[12] BLCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18205 rows and 427 columns
[13] BLCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 434 columns
> rownames( BLCA )
CharacterList of length 13
[["BLCA_CNASeq-20160128"]] character(0)
[["BLCA_CNASNP-20160128"]] character(0)
[["BLCA_CNVSNP-20160128"]] character(0)
[["BLCA_GISTIC_AllByGene-20160128"]] character(0)
[["BLCA_GISTIC_Peaks-20160128"]] 38 1 2 3 39 4 40 41 ... 69 70 34 35 36 37 71
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["BLCA_Mutation-20160128"]] character(0)
[["BLCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["BLCA_RNASeqGene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["BLCA_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
...
<3 more elements>
> colnames( BLCA )
CharacterList of length 13
[["BLCA_CNASeq-20160128"]] TCGA-BL-A0C8-01A-11D-A10R-02 ...
[["BLCA_CNASNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_CNVSNP-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_AllByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_Peaks-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2F-A9KO-01A-11D-A38F-01 ...
[["BLCA_Mutation-20160128"]] TCGA-BL-A0C8-01A-11D-A10S-08 ...
[["BLCA_RNASeq2Gene-20160128"]] TCGA-2F-A9KO-01A-11R-A38B-07 ...
[["BLCA_RNASeqGene-20160128"]] TCGA-BL-A0C8-01A-11R-A10U-07 ...
[["BLCA_RPPAArray-20160128"]] TCGA-2F-A9KO-01A-21-A459-20 ...
...
<3 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BLCA_CNASeq-20160128 1 Mb
2 BLCA_CNASNP-20160128 13.1 Mb
3 BLCA_CNVSNP-20160128 3 Mb
4 BLCA_GISTIC_AllByGene-20160128 80.7 Mb
5 BLCA_GISTIC_Peaks-20160128 0.4 Mb
6 BLCA_GISTIC_ThresholdedByGene-20160128 80.5 Mb
7 BLCA_Mutation-20160128 56.1 Mb
8 BLCA_RNASeq2Gene-20160128 69.4 Mb
9 BLCA_RNASeqGene-20160128 13 Mb
10 BLCA_RPPAArray-20160128 0.6 Mb
11 BLCA_miRNASeqGene-20160128 3.6 Mb
12 BLCA_RNASeq2GeneNorm-20160128 61.6 Mb
13 BLCA_Methylation-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)
232 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 180 180 1.12 0.992 1.33
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
34.00 60.00 69.00 68.08 76.00 90.00 1
vital_status:
0 1
230 182
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
19.0 235.8 410.5 552.8 654.5 3183.0 232
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-64.0 398.2 639.0 1016.7 1458.8 5050.0 182
tumor_tissue_site:
bladder
412
pathologic_stage:
stage i stage ii stage iii stage iv NA's
2 131 141 136 2
pathology_M_stage:
m0 m1 mx NA's
196 11 202 3
gender:
female male
108 304
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1999 2009 2011 2010 2012 2013 18
radiation_therapy:
no yes NA's
366 20 26
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.00 80.00 90.00 83.09 90.00 100.00 276
histological_type:
muscle invasive urothelial carcinoma (pt2 or above)
409
NA's
3
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.15 20.00 30.00 39.04 50.00 730.00 188
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.088 2.000 97.000 115
race:
asian black or african american white
44 23 327
NA's
18
ethnicity:
hispanic or latino not hispanic or latino NA's
9 371 32
Including an additional 1695 columns