Prostate adenocarcinoma
PRAD-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( PRAD )
ExperimentList class object of length 12:
[1] PRAD_CNASeq-20160128: RaggedExperiment with 23398 rows and 230 columns
[2] PRAD_CNASNP-20160128: RaggedExperiment with 573776 rows and 1029 columns
[3] PRAD_CNVSNP-20160128: RaggedExperiment with 117345 rows and 1023 columns
[4] PRAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[5] PRAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 58 rows and 492 columns
[6] PRAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 492 columns
[7] PRAD_Mutation-20160128: RaggedExperiment with 12348 rows and 332 columns
[8] PRAD_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 550 columns
[9] PRAD_RPPAArray-20160128: SummarizedExperiment with 195 rows and 352 columns
[10] PRAD_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 547 columns
[11] PRAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18265 rows and 550 columns
[12] PRAD_Methylation-20160128: SummarizedExperiment with 485577 rows and 549 columns
> rownames( PRAD )
CharacterList of length 12
[["PRAD_CNASeq-20160128"]] character(0)
[["PRAD_CNASNP-20160128"]] character(0)
[["PRAD_CNVSNP-20160128"]] character(0)
[["PRAD_GISTIC_AllByGene-20160128"]] character(0)
[["PRAD_GISTIC_Peaks-20160128"]] 29 30 1 31 32 33 34 ... 21 60 61 22 23 62 63
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["PRAD_Mutation-20160128"]] character(0)
[["PRAD_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["PRAD_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["PRAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>
> colnames( PRAD )
CharacterList of length 12
[["PRAD_CNASeq-20160128"]] TCGA-CH-5741-01A-11D-1572-02 ...
[["PRAD_CNASNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_CNVSNP-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_AllByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_Peaks-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-2A-A8VL-01A-21D-A376-01 ...
[["PRAD_Mutation-20160128"]] TCGA-2A-A8VL-01A-21D-A377-08 ...
[["PRAD_RNASeq2Gene-20160128"]] TCGA-2A-A8VL-01A-21R-A37L-07 ...
[["PRAD_RPPAArray-20160128"]] TCGA-2A-A8VL-01A-11-A43M-20 ...
[["PRAD_miRNASeqGene-20160128"]] TCGA-2A-A8VL-01A-21R-A37H-13 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 PRAD_CNASeq-20160128 0.7 Mb
2 PRAD_CNASNP-20160128 15.6 Mb
3 PRAD_CNVSNP-20160128 3.4 Mb
4 PRAD_GISTIC_AllByGene-20160128 96.6 Mb
5 PRAD_GISTIC_Peaks-20160128 0.4 Mb
6 PRAD_GISTIC_ThresholdedByGene-20160128 96.4 Mb
7 PRAD_Mutation-20160128 21.5 Mb
8 PRAD_RNASeq2Gene-20160128 88.7 Mb
9 PRAD_RPPAArray-20160128 0.6 Mb
10 PRAD_miRNASeqGene-20160128 4.6 Mb
11 PRAD_RNASeq2GeneNorm-20160128 79 Mb
12 PRAD_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)
488 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 10 10 3.02 1.99 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
41.00 56.00 61.00 61.02 66.00 78.00 11
vital_status:
0 1
488 10
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
146.0 743.8 1102.0 1579.0 2315.5 3502.0 488
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
23.0 523.5 926.0 1076.5 1458.0 5024.0 10
tumor_tissue_site:
prostate
498
pathology_N_stage:
n0 n1 NA's
346 79 73
gender:
male
498
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2009 2011 2010 2012 2013 31
radiation_therapy:
no yes NA's
395 59 44
histological_type:
prostate adenocarcinoma acinar type prostate adenocarcinoma, other subtype
483 15
residual_tumor:
r0 r1 r2 rx NA's
316 147 5 15 15
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0000 0.0000 0.0000 0.4447 0.0000 15.0000 91
gleason_score:
6 7 8 9 10
45 248 64 137 4
psa_value:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.030 0.100 1.742 0.110 323.000 57
days_to_psa:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-164.0 191.0 512.0 685.6 926.0 3447.0 53
race:
asian black or african american white
2 7 147
NA's
342
ethnicity:
not hispanic or latino NA's
152 346
Including an additional 1126 columns