Breast invasive carcinoma
BRCA-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( BRCA )
ExperimentList class object of length 15:
[1] BRCA_CNASeq-20160128: RaggedExperiment with 5298 rows and 38 columns
[2] BRCA_CNASNP-20160128: RaggedExperiment with 1132786 rows and 2209 columns
[3] BRCA_CNVSNP-20160128: RaggedExperiment with 284458 rows and 2199 columns
[4] BRCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[5] BRCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 1080 columns
[6] BRCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 1080 columns
[7] BRCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 849 columns
[8] BRCA_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 590 columns
[9] BRCA_Mutation-20160128: RaggedExperiment with 90490 rows and 993 columns
[10] BRCA_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 1212 columns
[11] BRCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 1212 columns
[12] BRCA_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 878 columns
[13] BRCA_RPPAArray-20160128: SummarizedExperiment with 226 rows and 937 columns
[14] BRCA_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 343 columns
[15] BRCA_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 885 columns
> rownames( BRCA )
CharacterList of length 15
[["BRCA_CNASeq-20160128"]] character(0)
[["BRCA_CNASNP-20160128"]] character(0)
[["BRCA_CNVSNP-20160128"]] character(0)
[["BRCA_GISTIC_AllByGene-20160128"]] character(0)
[["BRCA_GISTIC_Peaks-20160128"]] 29 30 1 2 31 3 32 4 ... 66 27 67 28 68 69 70
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["BRCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["BRCA_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["BRCA_Mutation-20160128"]] character(0)
[["BRCA_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
...
<5 more elements>
> colnames( BRCA )
CharacterList of length 15
[["BRCA_CNASeq-20160128"]] TCGA-A2-A0EU-01A-22D-A060-02 ...
[["BRCA_CNASNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_CNVSNP-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_AllByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_Peaks-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-3C-AAAU-01A-11D-A41E-01 ...
[["BRCA_miRNASeqGene-20160128"]] TCGA-3C-AAAU-01A-11R-A41G-13 ...
[["BRCA_mRNAArray-20160128"]] TCGA-A1-A0SD-01A-11R-A115-07 ...
[["BRCA_Mutation-20160128"]] TCGA-A1-A0SB-01A-11D-A142-09 ...
[["BRCA_RNASeq2Gene-20160128"]] TCGA-3C-AAAU-01A-11R-A41B-07 ...
...
<5 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 BRCA_CNASeq-20160128 0.2 Mb
2 BRCA_CNASNP-20160128 30.9 Mb
3 BRCA_CNVSNP-20160128 8.2 Mb
4 BRCA_GISTIC_AllByGene-20160128 207.9 Mb
5 BRCA_GISTIC_Peaks-20160128 0.8 Mb
6 BRCA_GISTIC_ThresholdedByGene-20160128 207.7 Mb
7 BRCA_miRNASeqGene-20160128 7.1 Mb
8 BRCA_mRNAArray-20160128 82.5 Mb
9 BRCA_Mutation-20160128 67.4 Mb
10 BRCA_RNASeq2Gene-20160128 192.3 Mb
11 BRCA_RNASeq2GeneNorm-20160128 192.3 Mb
12 BRCA_RNASeqGene-20160128 140 Mb
13 BRCA_RPPAArray-20160128 1.8 Mb
14 BRCA_Methylation_methyl27-20160128 4.9 Mb
15 BRCA_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)
947 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
151.00 151.00 3.48 2.83 4.50
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.0 49.0 59.0 58.6 68.0 90.0 16
vital_status:
0 1 NA's
945 152 1
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
116.0 700.5 1272.0 1644.7 2367.0 7455.0 947
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-7 440 761 1183 1572 8605 153
tumor_tissue_site:
breast NA's
1097 1
pathology_M_stage:
cm0 (i+) m0 m1 mx NA's
6 906 22 163 1
gender:
female male NA's
1085 12 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1988 2007 2009 2008 2010 2013 3
days_to_last_known_alive:
735 2576 NA's
1 1 1096
radiation_therapy:
no yes NA's
446 556 96
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.363 2.000 35.000 169
race:
american indian or alaska native asian
1 61
black or african american white
183 757
NA's
96
ethnicity:
hispanic or latino not hispanic or latino NA's
39 884 175
Including an additional 2667 columns