Ovarian serous cystadenocarcinoma
OV-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( OV )
ExperimentList class object of length 19:
[1] OV_CNACGH_CGH_hg_244a-20160128: RaggedExperiment with 128946 rows and 472 columns
[2] OV_CNACGH_CGH_hg_415k_g4124a-20160128: RaggedExperiment with 245847 rows and 674 columns
[3] OV_CNASNP-20160128: RaggedExperiment with 907765 rows and 1145 columns
[4] OV_CNVSNP-20160128: RaggedExperiment with 261680 rows and 1141 columns
[5] OV_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[6] OV_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 70 rows and 573 columns
[7] OV_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 573 columns
[8] OV_miRNAArray-20160128: SummarizedExperiment with 821 rows and 573 columns
[9] OV_mRNAArray_huex-20160128: SummarizedExperiment with 18632 rows and 575 columns
[10] OV_mRNAArray_TX_g4502a-20160128: SummarizedExperiment with 17814 rows and 577 columns
[11] OV_mRNAArray_TX_ht_hg_u133a-20160128: SummarizedExperiment with 12042 rows and 524 columns
[12] OV_Mutation-20160128: RaggedExperiment with 20219 rows and 316 columns
[13] OV_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 307 columns
[14] OV_RNASeqGene-20160128: SummarizedExperiment with 19990 rows and 299 columns
[15] OV_RPPAArray-20160128: SummarizedExperiment with 208 rows and 427 columns
[16] OV_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 461 columns
[17] OV_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18571 rows and 307 columns
[18] OV_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 591 columns
[19] OV_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 10 columns
> rownames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] character(0)
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] character(0)
[["OV_CNASNP-20160128"]] character(0)
[["OV_CNVSNP-20160128"]] character(0)
[["OV_GISTIC_AllByGene-20160128"]] character(0)
[["OV_GISTIC_Peaks-20160128"]] 34 1 2 35 3 36 4 37 ... 70 28 29 30 71 31 72
[["OV_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["OV_miRNAArray-20160128"]] DarkCorner dmr_285 ... NegativeControl SCorner3
[["OV_mRNAArray_huex-20160128"]] C9orf152 ELMO2 RPS11 ... SLC39A6 CTSC AQP7
[["OV_mRNAArray_TX_g4502a-20160128"]] ELMO2 CREB3L1 RPS11 ... AQP7 CTSC
...
<9 more elements>
> colnames( OV )
CharacterList of length 19
[["OV_CNACGH_CGH_hg_244a-20160128"]] TCGA-04-1331-01A-01D-0431-02 ...
[["OV_CNACGH_CGH_hg_415k_g4124a-20160128"]] TCGA-04-1353-01A-01D-1046-02 ...
[["OV_CNASNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_CNVSNP-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_AllByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_Peaks-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_GISTIC_ThresholdedByGene-20160128"]] TCGA-04-1331-01A-01D-0428-01 ...
[["OV_miRNAArray-20160128"]] TCGA-04-1331-01A-01T-0438-07 ...
[["OV_mRNAArray_huex-20160128"]] TCGA-04-1331-01A-01R-0435-03 ...
[["OV_mRNAArray_TX_g4502a-20160128"]] TCGA-09-0364-01A-02R-0363-07 ...
...
<9 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 OV_CNACGH_CGH_hg_244a-20160128 3.6 Mb
2 OV_CNACGH_CGH_hg_415k_g4124a-20160128 6.8 Mb
3 OV_CNASNP-20160128 24.6 Mb
4 OV_CNVSNP-20160128 7.3 Mb
5 OV_GISTIC_AllByGene-20160128 112 Mb
6 OV_GISTIC_Peaks-20160128 0.5 Mb
7 OV_GISTIC_ThresholdedByGene-20160128 111.7 Mb
8 OV_miRNAArray-20160128 3.8 Mb
9 OV_mRNAArray_huex-20160128 84.2 Mb
10 OV_mRNAArray_TX_g4502a-20160128 80.7 Mb
11 OV_mRNAArray_TX_ht_hg_u133a-20160128 49.7 Mb
12 OV_Mutation-20160128 10.3 Mb
13 OV_RNASeq2Gene-20160128 50.6 Mb
14 OV_RNASeqGene-20160128 48.1 Mb
15 OV_RPPAArray-20160128 0.8 Mb
16 OV_miRNASeqGene-20160128 2.7 Mb
17 OV_RNASeq2GeneNorm-20160128 45.8 Mb
18 OV_Methylation_methyl27-20160128 4.9 Mb
19 OV_Methylation_methyl450-20160128 75 Mb
---------------------------
Overall survival time-to-event summary (in years):
---------------------------
Call: survfit(formula = survival::Surv(colDat$days_to_death/365, colDat$vital_status) ~
-1)
247 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 343 343 2.94 2.76 3.17
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
26.00 51.00 59.00 59.78 69.00 89.00 21
vital_status:
0 1
246 344
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 567.5 1073.0 1147.4 1557.0 4624.0 247
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
16 266 842 1216 1931 5481 358
tumor_tissue_site:
omentum ovary peritoneum ovary NA's
3 575 2 10
gender:
female NA's
580 10
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1992 2001 2004 2004 2007 2013 10
radiation_therapy:
no yes NA's
556 5 29
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
40.00 60.00 80.00 75.83 80.00 100.00 506
histological_type:
serous cystadenocarcinoma NA's
580 10
residual_tumor:
r0 r1 r2 rx NA's
15 31 5 3 536
ethnicity:
hispanic or latino not hispanic or latino NA's
11 338 241
Including an additional 2869 columns