Uterine Carcinosarcoma
UCS-v2.0.1.RdA document describing the TCGA cancer code
Details
> experiments( UCS )
ExperimentList class object of length 11:
[1] UCS_CNASNP-20160128: RaggedExperiment with 54944 rows and 111 columns
[2] UCS_CNVSNP-20160128: RaggedExperiment with 19298 rows and 111 columns
[3] UCS_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[4] UCS_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 56 rows and 56 columns
[5] UCS_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 56 columns
[6] UCS_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 56 columns
[7] UCS_Mutation-20160128: RaggedExperiment with 11339 rows and 57 columns
[8] UCS_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 57 columns
[9] UCS_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 57 columns
[10] UCS_RPPAArray-20160128: SummarizedExperiment with 192 rows and 48 columns
[11] UCS_Methylation-20160128: SummarizedExperiment with 485577 rows and 57 columns
> rownames( UCS )
CharacterList of length 11
[["UCS_CNASNP-20160128"]] character(0)
[["UCS_CNVSNP-20160128"]] character(0)
[["UCS_GISTIC_AllByGene-20160128"]] character(0)
[["UCS_GISTIC_Peaks-20160128"]] 26 1 2 3 27 4 28 29 ... 21 22 56 57 23 24 58
[["UCS_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UCS_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UCS_Mutation-20160128"]] character(0)
[["UCS_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UCS_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["UCS_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
...
<1 more element>
> colnames( UCS )
CharacterList of length 11
[["UCS_CNASNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_CNVSNP-20160128"]] TCGA-N5-A4R8-10A-01D-A28T-01 ...
[["UCS_GISTIC_AllByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_Peaks-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_GISTIC_ThresholdedByGene-20160128"]] TCGA-N5-A4RA-01A-11D-A28Q-01 ...
[["UCS_miRNASeqGene-20160128"]] TCGA-N5-A4R8-01A-11R-A28Z-13 ...
[["UCS_Mutation-20160128"]] TCGA-N5-A4R8-01A-11D-A28R-08 ...
[["UCS_RNASeq2Gene-20160128"]] TCGA-N5-A4R8-01A-11R-A28V-07 ...
[["UCS_RNASeq2GeneNorm-20160128"]] TCGA-N5-A4R8-01A-11R-A28V-07 ...
[["UCS_RPPAArray-20160128"]] TCGA-N5-A4R8-01A-21-A41P-20 ...
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 UCS_CNASNP-20160128 1.5 Mb
2 UCS_CNVSNP-20160128 0.6 Mb
3 UCS_GISTIC_AllByGene-20160128 14.1 Mb
4 UCS_GISTIC_Peaks-20160128 0.1 Mb
5 UCS_GISTIC_ThresholdedByGene-20160128 13.9 Mb
6 UCS_miRNASeqGene-20160128 0.6 Mb
7 UCS_Mutation-20160128 19.7 Mb
8 UCS_RNASeq2Gene-20160128 11.5 Mb
9 UCS_RNASeq2GeneNorm-20160128 11.5 Mb
10 UCS_RPPAArray-20160128 0.1 Mb
11 UCS_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)
22 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
35.00 35.00 1.43 1.04 1.96
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
51.00 62.00 68.00 69.72 76.00 90.00
vital_status:
0 1
22 35
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
8.0 304.0 522.0 705.4 790.5 3115.0 22
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.0 591.2 828.0 1183.4 1647.5 4269.0 35
tumor_tissue_site:
uterus
57
gender:
female
57
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
2002 2007 2009 2009 2011 2012
radiation_therapy:
no yes NA's
29 25 3
histological_type:
uterine carcinosarcoma/ malignant mixed mullerian tumor (mmmt): nos
24
uterine carcinosarcoma/ mmmt: heterologous type
20
uterine carcinosarcoma/mmmt: homologous type
13
race:
asian black or african american white
3 9 44
NA's
1
ethnicity:
hispanic or latino not hispanic or latino NA's
1 43 13
Including an additional 632 columns