UCS-v2.1.0: Uterine Carcinosarcoma

In waldronlab/curatedTCGAData: Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Uterine Carcinosarcoma

Description

A 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_Mutation-20160128: RaggedExperiment with 11339 rows and 57 columns
 [7] UCS_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 57 columns
 [8] UCS_RPPAArray-20160128: SummarizedExperiment with 192 rows and 48 columns
 [9] UCS_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 56 columns
 [10] UCS_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18645 rows and 57 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_Mutation-20160128"]] character(0)
[["UCS_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UCS_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
[["UCS_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UCS_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
...
<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_Mutation-20160128"]] TCGA-N5-A4R8-01A-11D-A28R-08 ...
[["UCS_RNASeq2Gene-20160128"]] TCGA-N5-A4R8-01A-11R-A28V-07 ...
[["UCS_RPPAArray-20160128"]] TCGA-N5-A4R8-01A-21-A41P-20 ...
[["UCS_miRNASeqGene-20160128"]] TCGA-N5-A4R8-01A-11R-A28Z-13 ...
[["UCS_RNASeq2GeneNorm-20160128"]] TCGA-N5-A4R8-01 ... TCGA-QN-A5NN-01
...
<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_Mutation-20160128 19.7 Mb
7               UCS_RNASeq2Gene-20160128 11.5 Mb
8                 UCS_RPPAArray-20160128  0.1 Mb
9              UCS_miRNASeqGene-20160128  0.6 Mb
10          UCS_RNASeq2GeneNorm-20160128 10.4 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
[1,] 35     35   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

waldronlab/curatedTCGAData documentation built on Nov. 14, 2024, 1:23 p.m.