UVM-v2.1.0: Uveal Melanoma

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

Uveal Melanoma

Description

A document describing the TCGA cancer code

Details

> experiments( UVM )
ExperimentList class object of length 12:
 [1] UVM_CNASeq-20160128: RaggedExperiment with 6496 rows and 102 columns
 [2] UVM_CNASNP-20160128: RaggedExperiment with 69487 rows and 160 columns
 [3] UVM_CNVSNP-20160128: RaggedExperiment with 12973 rows and 160 columns
 [4] UVM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
 [5] UVM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 80 columns
 [6] UVM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 80 columns
 [7] UVM_Mutation-20160128: RaggedExperiment with 2174 rows and 80 columns
 [8] UVM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 80 columns
 [9] UVM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 12 columns
 [10] UVM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
 [11] UVM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 17345 rows and 80 columns
 [12] UVM_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns

> rownames( UVM )
CharacterList of length 12
[["UVM_CNASeq-20160128"]] character(0)
[["UVM_CNASNP-20160128"]] character(0)
[["UVM_CNVSNP-20160128"]] character(0)
[["UVM_GISTIC_AllByGene-20160128"]] character(0)
[["UVM_GISTIC_Peaks-20160128"]] 4 5 6 7 8 9 10 11 ... 2 16 17 18 19 20 21 3
[["UVM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["UVM_Mutation-20160128"]] character(0)
[["UVM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["UVM_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
[["UVM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
...
<2 more elements>

> colnames( UVM )
CharacterList of length 12
[["UVM_CNASeq-20160128"]] TCGA-RZ-AB0B-01A-11D-A40D-26 ...
[["UVM_CNASNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_CNVSNP-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_AllByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_Peaks-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_GISTIC_ThresholdedByGene-20160128"]] TCGA-RZ-AB0B-01A-11D-A39V-01 ...
[["UVM_Mutation-20160128"]] TCGA-RZ-AB0B-01A-11D-A39W-08 ...
[["UVM_RNASeq2Gene-20160128"]] TCGA-RZ-AB0B-01A-11R-A405-07 ...
[["UVM_RPPAArray-20160128"]] TCGA-V3-A9ZX-01A-21-A41Z-20 ...
[["UVM_miRNASeqGene-20160128"]] TCGA-RZ-AB0B-01A-11R-A40B-13 ...
...
<2 more elements>

Sizes of each ExperimentList element:

                                   assay size.Mb
1                    UVM_CNASeq-20160128  0.2 Mb
2                    UVM_CNASNP-20160128  1.9 Mb
3                    UVM_CNVSNP-20160128  0.4 Mb
4          UVM_GISTIC_AllByGene-20160128 18.5 Mb
5              UVM_GISTIC_Peaks-20160128  0.1 Mb
6  UVM_GISTIC_ThresholdedByGene-20160128 18.5 Mb
7                  UVM_Mutation-20160128 12.3 Mb
8               UVM_RNASeq2Gene-20160128 15.1 Mb
9                 UVM_RPPAArray-20160128  0.1 Mb
10             UVM_miRNASeqGene-20160128  0.8 Mb
11          UVM_RNASeq2GeneNorm-20160128 12.8 Mb
12              UVM_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)

   57 observations deleted due to missingness 
      n events median 0.95LCL 0.95UCL
[1,] 23     23   1.66    1.14    3.05


---------------------------
Available sample meta-data:
---------------------------

years_to_birth:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  22.00   51.00   61.50   61.65   74.25   86.00 

vital_status:
 0  1 
57 23 

days_to_death:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
   40.0   393.5   606.0   693.9  1029.0  1581.0      57 

days_to_last_followup:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
    4.0   495.0   821.0   861.9  1184.0  2600.0      23 

tumor_tissue_site:
choroid 
     80 



pathology_N_stage:
  n0   nx NA's 
  52   27    1 

pathology_M_stage:
  m0   m1  m1b   mx NA's 
  51    2    2   23    2 

gender:
female   male 
    35     45 

date_of_initial_pathologic_diagnosis:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   2007    2011    2012    2012    2013    2013 

radiation_therapy:
  no  yes NA's 
  76    3    1 

race:
white  NA's 
   55    25 

ethnicity:
    hispanic or latino not hispanic or latino                   NA's 
                     1                     52                     27 

Including an additional 448 columns

waldronlab/curatedTCGAData documentation built on Feb. 7, 2024, 1:12 p.m.