Uveal Melanoma
UVM.RdA document describing the TCGA cancer code
Details
> experiments( UVM )
ExperimentList class object of length 11:
[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_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 80 columns
[8] UVM_Mutation-20160128: RaggedExperiment with 2174 rows and 80 columns
[9] UVM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 80 columns
[10] UVM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 12 columns
[11] UVM_Methylation-20160128: SummarizedExperiment with 485577 rows and 80 columns
> rownames( UVM )
CharacterList of length 11
[["UVM_CNASeq-20160128"]] character(0)
[["UVM_CNASNP-20160128"]] character(0)
[["UVM_CNVSNP-20160128"]] character(0)
[["UVM_GISTIC_AllByGene-20160128"]] ACAP3 ACTRT2 ... WASIR1|ENSG00000185203.7
[["UVM_GISTIC_Peaks-20160128"]] chr1:19073360-24108626 ...
[["UVM_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["UVM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["UVM_Mutation-20160128"]] character(0)
[["UVM_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["UVM_RPPAArray-20160128"]] 14-3-3_beta 14-3-3_epsilon ... p90RSK_pT359_S363
...
<1 more element>
> colnames( UVM )
CharacterList of length 11
[["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_miRNASeqGene-20160128"]] TCGA-RZ-AB0B-01A-11R-A40B-13 ...
[["UVM_Mutation-20160128"]] TCGA-RZ-AB0B-01A-11D-A39W-08 ...
[["UVM_RNASeq2GeneNorm-20160128"]] TCGA-RZ-AB0B-01A-11R-A405-07 ...
[["UVM_RPPAArray-20160128"]] TCGA-V3-A9ZX-01A-21-A41Z-20 ...
...
<1 more element>
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 4.9 Mb
5 UVM_GISTIC_Peaks-20160128 0 Mb
6 UVM_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 UVM_miRNASeqGene-20160128 0.1 Mb
8 UVM_Mutation-20160128 12.3 Mb
9 UVM_RNASeq2GeneNorm-20160128 1.3 Mb
10 UVM_RPPAArray-20160128 0 Mb
11 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
23.00 23.00 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