Thymoma
THYM-v2.1.0.RdA document describing the TCGA cancer code
Details
> experiments( THYM )
ExperimentList class object of length 11:
[1] THYM_CNASNP-20160128: RaggedExperiment with 105646 rows and 248 columns
[2] THYM_CNVSNP-20160128: RaggedExperiment with 15571 rows and 248 columns
[3] THYM_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[4] THYM_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 16 rows and 123 columns
[5] THYM_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 123 columns
[6] THYM_Mutation-20160128: RaggedExperiment with 3064 rows and 123 columns
[7] THYM_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 122 columns
[8] THYM_RPPAArray-20160128: SummarizedExperiment with 192 rows and 90 columns
[9] THYM_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 126 columns
[10] THYM_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18286 rows and 122 columns
[11] THYM_Methylation-20160128: SummarizedExperiment with 485577 rows and 126 columns
> rownames( THYM )
CharacterList of length 11
[["THYM_CNASNP-20160128"]] character(0)
[["THYM_CNVSNP-20160128"]] character(0)
[["THYM_GISTIC_AllByGene-20160128"]] character(0)
[["THYM_GISTIC_Peaks-20160128"]] 1 8 9 10 11 12 13 14 2 15 3 4 16 5 17 18
[["THYM_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["THYM_Mutation-20160128"]] character(0)
[["THYM_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["THYM_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["THYM_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["THYM_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
...
<1 more element>
> colnames( THYM )
CharacterList of length 11
[["THYM_CNASNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_CNVSNP-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_AllByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_Peaks-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_GISTIC_ThresholdedByGene-20160128"]] TCGA-3G-AB0O-01A-22D-A422-01 ...
[["THYM_Mutation-20160128"]] TCGA-3G-AB0O-01A-22D-A423-09 ...
[["THYM_RNASeq2Gene-20160128"]] TCGA-3G-AB0O-01A-22R-A42C-07 ...
[["THYM_RPPAArray-20160128"]] TCGA-3G-AB0O-01A-11-A45R-20 ...
[["THYM_miRNASeqGene-20160128"]] TCGA-3G-AB0O-01A-22R-A42W-13 ...
[["THYM_RNASeq2GeneNorm-20160128"]] TCGA-3G-AB0O-01 ... TCGA-ZT-A8OM-01
...
<1 more element>
Sizes of each ExperimentList element:
assay size.Mb
1 THYM_CNASNP-20160128 2.9 Mb
2 THYM_CNVSNP-20160128 0.5 Mb
3 THYM_GISTIC_AllByGene-20160128 26.7 Mb
4 THYM_GISTIC_Peaks-20160128 0.1 Mb
5 THYM_GISTIC_ThresholdedByGene-20160128 26.6 Mb
6 THYM_Mutation-20160128 3.3 Mb
7 THYM_RNASeq2Gene-20160128 21.7 Mb
8 THYM_RPPAArray-20160128 0.2 Mb
9 THYM_miRNASeqGene-20160128 1.2 Mb
10 THYM_RNASeq2GeneNorm-20160128 19.3 Mb
11 THYM_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)
115 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
[1,] 9 9 2.34 1.04 NA
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
17.00 49.50 60.00 58.15 68.50 84.00 1
vital_status:
0 1
115 9
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
124 379 853 1423 2488 3488 115
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
14.0 725.2 1267.5 1486.3 1947.0 4575.0 10
tumor_tissue_site:
anterior mediastinum thymus
27 97
gender:
female male
60 64
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2000 2008 2010 2010 2012 2013 1
radiation_therapy:
no yes
81 43
race:
asian black or african american white
13 6 103
NA's
2
ethnicity:
hispanic or latino not hispanic or latino NA's
10 100 14
Including an additional 685 columns