Mesothelioma
MESO.RdA document describing the TCGA cancer code
Details
> experiments( MESO )
ExperimentList class object of length 9:
[1] MESO_CNASNP-20160128: RaggedExperiment with 90003 rows and 173 columns
[2] MESO_CNVSNP-20160128: RaggedExperiment with 18335 rows and 172 columns
[3] MESO_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[4] MESO_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 21 rows and 87 columns
[5] MESO_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 87 columns
[6] MESO_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 87 columns
[7] MESO_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 87 columns
[8] MESO_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
[9] MESO_Methylation-20160128: SummarizedExperiment with 485577 rows and 87 columns
> rownames( MESO )
CharacterList of length 9
[["MESO_CNASNP-20160128"]] character(0)
[["MESO_CNVSNP-20160128"]] character(0)
[["MESO_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["MESO_GISTIC_Peaks-20160128"]] chr1:1-31262836 ... chr22:29969457-30128393
[["MESO_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["MESO_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["MESO_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["MESO_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["MESO_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873
> colnames( MESO )
CharacterList of length 9
[["MESO_CNASNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_CNVSNP-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_AllByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_Peaks-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_GISTIC_ThresholdedByGene-20160128"]] TCGA-3H-AB3K-01A-11D-A39Q-01 ...
[["MESO_miRNASeqGene-20160128"]] TCGA-3H-AB3K-01A-11R-A404-13 ...
[["MESO_RNASeq2GeneNorm-20160128"]] TCGA-3H-AB3K-01A-11R-A40A-07 ...
[["MESO_RPPAArray-20160128"]] TCGA-3H-AB3K-01A-21-A45O-20 ...
[["MESO_Methylation-20160128"]] TCGA-3H-AB3K-01A-11D-A39S-05 ...
Sizes of each ExperimentList element:
assay size.Mb
1 MESO_CNASNP-20160128 2.5 Mb
2 MESO_CNVSNP-20160128 0.6 Mb
3 MESO_GISTIC_AllByGene-20160128 4.9 Mb
4 MESO_GISTIC_Peaks-20160128 0 Mb
5 MESO_GISTIC_ThresholdedByGene-20160128 4.9 Mb
6 MESO_miRNASeqGene-20160128 0.1 Mb
7 MESO_RNASeq2GeneNorm-20160128 1.3 Mb
8 MESO_RPPAArray-20160128 0 Mb
9 MESO_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)
14 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
73.00 73.00 1.25 1.11 1.67
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
28.00 57.00 64.00 62.99 69.00 81.00
vital_status:
0 1
13 74
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.0 253.0 457.0 584.1 789.0 2790.0 14
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
-8 499 1168 1091 1490 2359 74
tumor_tissue_site:
pleura
87
pathology_N_stage:
n0 n1 n2 n3 nx
44 10 26 3 4
pathology_M_stage:
m0 m1 mx
57 3 27
gender:
female male
16 71
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1999 2008 2010 2009 2012 2013
radiation_therapy:
no yes NA's
62 24 1
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.00 80.00 90.00 77.65 90.00 100.00 70
histological_type:
biphasic mesothelioma diffuse malignant mesothelioma - nos
23 5
epithelioid mesothelioma sarcomatoid mesothelioma
57 2
residual_tumor:
r0 r1 r2 rx NA's
17 3 15 11 41
race:
asian black or african american white
1 1 85
ethnicity:
not hispanic or latino NA's
73 14
Including an additional 636 columns