MESO-v2.1.0: Mesothelioma

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

Mesothelioma

Description

A document describing the TCGA cancer code

Details

> experiments( MESO )
ExperimentList class object of length 10:
 [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_RNASeq2Gene-20160128: SummarizedExperiment with 20501 rows and 87 columns
 [7] MESO_RPPAArray-20160128: SummarizedExperiment with 193 rows and 63 columns
 [8] MESO_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 87 columns
 [9] MESO_RNASeq2GeneNorm-20160128: SummarizedExperiment with 18192 rows and 87 columns
 [10] MESO_Methylation-20160128: SummarizedExperiment with 485577 rows and 87 columns

> rownames( MESO )
CharacterList of length 10
[["MESO_CNASNP-20160128"]] character(0)
[["MESO_CNVSNP-20160128"]] character(0)
[["MESO_GISTIC_AllByGene-20160128"]] character(0)
[["MESO_GISTIC_Peaks-20160128"]] 1 2 3 4 5 6 7 8 ... 14 15 16 17 18 19 20 21
[["MESO_GISTIC_ThresholdedByGene-20160128"]] character(0)
[["MESO_RNASeq2Gene-20160128"]] A1BG A1CF A2BP1 A2LD1 ... ZZZ3 psiTPTE22 tAKR
[["MESO_RPPAArray-20160128"]] 14-3-3_beta ... p90RSK_pT359_S363
[["MESO_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["MESO_RNASeq2GeneNorm-20160128"]] A1BG A2BP1 A2LD1 ... ZZEF1 ZZZ3 psiTPTE22
[["MESO_Methylation-20160128"]] cg00000029 cg00000108 ... rs966367 rs9839873

> colnames( MESO )
CharacterList of length 10
[["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_RNASeq2Gene-20160128"]] TCGA-3H-AB3K-01A-11R-A40A-07 ...
[["MESO_RPPAArray-20160128"]] TCGA-3H-AB3K-01A-21-A45O-20 ...
[["MESO_miRNASeqGene-20160128"]] TCGA-3H-AB3K-01A-11R-A404-13 ...
[["MESO_RNASeq2GeneNorm-20160128"]] TCGA-3H-AB3K-01 ... TCGA-ZN-A9VW-01
[["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 19.9 Mb
4              MESO_GISTIC_Peaks-20160128  0.1 Mb
5  MESO_GISTIC_ThresholdedByGene-20160128 19.8 Mb
6               MESO_RNASeq2Gene-20160128 16.2 Mb
7                 MESO_RPPAArray-20160128  0.1 Mb
8              MESO_miRNASeqGene-20160128  0.9 Mb
9           MESO_RNASeq2GeneNorm-20160128 14.3 Mb
10              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
[1,] 73     73   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

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