Esophageal carcinoma
ESCA.RdA document describing the TCGA cancer code
Details
> experiments( ESCA )
ExperimentList class object of length 12:
[1] ESCA_CNASeq-20160128: RaggedExperiment with 17059 rows and 104 columns
[2] ESCA_CNASNP-20160128: RaggedExperiment with 203186 rows and 373 columns
[3] ESCA_CNVSNP-20160128: RaggedExperiment with 60803 rows and 373 columns
[4] ESCA_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[5] ESCA_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 77 rows and 184 columns
[6] ESCA_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 184 columns
[7] ESCA_miRNASeqGene-20160128: SummarizedExperiment with 1046 rows and 198 columns
[8] ESCA_Mutation-20160128: RaggedExperiment with 58602 rows and 185 columns
[9] ESCA_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 196 columns
[10] ESCA_RNASeqGene-20160128: SummarizedExperiment with 26120 rows and 198 columns
[11] ESCA_RPPAArray-20160128: SummarizedExperiment with 192 rows and 126 columns
[12] ESCA_Methylation-20160128: SummarizedExperiment with 485577 rows and 202 columns
> rownames( ESCA )
CharacterList of length 12
[["ESCA_CNASeq-20160128"]] character(0)
[["ESCA_CNASNP-20160128"]] character(0)
[["ESCA_CNVSNP-20160128"]] character(0)
[["ESCA_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["ESCA_GISTIC_Peaks-20160128"]] chr1:23960869-31653987 ... chr22:1-18218209
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["ESCA_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["ESCA_Mutation-20160128"]] character(0)
[["ESCA_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
[["ESCA_RNASeqGene-20160128"]] AADACL3 AADACL4 AB007962 ... VCY XKRY ZFY
...
<2 more elements>
> colnames( ESCA )
CharacterList of length 12
[["ESCA_CNASeq-20160128"]] TCGA-IG-A3I8-01A-11D-A248-26 ...
[["ESCA_CNASNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_CNVSNP-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_AllByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_Peaks-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_GISTIC_ThresholdedByGene-20160128"]] TCGA-2H-A9GF-01A-11D-A37B-01 ...
[["ESCA_miRNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37J-13 ...
[["ESCA_Mutation-20160128"]] TCGA-2H-A9GF-01A-11D-A37C-09 ...
[["ESCA_RNASeq2GeneNorm-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
[["ESCA_RNASeqGene-20160128"]] TCGA-2H-A9GF-01A-11R-A37I-31 ...
...
<2 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 ESCA_CNASeq-20160128 0.5 Mb
2 ESCA_CNASNP-20160128 5.5 Mb
3 ESCA_CNVSNP-20160128 1.7 Mb
4 ESCA_GISTIC_AllByGene-20160128 4.9 Mb
5 ESCA_GISTIC_Peaks-20160128 0.1 Mb
6 ESCA_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 ESCA_miRNASeqGene-20160128 0.1 Mb
8 ESCA_Mutation-20160128 45 Mb
9 ESCA_RNASeq2GeneNorm-20160128 1.3 Mb
10 ESCA_RNASeqGene-20160128 1.7 Mb
11 ESCA_RPPAArray-20160128 0 Mb
12 ESCA_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)
108 observations deleted due to missingness
n events median 0.95LCL 0.95UCL
77.000 77.000 0.962 0.677 1.353
---------------------------
Available sample meta-data:
---------------------------
years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max.
27.00 54.00 61.00 62.46 72.00 90.00
vital_status:
0 1
108 77
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
9.0 180.0 351.0 495.2 650.0 2532.0 108
days_to_last_followup:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
4.0 336.5 402.5 570.1 696.8 3714.0 77
tumor_tissue_site:
esophagus
185
pathology_M_stage:
m0 m1 m1a mx NA's
136 4 5 18 22
gender:
female male
27 158
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1998 2007 2011 2009 2012 2013 7
radiation_therapy:
no yes NA's
124 43 18
karnofsky_performance_score:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
20.00 60.00 80.00 73.82 90.00 100.00 117
histological_type:
esophagus adenocarcinoma, nos esophagus squamous cell carcinoma
89 96
number_pack_years_smoked:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
1.00 17.62 30.00 34.48 47.25 102.00 87
residual_tumor:
r0 r1 r2 rx NA's
137 13 2 7 26
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 1.000 2.526 4.000 21.000 50
race:
asian black or african american white
46 5 114
NA's
20
ethnicity:
hispanic or latino not hispanic or latino NA's
6 88 91
Including an additional 940 columns