Colon adenocarcinoma
COAD.RdA document describing the TCGA cancer code
Details
> experiments( COAD )
ExperimentList class object of length 14:
[1] COAD_CNASeq-20160128: RaggedExperiment with 40530 rows and 136 columns
[2] COAD_CNASNP-20160128: RaggedExperiment with 459490 rows and 914 columns
[3] COAD_CNVSNP-20160128: RaggedExperiment with 90534 rows and 914 columns
[4] COAD_GISTIC_AllByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[5] COAD_GISTIC_Peaks-20160128: RangedSummarizedExperiment with 66 rows and 449 columns
[6] COAD_GISTIC_ThresholdedByGene-20160128: SummarizedExperiment with 24776 rows and 449 columns
[7] COAD_miRNASeqGene-20160128: SummarizedExperiment with 705 rows and 221 columns
[8] COAD_mRNAArray-20160128: SummarizedExperiment with 17814 rows and 172 columns
[9] COAD_Mutation-20160128: RaggedExperiment with 62530 rows and 154 columns
[10] COAD_RNASeq2GeneNorm-20160128: SummarizedExperiment with 20501 rows and 191 columns
[11] COAD_RNASeqGene-20160128: SummarizedExperiment with 20502 rows and 10 columns
[12] COAD_RPPAArray-20160128: SummarizedExperiment with 208 rows and 360 columns
[13] COAD_Methylation_methyl27-20160128: SummarizedExperiment with 27578 rows and 202 columns
[14] COAD_Methylation_methyl450-20160128: SummarizedExperiment with 485577 rows and 333 columns
> rownames( COAD )
CharacterList of length 14
[["COAD_CNASeq-20160128"]] character(0)
[["COAD_CNASNP-20160128"]] character(0)
[["COAD_CNVSNP-20160128"]] character(0)
[["COAD_GISTIC_AllByGene-20160128"]] ACAP3 ... WASIR1|ENSG00000185203.7
[["COAD_GISTIC_Peaks-20160128"]] chr1:26527443-27650365 ...
[["COAD_GISTIC_ThresholdedByGene-20160128"]] ACAP3 ...
[["COAD_miRNASeqGene-20160128"]] hsa-let-7a-1 hsa-let-7a-2 ... hsa-mir-99b
[["COAD_mRNAArray-20160128"]] ELMO2 CREB3L1 RPS11 PNMA1 ... SNRPD2 AQP7 CTSC
[["COAD_Mutation-20160128"]] character(0)
[["COAD_RNASeq2GeneNorm-20160128"]] A1BG A1CF A2BP1 ... ZZZ3 psiTPTE22 tAKR
...
<4 more elements>
> colnames( COAD )
CharacterList of length 14
[["COAD_CNASeq-20160128"]] TCGA-A6-2671-01A-01D-1405-02 ...
[["COAD_CNASNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_CNVSNP-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_AllByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_Peaks-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_GISTIC_ThresholdedByGene-20160128"]] TCGA-3L-AA1B-01A-11D-A36W-01 ...
[["COAD_miRNASeqGene-20160128"]] TCGA-A6-2675-01A-02T-1722-13 ...
[["COAD_mRNAArray-20160128"]] TCGA-A6-2671-11A-01R-1758-07 ...
[["COAD_Mutation-20160128"]] TCGA-A6-2672-01A-01W-0833-10 ...
[["COAD_RNASeq2GeneNorm-20160128"]] TCGA-A6-2671-01A-01R-1410-07 ...
...
<4 more elements>
Sizes of each ExperimentList element:
assay size.Mb
1 COAD_CNASeq-20160128 1.1 Mb
2 COAD_CNASNP-20160128 12.5 Mb
3 COAD_CNVSNP-20160128 2.7 Mb
4 COAD_GISTIC_AllByGene-20160128 4.9 Mb
5 COAD_GISTIC_Peaks-20160128 0.1 Mb
6 COAD_GISTIC_ThresholdedByGene-20160128 4.9 Mb
7 COAD_miRNASeqGene-20160128 0.1 Mb
8 COAD_mRNAArray-20160128 1.1 Mb
9 COAD_Mutation-20160128 23.6 Mb
10 COAD_RNASeq2GeneNorm-20160128 1.3 Mb
11 COAD_RNASeqGene-20160128 1.3 Mb
12 COAD_RPPAArray-20160128 0 Mb
13 COAD_Methylation_methyl27-20160128 4.9 Mb
14 COAD_Methylation_methyl450-20160128 75 Mb
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Available sample meta-data:
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years_to_birth:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
31.00 58.00 68.00 66.95 77.00 90.00 2
tumor_tissue_site:
colon NA's
456 1
date_of_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
1998 2007 2009 2008 2010 2013
radiation_therapy:
no yes NA's
378 9 70
number_of_lymph_nodes:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
0.000 0.000 0.000 2.058 2.000 50.000 25
race:
american indian or alaska native asian
1 11
black or african american white
59 213
NA's
173
ethnicity:
hispanic or latino not hispanic or latino NA's
4 270 183
Including an additional 2604 columns