Hello community,
Is there a way to get the information on what assays were used to generate the data in the ExperimentsList
slot of the curatedTCGAData
MAEs?
For instance, in BioC 3.12, these are the list of experiments I see for BRCA
:
> curatedTCGAData("BRCA",dry.run=TRUE)
snapshotDate(): 2020-10-27
See '?curatedTCGAData' for 'diseaseCode' and 'assays' inputs
ah_id title file_size rdataclass rdatadateadded rdatadateremoved
1 EH584 BRCA_CNASeq-20160128 0 Mb RaggedExperiment 2017-10-10 <NA>
2 EH585 BRCA_CNASNP-20160128 9.8 Mb RaggedExperiment 2017-10-10 <NA>
3 EH586 BRCA_CNVSNP-20160128 2.8 Mb RaggedExperiment 2017-10-10 <NA>
4 EH588 BRCA_GISTIC_AllByGene-20160128 1.3 Mb SummarizedExperiment 2017-10-10 <NA>
5 EH2121 BRCA_GISTIC_Peaks-20160128 0 Mb RangedSummarizedExperiment 2019-01-09 <NA>
6 EH589 BRCA_GISTIC_ThresholdedByGene-20160128 0.4 Mb SummarizedExperiment 2017-10-10 <NA>
7 EH2122 BRCA_Methylation_methyl27-20160128_assays 63.2 Mb SummarizedExperiment 2019-01-09 <NA>
8 EH2123 BRCA_Methylation_methyl27-20160128_se 0.4 Mb SummarizedExperiment 2019-01-09 <NA>
9 EH2124 BRCA_Methylation_methyl450-20160128_assays 2613.2 Mb RaggedExperiment 2019-01-09 <NA>
10 EH2125 BRCA_Methylation_methyl450-20160128_se 6.1 Mb SummarizedExperiment 2019-01-09 <NA>
11 EH593 BRCA_miRNASeqGene-20160128 0.6 Mb SummarizedExperiment 2017-10-10 <NA>
12 EH594 BRCA_mRNAArray-20160128 27.3 Mb SummarizedExperiment 2017-10-10 <NA>
13 EH595 BRCA_Mutation-20160128 4.5 Mb RaggedExperiment 2017-10-10 <NA>
14 EH596 BRCA_RNASeq2GeneNorm-20160128 64.5 Mb SummarizedExperiment 2017-10-10 <NA>
15 EH597 BRCA_RNASeqGene-20160128 30 Mb SummarizedExperiment 2017-10-10 <NA>
16 EH598 BRCA_RPPAArray-20160128 1.6 Mb SummarizedExperiment 2017-10-10 <NA>
Is there a way right in the curatedTCGAData
package to find out, for example, what type of microarrays were used for the BRCA_mRNAArray-20160128
data? Or what type of sequencer for the *Seq*
assays?
Thanks, Shraddha