curatedTCGAData: How to get metadata about assays
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@shraddhapai-10725
Last seen 6 days ago
Canada

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

curatedTCGAData • 841 views
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@marcel-ramos-7325
Last seen 28 days ago
United States

Hi Shraddha,

Thanks for your question. Please see ?curatedTCGAData for a description of the assay types in the package. You can also have a look at the getLinks function in RTCGAToolbox to track down the source of the data, e.g.

> getLinks("BRCA", CNASeq = TRUE)
                                                                                                                                      href 
"gdac.broadinstitute.org_BRCA.Merge_cna__illuminahiseq_dnaseqc__hms_harvard_edu__Level_3__segmentation__seg.Level_3.2016012800.0.0.tar.gz"

You can then look at this link to find more documentation on the data: http://firebrowse.org/?cohort=BRCA&download_dialog=true

Note. I updated your post to include the correct tag.

Best regards,

Marcel

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