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waldronlab / curatedTCGAData

Curated Data From The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects
https://bioconductor.org/packages/curatedTCGAData
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Missing GISTIC data for SKCM #29

Closed pcheng84 closed 5 years ago

pcheng84 commented 5 years ago

Hi Marcel and Levi,

I noticed some of the cancers were missing the GISTIC data like SKCM and LAML. I was wondering when these will be uploaded>

curatedTCGAData("SKCM", "GISTIC", FALSE) Error in curatedTCGAData("SKCM", "GISTIC", FALSE) : Cancer and data type combination(s) not available

Thanks, Phil

LiNk-NY commented 5 years ago

Hi Phil, @pcheng84

It looks like RTCGAToolbox only serves Peaks data for those cancer types. There might be a bug somewhere in the code. Can you provide a link to the dataset for download from gdac.broadinstitute.org? It could be that getFirehoseData is not fetching the right URL for these cancer types.

Best, Marcel

pcheng84 commented 5 years ago

Here is the link for SKCM http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/SKCM-TM/20160128/gdac.broadinstitute.org_SKCM-TM.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz

and for LAML http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/LAML-TB/20160128/gdac.broadinstitute.org_LAML-TB.CopyNumber_Gistic2.Level_4.2016012800.0.0.tar.gz

LiNk-NY commented 5 years ago

Thanks @pcheng84 , I'll send in a patch through RTCGAToolbox this week. More info to come.

LiNk-NY commented 5 years ago

Hi Phil, @pcheng84 I've sent in the patch to RTCGAToolbox and can be seen here: https://github.com/LiNk-NY/RTCGAToolbox/commit/cf8cad1111ed0d285467d5927195bb4121bcc129

It will take some time for it to show up on curatedTCGAData since it's part of a pipeline. Entries will have to be added to ExperimentHub for these datasets.

For now, you can use RTCGAToolbox::biocExtract to get these in somewhat workable shape. 

library(RTCGAToolbox)
sk <- getFirehoseData("SKCM", GISTIC = TRUE)
GIST <- biocExtract(sk, "GISTIC")

Best, Marcel

pcheng84 commented 5 years ago

Hi Marcel,

Great! Thanks for the hotfix!

Cheers, Phil

LiNk-NY commented 5 years ago

Hi Phil, @pcheng84

This has been resolved in version 1.5.11. Or the Release version to come out soon 1.6.0. In any event, you can use the GitHub version to reliably obtain LAML and SKCM GISTIC datasets. Thanks!

Marcel