Missing GISTIC data for SKCM
Closed this issue · 6 comments
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
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
Thanks @pcheng84 , I'll send in a patch through RTCGAToolbox
this week. More info to come.
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
Hi Marcel,
Great! Thanks for the hotfix!
Cheers,
Phil