Entering edit mode
António Miguel de Jesus Domingues
▴
510
@antonio-miguel-de-jesus-domingues-5182
Last seen 10 months ago
Germany
Hi all,
I am trying to use GenomicDataCommons
to retrieve RPPA data and associated patient clinical data for all cancer types in CGD. I am able to find and download the relevant files with:
library("GenomicDataCommons")
library("BiocParallel")
options(MulticoreParam=MulticoreParam(workers=4))
stopifnot(GenomicDataCommons::status()$status=="OK")
ge_manifest <- files() %>%
filter(type == 'protein_expression') %>%
filter(access == "open") %>%
filter(platform == "RPPA") %>%
manifest()
head(ge_manifest)
fnames <- gdcdata(ge_manifest$id, progress=TRUE)
fnames <- bplapply(ge_manifest$id, gdcdata, progress=FALSE)
rppa_scores <- bplapply(fnames, fread)
But I am not able to figure out how to obtain the clinical data. ge_manifest
contains file ids which don't retrieve the patient data, and inside each _RPPA_data.tsv
there is no obvious patient id column:
AGID lab_id catalog_number set_id peptide_target protein_expression
Any ideas on how to retrieve the patient data for those samples?