severe missingness in ovarian pData?
Opened this issue · 3 comments
From @vjcitn on June 4, 2016 20:57
ov is the readRDS of what we have in the S3 bucket
table(pData(ov)$radiation_therapy, exclude=NULL)
no yes
557 5 29
table(pData(ov)$chemo_therapy)
< table of extent 0 >
table(pData(ov)$tumor_stage)
< table of extent 0 >
Copied from original issue: waldronlab/MultiAssayExperiment#132
From @lwaldron on June 5, 2016 1:1
The clinical data are messy, and we're working on merging the different datasets available to produce something more complete. It looks like it's not done yet for OVC, but in the meantime you could use:
patient.stage_event.clinical_stage
stage iiic:408
stage iv : 89
stage iiib: 25
stage iic : 20
stage ic : 11
(Other) : 23
NA's : 15
and assume that every OVC patient received platinum and taxol chemotherapy.
From @lwaldron on June 5, 2016 1:3
I mean, it's not done yet in the MAE for any cancers, but for about 20 cancers we have a merged version of the clinical data prepared already. By the way, cBioPortal provides only a few clinical variables which are quite an incomplete selection, although that may have some advantage over providing hundreds of variables...