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meyer-lab-cshl / plinkQC

R package for quality control of plink genetic datasets
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markerQC #33

Closed umasaxena closed 3 years ago

umasaxena commented 4 years ago

Hello, I am working on a project with UKB data and I would like to look at a select marker QC on genotyped data. I was unable to locate a specific func or object where I can pass the probes.tsv with marker probe IDs. Generally I would use Plink2 function '--extract' and for selection of specific samples, I would do '--keep' whilst passing FIID & IID. Does it this feature exist ? If not, would it be possible to add. Thanks

HannahVMeyer commented 3 years ago

There is currently no option to do QC on a specific set of markers by providing a list. You could however create the file as you described above and run the QC on this pre-selected subset of markers.

HannahVMeyer commented 3 years ago

on its way to CRAN, closing this issue now.