markerQC

[umasaxena]

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]

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]

on its way to CRAN, closing this issue now.