search

hansenlab / bsseq

Devel repository for bsseq
36 stars 26 forks source link

exclude "Y" chromosome from bsseq object #129

Closed demis001 closed 1 year ago

demis001 commented 1 year ago

Please explain how to exclude the "Y" chromosome data from the "bsseq" object. I want to exclude the "Y" range data and coverage simultaneously.

Best, Dereje Jima

PeteHaitch commented 1 year ago

If you're BSseq object is called bsseq, then bsseq[seqnames(bsseq) != "chrY", ]or bsseq[seqnames(bsseq) != "Y", ] will do it (depending on what the Y chromosome is named in your data). General question like this are better posted to https://support.bioconductor.org/.

demis001 commented 1 year ago

@PeteHaitch I just registered to bioconductor.org, and the site couldn't allow me to create a new post. I want to bother you one more time. I initially filtered CpG loci with a median coverage of 4 or greater with 50% or less missing value among all participants. Would you please guide me on how to apply imputation to both "M" and "Cov" in the BSseq object?

PeteHaitch commented 1 year ago

I've never used imputation.