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Published 20 hours ago • verified publisher icon jianhong

factorFootprints 'seqnames' issue

Open mmilevskiy opened this issue 5 years ago • 5 comments

Hi @jianhong

I am having an issue with the factorFootprints coding. I can run everything up to this point fine, but when I try to run this through, I get the following error. Our bioinformatics team have looked into it but can't figure it out. Any thoughts you have would be much appreciated.

Thanks,

library(BSgenome.Mmusculus.UCSC.mm10) library(MotifDb) CTCF <- query(MotifDb, c("CTCF")) CTCF <- as.list(CTCF) sigs <- factorFootprints(shiftedBamfile, pfm=CTCF[[1]], genome=genome, min.score="90%", seqlev=seqlev, upstream=100, downstream=100) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'seqnames' for signature '"NULL"'

mmilevskiy avatar Jun 27 '19 05:06 mmilevskiy

I am also getting this issue

ianbed avatar Aug 02 '19 19:08 ianbed

May I know the seqlev you set?

jianhong avatar Aug 03 '19 11:08 jianhong

Hi @jianhong

I am using chromosome 19 as a first pass, but ideally want the entire genome once its working.

seqlev <- "chr19"

mmilevskiy avatar Aug 05 '19 02:08 mmilevskiy

I have the same error when I tried to run the function for any chromosome of 10-22, X and Y. But the function worked completely fine for any chromosome 1-9. Cannot understand why it could happen?

NgocTNguyen avatar Oct 13 '20 08:10 NgocTNguyen

Currently I fixed it by paste ^ and $ into exclude parameter of matchPWM. It will be release in bioconductor soon. Thank you for reporting the bug.

Jianhong.

jianhong avatar Oct 16 '20 14:10 jianhong