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Published 20 hours ago • verified publisher icon Simon-Coetzee

motifbreakR() never returns a result

Open 5Aki1 opened this issue 2 years ago • 3 comments

Hi! I am not sure if there is a bug somewhere, but I can't seem to get motifbreakR() to return anything except for "Warning: No SNP/Motif Interactions reached threshold". This includes the practical example found in the documentation

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5Aki1 avatar Sep 20 '22 22:09 5Aki1

Hi! I am getting the issue when I run the vignette/documentation - were you able to fix this? I used both dbSNP package 142 and 144 but still do not see any SNP/Motif interactions that reach the threshold.

ashvinravi avatar Oct 10 '22 16:10 ashvinravi

I believe I have tracked down some code where all changes were being called neutral when using motifbreakr with score based thresholding, rather than p-value thresholding. It has been fixed here on github and should be making it's way out to bioc shortly.

Simon-Coetzee avatar Oct 11 '22 18:10 Simon-Coetzee

It actually started to work for me now - when I use variants[1:n], where n=range of SNPs, I get results so it may be something with the snpList formatting as well. Thank you for getting back to me regardless!

ashvinravi avatar Oct 11 '22 19:10 ashvinravi