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Simon-Coetzee / motifBreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
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motifbreakR() never returns a result #44

Closed 5Aki1 closed 3 months ago

5Aki1 commented 1 year ago

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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ashvinravi commented 1 year ago

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.

Simon-Coetzee commented 1 year ago

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.

ashvinravi commented 1 year ago

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!