Simon Coetzee

Firstly, yes you have exposed a bug, particularly on the Zfp410 example. Your first example, however, I believe is working as intended. I think I have it confusingly labeled, however...

Perhaps your SNP coordinates are off by one? If you have an example of your prom_flank.bed I'll take a look.

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...

This work is currently underway, I'll post here when the code is rolled out

Okay so I think I figured out what was going wrong with that SNP, it's right on the edge of a region in the reference genome full of NNNNN, which...

Okay, I think i resolved that, the motifList object wasn't validating at the end b/c it now had 5 rows (including the Ns), so I have that clean up before...

Indels are not currently under the purview of motifbreakR, but an update currently in the works will support indels in addition to SNVs. I will keep you updated here.

May I please have a sample of a few lines from a bed file you're interested in using? And I'd like to confirm that you're using hg19?

You're missing the ghostcript binary required to generate figures. Instructions on ghostscript can be found here: https://github.com/Simon-Coetzee/motifBreakR#install

I'm not sure the exact cause of this problem, but some of our dependencies changed, and I'm working on refactoring the plotting code currently. Expect and update soon.