Hello,

I have calculated the enrichment for a set of position weight matrices in two sets of sequences and want to determine which motifs are differentially enriched between the sets. I am using the PWMEnrich package and see there is a function motifDiffEnrichment() to do this, but I'm unclear about what the difference statistic that is the output of that function means, or how to determine a cutoff for which motifs to consider differentially enriched between the groups. Can anyone weigh in, or suggest a better way to get this info?

Thanks,

Amanda