Hi Robert, Hope this finds you well! I was playing with PWMEnrich and found what might be a bug in the sequenceReport() function. In short, if you invoke sequenceReport() from within another function, it searches for a global variable of class 'MotifEnrichmentResults' named 'res', instead of using the 'MotifEnrichmentResults' object provided as first argument. ### # this will work: library(PWMEnrich) library(PWMEnrich.Hsapiens.background) data(PWMLogn.hg19.MotifDb.Hsap) dss <- DNAStringSet(c("CACCAGGATTAACATCGGGATGATCGATGCTAGATCA", "CAGATAGCCATGACAGGGTACCAA")) res <- motifEnrichment(dss, PWMLogn.hg19.MotifDb.Hsap) rprt <- sequenceReport(res, 1) # clean up: rm(res, rprt) # but this will fail: findMotifs <- function(x) { res <- motifEnrichment(x, PWMLogn.hg19.MotifDb.Hsap) rprt <- sequenceReport(res, 1) } rprt <- findMotifs(dss) # the workaround is to use global assignment in the function; # the 'MotifEnrichmentResults' object needs to be names 'res' for the workaround to work. findMotifs <- function(x) { res <<- motifEnrichment(x, PWMLogn.hg19.MotifDb.Hsap) rprt <- sequenceReport(res, 1) } rprt <- findMotifs(dss) ### Can you reproduce this? HTH! Best, -- Enrico Ferrero [[alternative HTML version deleted]]