motifDiffEnrichment {PWMEnrich} | R Documentation |
Test for differential enrichment between two groups of sequences
motifDiffEnrichment( sequences1, sequences2, pwms, score = "autodetect", bg = "autodetect", cutoff = log2(exp(4)), verbose = TRUE, res1 = NULL, res2 = NULL )
sequences1 |
First set of sequences. Can be either a single sequence (an object of class DNAString), or a list of DNAString objects, or a DNAStringSet object. |
sequences2 |
Second set of sequences. Can be either a single sequence (an object of class DNAString), or a list of DNAString objects, or a DNAStringSet object. |
pwms |
this parameter can take multiple values depending on the scoring scheme and background correction used.
When the
|
score |
this parameter determines which scoring scheme to use. Following scheme as available:
|
bg |
this parameter determines which background correction to use, if any.
|
cutoff |
the score cutoff for a significant motif hit if scoring scheme "cutoff" is selected. |
verbose |
if to produce verbose output |
res1 |
the output of |
res2 |
the output of |
This function calls motifEnrichment
on two groups of sequences and calculates
the difference statistics when possible.
if(requireNamespace("PWMEnrich.Dmelanogaster.background")){ # load the background file for drosophila and lognormal correction data(PWMLogn.dm3.MotifDb.Dmel, package = "PWMEnrich.Dmelanogaster.background") # get the differential enrichment diff = motifDiffEnrichment(DNAString("TGCATCAAGTGTGTAGTGTGAGATTAGT"), DNAString("TGAACGAGTAGGACGATGAGAGATTGATG"), PWMLogn.dm3.MotifDb.Dmel, verbose=FALSE) # motifs differentially enriched in the first sequence (with lognormal background correction) head(sort(diff$group.bg, decreasing=TRUE)) # motifs differentially enriched in the second sequence (with lognormal background correction) head(sort(diff$group.bg)) }