groupReport,MotifEnrichmentResults-method {PWMEnrich}R Documentation

Generate a motif enrichment report for the whole group of sequences together

Description

Generate a motif enrichment report for the whole group of sequences together

Usage

## S4 method for signature 'MotifEnrichmentResults'
groupReport(obj, top = 0.05, bg = TRUE, by.top.motifs = FALSE, ...)

Arguments

obj

a MotifEnrichmentResults object

top

what proportion of top motifs should be examined in each individual sequence (by default 0.05, i.e. 5%)

bg

if to use background corrected P-values to do the ranking (if available)

by.top.motifs

if to rank by the proportion of sequences where the motif is within 'top' percentage of motifs

...

unused

Value

a MotifEnrichmentReport object containing a table with the following columns:

Examples

if(requireNamespace("PWMEnrich.Dmelanogaster.background")){
   ###
   # load the pre-compiled lognormal background
   data(PWMLogn.dm3.MotifDb.Dmel, package = "PWMEnrich.Dmelanogaster.background")

   # scan two sequences for motif enrichment
   sequences = list(DNAString("GAAGTATCAAGTGACCAGTAAGTCCCAGATGA"), 
     DNAString("AGGTAGATAGAACAGTAGGCAATGAAGCCGATG"))

   res = motifEnrichment(sequences, PWMLogn.dm3.MotifDb.Dmel)

   # produce a report for all sequences taken together
   r.default = groupReport(res)

   # produce a report where the last column takes top 1% motifs
   r = groupReport(res, top=0.01)

   # view the results
   r

   # plot the top 10 most enriched motifs
   plot(r[1:10])

}

[Package PWMEnrich version 4.28.1 Index]