PWMEnrich (version 4.8.2)

groupReport,MotifEnrichmentResults-method: 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

Arguments

obj

a MotifEnrichmentResults object

top

what proportion of top motifs should be examined in each individual sequence (by default 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:

• 'rank' - The rank of the PWM's enrichment in the whole group of sequences together
• 'target' - The name of the PWM's target gene, transcript or protein complex.
• 'id' - The unique identifier of the PWM (if set during PWM creation).
• 'raw.score' - The raw score before P-value calculation
• 'p.value' - The P-value of motif enrichment (if available)
• 'top.motif.prop' - The proportion (between 0 and 1) of sequences where the motif is within top proportion of enrichment motifs.

Examples

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

   # 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])

}