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:

• '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(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])

}

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