sequenceReport-MotifEnrichmentResults-method: Generate a motif enrichment report for a single sequence
In PWMEnrich: PWM enrichment analysis

Description Usage Arguments Value Examples

Generate a motif enrichment report for a single sequence

1 2	## S4 method for signature 'MotifEnrichmentResults' sequenceReport(obj, seq.id, bg = TRUE, ...)

`obj`	a MotifEnrichmentResults object
`seq.id`	the sequence index or name
`bg`	if to use background corrected P-values to do the ranking (if available)
`...`	unused

a MotifEnrichmentReport object containing a table with the following columns:

'rank' - The rank of the PWM's enrichment in the sequence
'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)

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)

   # reports for the two sequences
   r1 = sequenceReport(res, 1)
   r2 = sequenceReport(res, 2)

   # view the results
   r1
   r2

   # plot the top 10 most enriched motifs in the first, and then second sequence
   plot(r1[1:10])
   plot(r2[1:10])

}