PWMEnrich (version 4.8.2)

sequenceReport,MotifEnrichmentResults-method: Generate a motif enrichment report for a single sequence

Description

Generate a motif enrichment report for a single sequence

Arguments

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

Value

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)

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)

   # 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])

}