| sequenceReport,MotifEnrichmentResults-method {PWMEnrich} | R Documentation |
Generate a motif enrichment report for a single sequence
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(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])
}