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]) }