groupReport,MotifEnrichmentResults-method {PWMEnrich} | R Documentation |
Generate a motif enrichment report for the whole group of sequences together
## S4 method for signature 'MotifEnrichmentResults' groupReport(obj, top = 0.05, bg = TRUE, by.top.motifs = FALSE, ...)
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 |
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.
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]) }