makePWMPvalCutoffBackgroundFromSeq {PWMEnrich} | R Documentation |
This function creates a P-value cutoff background for motif enrichment.
makePWMPvalCutoffBackgroundFromSeq( bg.seq, motifs, p.value = 0.001, bg.pseudo.count = 1, bg.source = "", verbose = TRUE )
bg.seq |
a set of background sequences, either a list of DNAString object or DNAStringSet object |
motifs |
a set of motifs, either a list of frequency matrices, or a list of PWM objects. If frequency matrices are given, the background distribution is fitted from bg.seq. |
p.value |
the P-value used to find cuttoffs for each of the motifs |
bg.pseudo.count |
the pseudo count which is shared between nucleotides when frequency matrices are given |
bg.source |
textual description of background source |
verbose |
if to print verbose output |
an object of type PWMCutoffBackground
## Not run: if(requireNamespace("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel.PFM, package = "PWMEnrich.Dmelanogaster.background") # use the empirical background to pick a threshold and make cutoff background makePWMPvalCutoffBackground(Dmelanogaster$upstream2000, 0.001) } ## End(Not run)