makePWMPvalCutoffBackground {PWMEnrich} | R Documentation |
This function takes already calculated empirical background distribution and chooses cutoff for each motif based on P-value cutoff for individual sites.
makePWMPvalCutoffBackground(bg.p, p.value = 0.001, bg.source = "")
bg.p |
an object of class PWMEmpiricalBackground |
p.value |
the P-value used to find cuttoffs for each of the motifs |
bg.source |
textual description of background source |
an object of type PWMCutoffBackground
## Not run: if(requireNamespace("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel.PFM, package = "PWMEnrich.Dmelanogaster.background") # make empirical background - here we use only 100 sequences for illustrative purposes if(requireNamespace("BSgenome.Dmelanogaster.UCSC.dm3")) bg.p = makePWMEmpiricalBackground(Dmelanogaster$upstream2000[1:100], MotifDb.Dmel.PFM) # use the empirical background to pick a threshold and make cutoff background makePWMPvalCutoffBackground(bg.p, 0.001) } ## End(Not run)