makePWMCutoffBackground {PWMEnrich} | R Documentation |
Make a background based on number of motifs hits above a certain threshold.
makePWMCutoffBackground( bg.seq, motifs, cutoff = log2(exp(4)), 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. |
cutoff |
the cutoff at which the background should be made, i.e. at which a motif hit is called significant |
bg.pseudo.count |
the pseudo count which is shared between nucleotides when frequency matrices are given |
bg.source |
a free-form textual description of how the background was generated |
verbose |
if to produce verbose output |
## Not run: if(requireNamespace("PWMEnrich.Dmelanogaster.background")){ data(MotifDb.Dmel.PFM, package = "PWMEnrich.Dmelanogaster.background") # make background for MotifDb motifs using 2Kb promoters of all D. melanogaster transcripts # using a cutoff of 5 if(requireNamespace("BSgenome.Dmelanogaster.UCSC.dm3")) makePWMCutoffBackground(Dmelanogaster$upstream2000, MotifDb.Dmel.PFM, cutoff=log2(exp(5))) } ## End(Not run)