PWMEnrich (version 4.8.2)

makePWMCutoffBackground: Make a cutoff background

Description

Make a background based on number of motifs hits above a certain threshold.

Usage

makePWMCutoffBackground(bg.seq, motifs, cutoff = log2(exp(4)), bg.pseudo.count = 1, bg.source = "", verbose = TRUE)

Arguments

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

Examples

## Not run: 
# if(require("PWMEnrich.Dmelanogaster.background")){
#    data(MotifDb.Dmel.PFM)
# 
#    # make background for MotifDb motifs using 2kb promoters of all D. melanogaster transcripts using cutoff of 5
# 	  if(require("BSgenome.Dmelanogaster.UCSC.dm3"))
#      makePWMCutoffBackground(Dmelanogaster$upstream2000, MotifDb.Dmel.PFM, cutoff=log2(exp(5)))
# }
# ## End(Not run)