makePWMCutoffBackground: Make a cutoff background

Description Usage Arguments Examples

View source: R/background.R

Description

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

Usage

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  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

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## 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)

PWMEnrich documentation built on Nov. 1, 2018, 2:25 a.m.