makePWMGEVBackground: Make a GEV background distribution

In PWMEnrich: PWM enrichment analysis

Description

Construct a lognormal background distribution for a set of sequences. Sequences concatenated are binned in 'bg.len' chunks and lognormal distribution fitted to them.

Usage

makePWMGEVBackground(
  bg.seq,
  motifs,
  bg.pseudo.count = 1,
  bg.len = seq(200, 2000, 200),
  bg.source = "",
  verbose = TRUE,
  fit.log = 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.
bg.pseudo.count	the pseudo count which is shared between nucleotides when frequency matrices are given
bg.len	the length range of background chunks
bg.source	a free-form textual description of how the background was generated
verbose	if to produce verbose output
fit.log	if to fit log odds (instead of odds)

Examples

## 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 
	  if(requireNamespace("BSgenome.Dmelanogaster.UCSC.dm3")) 
     makePWMGEVBackground(Dmelanogaster$upstream2000, MotifDb.Dmel.PFM)
}

## End(Not run)

PWMEnrich documentation built on Nov. 8, 2020, 7:45 p.m.