makePWMLognBackground: Make a lognormal 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

makePWMLognBackground(
  bg.seq,
  motifs,
  bg.pseudo.count = 1,
  bg.len = 250,
  bg.len.sizes = 2^(0:4),
  bg.source = "",
  verbose = TRUE,
  algorithm = "default"
)

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	background sequences will be split into tiles of this length (default: 250bp)
bg.len.sizes	background tiles will be joined into bigger tiles containing this much smaller tiles. The default is 2^(0:4), which with bg.len translates into 250bp, 500bp, 1000bp, 1500bp, 2000bp, 4000bp. Note this is only used in the "human" algorithm.
bg.source	a free-form textual description of how the background was generated
verbose	if to produce verbose output
algorithm	type of algorithm to use, valid values are: "default" and "human".

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")) 
     makePWMLognBackground(Dmelanogaster$upstream2000, MotifDb.Dmel.PFM)
}

## End(Not run)

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