makePWMGEVBackground {PWMEnrich} | R Documentation

## Make a GEV background distribution

### 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)

[Package PWMEnrich version 4.28.1 Index]