makePWMLognBackground {PWMEnrich} | R Documentation

## Make a lognormal 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

    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)

[Package PWMEnrich version 4.30.0 Index]