makePWMEmpiricalBackground {PWMEnrich} | R Documentation

## Make an empirical P-value background

### Description

Make a background appropriate for empirical P-value calculation. The provided set of background sequences is contcatenated into a single long sequence which is then scanned with the motifs and raw scores are saved. This object can be very large.

### Usage

      makePWMEmpiricalBackground(bg.seq, motifs,
        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.
`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
`...` | currently unused (this is for convenience for makeBackground function)

### Details

For reliable P-value calculation the size of the background set needs to be at least seq.len / min.P.value. For instance, to get P-values at a resolution of 0.001 for a single sequence of 500bp, we would need a background of at least 500/0.001 = 50kb. This ensures that we can make 1000 independent 500bp samples from this background to properly estimate the P-value. For a group of sequences, we would take seq.len to be the total length of all sequences in a group.

### Examples

    ## Not run:
    if(require("PWMEnrich.Dmelanogaster.background")){
       data(MotifDb.Dmel.PFM)

       # make empirical background by saving raw scores for each bp in the sequence - this can be very large in memory!
    	  if(require("BSgenome.Dmelanogaster.UCSC.dm3"))
         makePWMEmpiricalBackground(Dmelanogaster$upstream2000[1:100], MotifDb.Dmel.PFM)
    }

    ## End(Not run)

[Package PWMEnrich version 4.24.2 Index]