motifEcdf {PWMEnrich}R Documentation

Calculate the empirical distribution score distribution for a set of motifs

Description

Calculate the empirical distribution score distribution for a set of motifs

Usage

motifEcdf(
  motifs,
  organism = NULL,
  bg.seq = NULL,
  quick = FALSE,
  pseudo.count = 1
)

Arguments

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.

organism

either a name of the organisms for which the background should be compiled (supported names are "dm3", "mm9" and "hg19"), or a BSgenome object (see BSgenome package).

bg.seq

a set of background sequence (either this or organism needs to be specified!). Can be a DNAString or DNAStringSet object.

quick

if to do the fitting only on a small subset of the data (only in combination with organism). Useful only for code testing!

pseudo.count

the pseudo count which is shared between nucleotides when frequency matrices are given

Value

a list of ecdf objects (see help page for ecdf for usage).


[Package PWMEnrich version 4.26.0 Index]