motifEcdf: Calculate the empirical distribution score distribution for a...

In PWMEnrich: PWM enrichment analysis

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).

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