homerWrapper: Homer Wrapper

In alexjgriffith/CCCA: Cross Condition ChIP Analyisis

Description

This is only a wrapper for the DENOVO functionality of homer2, homer must be installed on the system before this can be used.

Usage

homerWrapper(sequences, foreground, background, homerLocation,
  motifsFile = FALSE, opts = "-S 25 -len 6")

Arguments

sequences	Biostring dnastring object
foreground	The foreground subset of sequences, list
background	The background subset of sequences, list
homerLocation	The locatoin of the homer executable on your system
motifsFile	The file to save the motifs in, if none then the motifs are note saved
opts	A string of additional parameters to be passed to homer

Value

a pwm of the motifs found.

alexjgriffith/CCCA documentation built on May 10, 2019, 8:52 a.m.