homer_known: Parse HOMER motif files

In anilchalisey/parseR: Pipeline for Analysis of RNA-seq in R

Description

homer_known is a function to parse the 'known' motifs identified by HOMER.

homer_denovo is a function to parse the 'denovo' motifs identified by HOMER.

Usage

homer_known(motif_dir = "motifs")

homer_denovo(motif_dir = "motifs")

Arguments

motif_dir

Directory in which the motif files created by HOMER are located

Value

An R object with the known motifs in an easily readable format.

An R object with the de novo motifs in an easily readable format.

Examples

## Not run: 
motifdir <- system.file("extdata", "motifs.tar.gz", package = "dealr")
extract <- sprintf("tar -xvzf %s", motifdir)
system(extract)
motifs <- list.files("motifs")
hk <- homer_known("motifs")
hd <- homer_denovo("motifs")
compress <- sprintf("tar -cvzf %s %s", motifs, motifdir)
system(compress)
unlink("motifs", recursive = TRUE)

## End(Not run)

anilchalisey/parseR documentation built on May 7, 2019, 7:45 a.m.