maRge (Motif Analysis in R for Genomic Exploration)

[WARNING: PACKAGE UNDER CONSTRUCTION]

Description

maRge is a package developed for simplifying motif analysis of genomic regions. On one side, it provides a wrap to HOMER de novo motif analysis. On the other side, it provides easy tools to query a region for transcription factor binding motifs.

Installation

## install.packages("devtools")
devtools::install_github("mirthelle/maRge")
library(maRge)

Functionality

Run HOMER from R

We have implemented several functions for running HOMER programs from (they are actually just calls to the system with the command line specified in the arguments of the function).

• deNovoMotifHOMER. Runs findMotifsGenome.pl to obtain lists of motifs enriched in your set of regions.
• countSignHOMER. This function is usefull when you want to use de novo motifs for your analysis. It returns the number of significant de novo motifs that were found in your data, so you can extract the rows from the dataframe in downstream analysis.
• catSignMotifsHOMER. Creates a single .motif file containing all the sequences that were found significant in the analysis.

Query a single region for TF Motifs

Generation of Transcription Factor Regulatory Networks