FindMotifs: FindMotifs

In fmi-basel/gbuehler-MiniChip: MiniChip

FindMotifs

Description

Finds enriched motifs in supplied regions (peaks) using MEME and HOMER.

Usage

FindMotifs(
  peaks,
  peaknames = "mypeaks",
  genome,
  topn = 100,
  width = 100,
  runMEME = FALSE,
  runHOMER = FALSE,
  revcomp = TRUE,
  genomepath
)

Arguments

peaks	A Granges object containing your positions of interest. Must include seqnames (chromosomes), start, end, unique peak (row) name.
peaknames	A character scalar that describes your peaks. Default is "mypeaks".
genome	BSGenome object. Required parameter. For example,use BSgenome.Mmusculus.UCSC.mm10 for mouse.
topn	Numeric scalar or vector indicating the number of top peaks (counted from the top row of the GRanges object) to use for motif finding. Default is 100. If a vector is supplied (eg. c(100,1000)), then the function generates a MEME and a HOMER input file (and runs MEME/HOMER) for each element (eg. the 100 top peaks, then the 1000 top peaks).
width	Numeric scalar indicating the width of the peak (around the center of each range) to use for motif finding. Default is 100.
runMEME	Logical scalar, indicating whether the MEME motif finding should be run. Default = FALSE.
runHOMER	Logical scalar, indicating whether the HOMER motif finding should be run. Default = FALSE.
revcomp	Logical scalar, indicating whether the MEME motif finding should use both strands (TRUE, Default), or only the provided strand (FALSE).
genomepath	Character string giving the full path to the genome that HOMER should use for extracting peak sequences. Only required if runHOMER = TRUE. For example, for mm10 genome use: "/work/gbioinfo/DB/genomes/mm10".

Details

Finds enriched motifs in supplied regions (peaks) in the supplied genome using MEME and HOMER. It will write a fasta file with the peak sequences (for MEME Input) and a bed file with the peak coordinates (for HOMER Input). If runMEME and/or runHOMER is set to TRUE it will also run the MEME and/or HOMER analysis (requires MEME and/or HOMER to be installed).

Value

Saves the outputs of MEME and HOMER.

Examples

library(BSgenome.Mmusculus.UCSC.mm10)
peaks <- GenomicRanges::GRanges(
seqnames = Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)),
ranges = IRanges(50101:50110, end = 51111:51120),
strand = Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
summit = 1:10, name = head(letters, 10))
FindMotifs(peaks,genome=BSgenome.Mmusculus.UCSC.mm10,topn=2)
unlink("mypeaks.*")

fmi-basel/gbuehler-MiniChip documentation built on June 13, 2025, 6:15 a.m.