runHomer: Motif Analysis Using Homer

In r3fang/SnapATAC: Single Nucleus Analysis Package for ATAC-Seq

Motif Analysis Using Homer

Description

Program will find de novo and known motifs in regions in the genome using HOMER

Usage

runHomer(obj, result.dir, mat, path.to.homer, genome, num.cores, motif.length,
  scan.size, optimize.count, background, local.background, only.known,
  only.denovo, fdr.num, cache, keep.minimal, ...)

Arguments

obj	A snap object.
result.dir	Directory to store Homer results.
mat	matrix to use c("pmat", "bmat").
path.to.homer	Directory path to "findMotifsGenome.pl" excutable file.
genome	Genome hg19 for human and mm10 for mouse.
num.cores	Number of cores to use [10].
motif.length	Motif length (default=8,10,12). NOTE: values greater 12 may cause the program to run out of memory.
scan.size	fragment size to use for motif finding [200].
optimize.count	global optimization: searches for strings with # mismatches [2].
background	Genomic positions to be used as background. Removes background positions overlapping with target positions [automatic]
local.background	Wehther to use local background [FALSE]
only.known	Only to search for known motifs [TRUE]
only.denovo	Only to search for de novo motifs [FALSE].
fdr.num	Calculate empirical FDR for de novo discovery #=number of randomizations [5].
cache	Size in MB for statistics cache [500].
keep.minimal	Keep minimal version of output [FALSE].
...	Arguments passed to "findMotifsGenome.pl".

r3fang/SnapATAC documentation built on March 29, 2022, 4:33 p.m.