run_homer: Run HOMER for promoter motif enrichment

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

Description

Function to run the HOMER tool for motif finding. This function searches motifs enriched in the promoters of the gene list provided.

Usage

run_homer(genelist, genome = "human", output_dir, len = NULL, bg = NULL,
  start = NULL, end = NULL, nomask = FALSE, S = NULL, mis = NULL,
  noconvert = FALSE, norevopp = FALSE, nomotif = FALSE, basic = FALSE,
  bits = FALSE, nocheck = FALSE, noknown = FALSE, b = FALSE,
  nogo = TRUE, humanGO = TRUE, noweight = FALSE, noredun = FALSE,
  g = FALSE, cpg = FALSE, rand = FALSE, fdr = NULL, p = NULL)

Arguments

genelist	Vector of the genes in which to look for enrichment.
genome	The reference genome [default = "human"].
output_dir	The directory in which to output the results.
len	Length of motifs to be found [default = c(8, 10, 12)].
bg	File of gene IDs to use as background. By default HOMER uses all other promoters as the background set.
start	Number of base pairs upstream of the promoter start site to begin looking [default = -300].
end	Number of base pairs downstream of the promoter start site to stop looking [default = +50].
nomask	Use unmasked version of the genome [default = FALSE].
S	Number of motifs of each length to find [default = 25].
mis	Number of mismatches allowed [default = 2].
noconvert	Do not convert input files into unigene ids [default = FALSE].
norevopp	Do not search the revese strand for motifs [default = FALSE].
nomotif	Do not search for de novo motifs [default = FALSE].
basic	Do not check de novo motifs dor similarity to known [default = FALSE].
bits	Scale sequence logos by information content [default = FALSE].
nocheck	Do not check for similarity between de novo and known motifs [default = FALSE].
noknown	Do not check for known motif enrichment [default = FALSE].
b	Use binomial distribution to calculate p-values [default = FALSE; uses hypergeometric instead].
nogo	Do not search for GO enrichment [default = TRUE].
humanGO	Convert IDs to human for GO analysis [default = TRUE].
noweight	Do not perform GC correction [default = FALSE].
noredun	Do not remove predetermined redundant promoters/sequences [default = FALSE].
g	Input file is a group file, i.e. 1st column = id, 2nd = 0 or 1 [1=target,0=back] [default = FALSE].
cpg	Use CpG% instead of GC% for sequence normalization [default = FALSE].
rand	randomise labels for target and backgound sequences [default = FALSE].
fdr	Numerical indicating number of randomisations to perform for empirical FDR calculation for de novo discovery. [default = NULL; no fdr calculation]
p	Number of processors to use [default = 1]

Value

Output from HOMER, and also an R list object of results.

Examples

## Not run: 
motif_results <- homer_motifs(de_genes, genome = "human", output_dir = "motifs")

## End(Not run)

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