findMotifRegion: Use Hocomoco motif and homer to identify motifs in a given...

Description Usage Arguments Examples

View source: R/Small.R

Description

To find for each probe the know motif we will use HOMER software (http://homer.salk.edu/homer/). Homer and genome should be installed before this function is executed Step: 1 - get DNA methylation probes annotation with the regions 2 - Make a bed file from it 3 - Execute section: Finding Instance of Specific Motifs from http://homer.salk.edu/homer/ngs/peakMotifs.html to the HOCOMOCO TF motifs Also, As HOMER is using more RAM than the available we will split the files in to 100k probes. Obs: for each probe we create a winddow of 500 bp (-size 500) around it. This might lead to false positives, but will not have false negatives. The false posives will be removed latter with some statistical tests.

Usage

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findMotifRegion(regions, output.filename = "mapped_motifs_regions.txt",
  region.size = NULL, genome = "hg38", cores = 1)

Arguments

regions

A GRanges object. Names will be used as the identifier.

output.filename

Final file name

region.size

If NULL the motif will be mapped to the region. If set a window around its center will be considered. For example if region.size is 500, then +-250bp round it will be searched.

genome

Homer genome (hg38, hg19)

cores

A interger which defines the number of cores to be used in parallel process. Default is 1: no parallel process.

Examples

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## Not run: 
 # use the center of the region and +-250bp around it
 gr0 <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), 
                    c(1, 3, 2, 4)
                    ), 
               IRanges(1:10, width=10:1)
               )
 names(gr0) <- paste0("ID",c(1:10))
 findMotifRegion(regions = gr0, region.size = 500, genome = "hg38", cores = 1)
 
 # use the region size itself
 gr1 <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), 
                IRanges(1:10, width=sample(200:1000,10)))
 names(gr1) <- paste0("ID",c(1:10))
 findMotifRegion(regions = gr0, genome = "hg38", cores = 1)

## End(Not run)

ELMER documentation built on June 29, 2018, 10 a.m.