findMotifRegion {ELMER} | R Documentation

## Use Hocomoco motif and homer to identify motifs in a given region

### 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

    findMotifRegion(
      regions,
      output.filename = "mapped_motifs_regions.txt",
      region.size = NULL,
      genome = "hg38",
      nstep = 10000,
      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)
`nstep` | Number of regions to evaluate in homer, the bigger, more memory it will use at each step.
`cores` | A interger which defines the number of cores to be used in parallel process. Default is 1: no parallel process.

### Examples

    ## 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)

[Package ELMER version 2.11.1 Index]