findMotifRegion {ELMER} | R Documentation |
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.
findMotifRegion(regions, output.filename = "mapped_motifs_regions.txt", region.size = NULL, genome = "hg38", cores = 1)
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. |
## 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)