Prepare and run HOMER motif enrichment analysis.

Run complete HOMER motif enrichment analysis, consisting of calls to prepareHomer, system2 and parseHomerOutput. This function requires HOMER to be installed (see http://homer.ucsd.edu/homer/index.html) and the path to the tool to be provided (homerfile argument).

Usage

calcBinnedMotifEnrHomer(
  gr,
  b,
  genomedir,
  outdir,
  motifFile,
  homerfile = findHomer(),
  regionsize = "given",
  pseudocount.log2enr = 8,
  p.adjust.method = "BH",
  Ncpu = 2L,
  verbose = FALSE,
  verbose.Homer = FALSE
)

Arguments

gr

A GRanges object (or an object that can be coerced to one) with the genomic regions to analyze.

b

A vector of the same length as gr that groups its elements into bins (typically a factor, such as the one returned by bin).

genomedir

Directory containing sequence files in Fasta format (one per chromosome).

outdir

A path specifying the folder into which the output files will be written.

motifFile

A file with HOMER formatted PWMs to be used in the enrichment analysis.

homerfile

Path and file name of the findMotifsGenome.pl HOMER script.

regionsize

The peak size to use in HOMER ("given" keeps the coordinate region, an integer value will keep only that many bases in the region center).

pseudocount.log2enr

A numerical scalar with the pseudocount to add to foreground and background counts when calculating log2 motif enrichments

p.adjust.method

A character scalar selecting the p value adjustment method (used in p.adjust).

Ncpu

Number of parallel threads that HOMER can use.

verbose

A logical scalar. If TRUE, print progress messages.

verbose.Homer

A logical scalar. If TRUE, print the console output when running Homer.

Value

A SummarizedExperiment object with motifs in rows and bins in columns, containing seven assays:

negLog10P

: -log10 P values

negLog10Padj

: -log10 adjusted P values

pearsonResid

: motif enrichments as Pearson residuals

expForegroundWgtWithHits

: expected number of foreground sequences with motif hits

log2enr

: motif enrichments as log2 ratios

sumForegroundWgtWithHits

: Sum of foreground sequence weights in a bin that have motif hits

sumBackgroundWgtWithHits

: Sum of background sequence weights in a bin that have motif hits

The rowData of the object contains annotations (name, PFMs, PWMs and GC fraction) for the motifs, while the colData slot contains summary information about the bins.

See also

The functions that are wrapped: prepareHomer, system2 and parseHomerOutput, bin for binning of regions

Examples

if (!is.na(findHomer())){

  # genome
  genome <-  system.file("extdata", "exampleGenome.fa", package = "monaLisa")

  # create motif file for Homer
  motiffile <- tempfile()
  motifIDs <- c("MA0139.1", "MA1102.1", "MA0740.1")
  dumpJaspar(filename = motiffile, pkg = "JASPAR2020",
             opts = list(ID = motifIDs))

  # GRanges of regions used in binned motif enrichment analysis
  gr <- GenomicRanges::tileGenome(
      seqlengths = c(chr1 = 10000L, chr2 = 10000L, chr3 = 10000L),
      tilewidth = 200, cut.last.tile.in.chrom = TRUE)

  # create bins (motif enrichment analysis will be per bin)
  bins <- factor(GenomicRanges::seqnames(gr))
  table(bins)

  # run calcBinnedMotifEnrHomer
  outdir <- tempfile()
  se <- calcBinnedMotifEnrHomer(gr = gr, b = bins, genomedir = genome,
      outdir = outdir, motifFile = motiffile)
  list.files(outdir)

  }