assign_peaks: Assign peak midpoints to defined gene loci.
In chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Description Usage Arguments Details Value Examples

Determine the midpoints of a set of input regions peaks and the overlap of the midpoints with a given locus definition locusdef. Also report the TSS that is nearest each region (peak) overlapping a defined locus and its distance.

1	assign_peaks(peaks, locusdef, tss, weighting = NULL)

`peaks`	A `GRanges` object representing regions to be used for enrichment.
`locusdef`	A locus definition object from `chipenrich.data`.
`tss`	A `GRanges` object representing the TSSs for the genome build. Includes `mcols` for Entrez Gene ID `gene_id` and gene symbol `symbol`.
`weighting`	A string defining what weighting option they want. Current options are 'multiAssign', 'signalValue', and 'logSignal Value'. Default is NULL.

Typically, this function will not be used alone, but inside chipenrich().

A data.frame with columns for peak_id, chr, peak_start, peak_end, gene_locus_start, gene_locus_end, gene_id, nearest_tss, nearest_tss_gene, dist_to_tss, nearest_tss_gene_strand. The result is used in num_peaks_per_gene().

data('locusdef.hg19.nearest_tss', package = 'chipenrich.data')
data('tss.hg19', package = 'chipenrich.data')

file = system.file('extdata', 'test_assign.bed', package = 'chipenrich')
peaks = read_bed(file)

assigned_peaks = assign_peaks(
	peaks = peaks,
	locusdef = locusdef.hg19.nearest_tss,
	tss = tss.hg19)