Gene Set Enrichment For ChIP-seq Peak Data

Documentation for package ‘chipenrich’ version 1.12.1

chipenrich-package	Run ChIP-Enrich on a dataset of ChIP-seq peaks
assign_peaks	Assign peak midpoints to defined gene loci.
assign_peak_segments	Assign whole peaks to all overlapping defined gene loci.
calc_peak_gene_overlap	Add peak overlap and ratio to result of 'num_peaks_per_gene()'
chipenrich	Run ChIP-Enrich on a dataset of ChIP-seq peaks
load_peaks	Convert BEDX+Y data.frames and into GRanges
num_peaks_per_gene	Aggregate peak assignments over the 'geneid' column
plot_dist_to_tss	Plot histogram of distance from peak to nearest TSS
plot_gene_coverage	Plot probability of peak being assigned to a gene vs. gene length
plot_spline_length	Plot probability of peak being assigned to a gene vs. gene length
read_bed	Read BEDX+Y files and convert into GRanges
read_bedgff	Read BEDGFF files and convert into GRanges
supported_genesets	Display supported genesets for gene set enrichment.
supported_genomes	Display supported genomes.
supported_locusdefs	Display supported locus definitions
supported_methods	Display supported gene set enrichment methods.
supported_read_lengths	Display supported read lengths for mappability