# Gene Set Enrichment For ChIP-seq Peak Data

## Documentation for package ‘chipenrich’ version 2.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

assign_peaks | Assign peak midpoints to defined gene loci.
assign_peak_segments | Assign whole peaks to all overlapping defined gene loci.
broadenrich | Run Broad-Enrich on broad genomic regions
calc_peak_gene_overlap | Add peak overlap and ratio to result of 'num_peaks_per_gene()'
chipenrich | Run ChIP-Enrich on narrow genomic regions
chipenrich_package | chipenrich: Gene Set Enrichment For ChIP-seq Peak Data and Other Genomic Regions
filter_genesets | Function to filter genesets by locus definition and size
genome_to_organism | Get the correct organism code based on genome
genome_to_orgdb | Get Entrez ID to gene symbol mappings for custom locus definitions
get_test_method | Get the test function name from the method name
hybridenrich | Running Hybrid test, either from scratch or using two results files
load_peaks | Convert a BEDX+Y data.frame and into GRanges
num_peaks_per_gene | Aggregate peak assignments over the 'gene_id' column
peaks2genes | Run the test process up to, but not including the enrichment tests.
plot_chipenrich_spline | QC plot for ChIP-Enrich
plot_dist_to_tss | Plot histogram of distance from peak to nearest TSS
plot_gene_coverage | QC plot for Broad-Enrich
plot_polyenrich_spline | QC plot for Poly-Enrich
polyenrich | Run Poly-Enrich on narrow genomic regions
postprocess_peak_grs | A helper function to post-process peak GRanges
post_process_enrichments | Post process the 'data.frame' of enrichment results
proxReg | Run Proximity Regulation test on a set of narrow genomic regions
read_bed | Read files containing peaks or genomic regions
read_geneset | Function to read custom gene sets from file
read_ldef | Function to read custom locus definition from file
read_mappa | Function to read custom mappability files
recode_peaks | Recode a vector of number of peaks to binary based on threshold
reset_ncores_for_windows | Reset n_cores for Windows
setup_genesets | Function to setup genesets
setup_locusdef | Function to setup locus definitions
setup_mappa | Function to setup mappability
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