Man pages for Bioconductor-mirror/chipenrich
Gene Set Enrichment For ChIP-seq Peak Data

assign_peaksAssign peak midpoints to defined gene loci.
assign_peak_segmentsAssign whole peaks to all overlapping defined gene loci.
broadenrichRun Broad-Enrich on broad genomic regions
calc_peak_gene_overlapAdd peak overlap and ratio to result of...
chipenrichRun ChIP-Enrich on narrow genomic regions
chipenrich_packagechipenrich: Gene Set Enrichment For ChIP-seq Peak Data
filter_genesetsFunction to filter genesets by locus definition and size
genome_to_organismGet the correct organism code based on genome
genome_to_orgdbGet Entrez ID to gene symbol mappings for custom locus...
get_test_methodGet the test function name from the method name
load_peaksConvert a BEDX+Y data.frame and into GRanges
num_peaks_per_geneAggregate peak assignments over the 'gene_id' column
plot_chipenrich_splineQC plot for ChIP-Enrich
plot_dist_to_tssPlot histogram of distance from peak to nearest TSS
plot_gene_coverageQC plot for Broad-Enrich
plot_polyenrich_splineQC plot for Poly-Enrich
polyenrichRun Poly-Enrich on narrow genomic regions
post_process_enrichmentsPost process the 'data.frame' of enrichment results
postprocess_peak_grsA helper function to post-process peak GRanges
read_bedRead files containing peaks or genomic regions
read_genesetFunction to read custom gene sets from file
read_ldefFunction to read custom locus definition from file
read_mappaFunction to read custom mappability files
recode_peaksRecode a vector of number of peaks to binary based on...
reset_ncores_for_windowsReset n_cores for Windows
setup_genesetsFunction to setup genesets
setup_locusdefFunction to setup locus definitions
setup_mappaFunction to setup mappability
supported_genesetsDisplay supported genesets for gene set enrichment.
supported_genomesDisplay supported genomes.
supported_locusdefsDisplay supported locus definitions
supported_methodsDisplay supported gene set enrichment methods.
supported_read_lengthsDisplay supported read lengths for mappability
Bioconductor-mirror/chipenrich documentation built on June 1, 2017, 5:31 a.m.