Gene Set Enrichment For ChIP-seq Peak Data


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Documentation for package ‘chipenrich’ version 1.12.1

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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