plot_gene_coverage: QC plot for Broad-Enrich
In chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Description Usage Arguments Value Examples

Create a plot showing the relationship between locus length and the proportion of gene loci covered by peaks.

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plot_gene_coverage(peaks, locusdef = "nearest_tss",
  genome = supported_genomes(), mappability = NULL, legend = TRUE,
  xlim = NULL)

`peaks`	Either a file path or a `data.frame` of peaks in BED-like format. If a file path, the following formats are fully supported via their file extensions: .bed, .broadPeak, .narrowPeak, .gff3, .gff2, .gff, and .bedGraph or .bdg. BED3 through BED6 files are supported under the .bed extension. Files without these extensions are supported under the conditions that the first 3 columns correspond to 'chr', 'start', and 'end' and that there is either no header column, or it is commented out. If a `data.frame` A BEDX+Y style `data.frame`. See `GenomicRanges::makeGRangesFromDataFrame` for acceptable column names.
`locusdef`	One of: 'nearest_tss', 'nearest_gene', 'exon', 'intron', '1kb', '1kb_outside', '1kb_outside_upstream', '5kb', '5kb_outside', '5kb_outside_upstream', '10kb', '10kb_outside', '10kb_outside_upstream'. For a description of each, see the vignette or `supported_locusdefs`. Alternately, a file path for a custom locus definition. NOTE: Must be for a `supported_genome()`, and must have columns 'chr', 'start', 'end', and 'gene_id' or 'geneid'. For an example custom locus definition file, see the vignette.
`genome`	One of the `supported_genomes()`.
`mappability`	One of `NULL`, a file path to a custom mappability file, or an `integer` for a valid read length given by `supported_read_lengths`. If a file, it should contain a header with two column named 'gene_id' and 'mappa'. Gene IDs should be Entrez IDs, and mappability values should range from 0 and 1. For an example custom mappability file, see the vignette. Default value is NULL.
`legend`	If true, a legend will be drawn on the plot.
`xlim`	Set the x-axis limit. NULL means select x-lim automatically.

A trellis plot object.

# Spline plot for E2F4 example peak dataset.
data(peaks_H3K4me3_GM12878, package = 'chipenrich.data')

# Create the plot for a different locus definition
# to compare the effect.
plot_gene_coverage(peaks_H3K4me3_GM12878, locusdef = 'nearest_gene', genome = 'hg19')