plot_dist_to_tss: Plot histogram of distance from peak to nearest TSS
In chipenrich: Gene Set Enrichment For ChIP-seq Peak Data

Description Usage Arguments Value Examples

Create a histogram of the distance from each peak to the nearest transcription start site (TSS) of any gene.

1	plot_dist_to_tss(peaks, genome = supported_genomes())

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.

genome

One of the supported_genomes().

A trellis plot object.

# Create histogram of distance from peaks to nearest TSS.
data(peaks_E2F4, package = 'chipenrich.data')
peaks_E2F4 = subset(peaks_E2F4, peaks_E2F4$chrom == 'chr1')
plot_dist_to_tss(peaks_E2F4, genome = 'hg19')