plot_chipenrich_spline {chipenrich} | R Documentation |
A plot showing an approximation of the empirical spline used to model the relationship between a gene having a peak and the locus length. For visual clarity, genes are binned into groups of 25 after sorting by locus length. Expected fits assuming independence of locus length and presence of a peak, and assuming proportionality of locus length and presence of a peak are given to demonstrate deviation from either for the dataset.
plot_chipenrich_spline( peaks, locusdef = "nearest_tss", genome = supported_genomes(), mappability = NULL, legend = TRUE, xlim = NULL )
peaks |
Either a file path or a |
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 |
genome |
One of the |
mappability |
One of |
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_E2F4, package = 'chipenrich.data') # Create the plot for a different locus definition # to compare the effect. plot_chipenrich_spline(peaks_E2F4, locusdef = 'nearest_gene', genome = 'hg19')