duplicatedSitesPlot: Plot the number of overlaps when assigning crosslink sites to...

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

Plot the number of overlaps when assigning crosslink sites to genes

Description

A diagnostic function that plots the number of crosslink sites with their respective overlapping rate. The function pureClipGeneWiseFilter is expected to be executed prior to calling this plot function.

Usage

duplicatedSitesPlot(object)

Arguments

object

a BSFDataSet object

Value

a plot of type ggplot

See Also

pureClipGeneWiseFilter

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
# Load GRanges with genes
load(list.files(files, pattern = ".rds$", full.names = TRUE)[1])
# apply 5% gene-wise filter
bds = pureClipGeneWiseFilter(object = bds, anno.genes = gns, cutoff = 0.5,
 overlaps = "keepSingle")
duplicatedSitesPlot(bds)

ZarnackGroup/BindingSiteFinder documentation built on May 31, 2024, 3:29 a.m.