supportRatioPlot: Plot that shows the binding site support ratio

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

Plot that shows the binding site support ratio

Description

Function that shows a ratio to determine how well a given binding site with is supported by the crosslink coverage of the data. Ratios are computed using the supportRatio function.

Usage

supportRatioPlot(object, bsWidths, bsFlank = NA, ...)

Arguments

object	a BSFDataSet object
bsWidths	a numeric vector indicating the different binding site width to compute the ratio for
bsFlank	optional; a numeric vector of the same length as bsWidth used to specify the width of the flanking regions
...	further arguments passed to makeBindingSites

Details

The higher the ratio, the more does the given binding site width captures the enrichment of crosslinks compared the the local surrounding. A ratio equal to 1 would mean no enrichemnt at all.

Value

an object of class ggplot2

Examples

# load data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))

suppressWarnings(supportRatioPlot(bds, bsWidths = c(3,7),
minWidth = 1, minClSites = 1, minCrosslinks = 2))

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