estimateBsWidthPlot: Plot the signal-to-flank score for varying gene-wise filter...

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

Plot the signal-to-flank score for varying gene-wise filter and binding site width

Description

A diagnostic function that plots the the signal-to-flank score as a mean for each binding site width and gene-wise filter as indicated when executing estimateBsWidth. Additionally a mean of means visualizes the overall trend and a red line indicates the suggested optimal binding site width. The function estimateBsWidth is expected to be executed prior to calling this plot function.

Usage

estimateBsWidthPlot(object)

Arguments

object

a BSFDataSet object

Value

a plot of type ggplot

See Also

estimateBsWidth

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
load(list.files(files, pattern = ".rds$", full.names = TRUE)[1])
bds = estimateBsWidth(bds, anno.genes = gns, est.maxBsWidth = 19,
 geneResolution = "coarse", bsResolution = "coarse", est.subsetChromosome = "chr22")
estimateBsWidthPlot(bds)

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.