reproducibilityScatterPlot: Plot that shows binding site reproducibility as scatter

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

Plot that shows binding site reproducibility as scatter

Description

Function compute the number of crosslinks per binding site on a log2 scale for each sample. Samples are pairwise correlated as a scatter and pairwise pearson correlation is shown.

Usage

reproducibilityScatterPlot(object, quiet = FALSE)

Arguments

object	a BSFDataSet object
quiet	logical; whether to print messages

Details

Unlike most plotting functions, this function is actively calculating the values to plot.

Value

an object of class ggplot2

See Also

BSFind, reproducibilityFilter

Examples

# load data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
bds <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2,
minCrosslinks = 2, minClSites = 3, sub.chr = "chr22")
reproducibilityScatterPlot(bds)

ZarnackGroup/BindingSiteFinder documentation built on May 2, 2024, 12:38 a.m.