reproducibilityCutoffPlot: Plot to that shows how many replicates support each binding...

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

Plot to that shows how many replicates support each binding site

Description

Plotting function for settings specified in reproducibilityFilter.

Usage

reproducibilityCutoffPlot(
  object,
  cutoff = 0.05,
  min.crosslinks = 1,
  max.range = 20,
  ...
)

Arguments

object	a BSFDataSet object
cutoff	a vector of length = 1, or of length = levels(meta$conditions) with a single number (between 0-1) indicating the quantile cutoff
min.crosslinks	numeric of length = 1, defines the lower boundary for the minimum number of crosslinks a binding site has to be supported by all replicates, regardless of the replicate specific quantile threshold
max.range	maximum number of crosslinks per sites that should be shown
...	further arguments passed to ggplot

Value

a plot of type ggplot2 showing the per replicate reproducibility cutoffs based on a given quantile threshold

See Also

reproducibilityFilter

Examples

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

# merge binding sites
bds <- makeBindingSites(object = bds, bsSize = 9, minWidth = 2,
minCrosslinks = 2, minClSites = 1)

# use the same cutoff for both conditions
suppressWarnings(reproducibilityCutoffPlot(bds, max.range = 20, cutoff = c(0.05)))

# use different cutoffs for each condition
suppressWarnings(reproducibilityCutoffPlot(bds, max.range = 20, cutoff = c(0.1)))

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