plotBsMA: MA style plot

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

MA style plot

Description

Wrapper that plots differential binding results as MA plot. For each binding site the estimated baseMean (log2) is shown on X and the fold-change (log2) is shown on Y.

Usage

plotBsMA(object, what = c("bs", "bg"), sig.threshold = 0.05)

Arguments

object	a BSFDataSet object with results calculated by calculateBsFoldChange
what	character; whether to show results for binding sites or the background (one of: 'bs', 'bg')
sig.threshold	numeric; what P value significance level to use (default = 0.05)

Value

a plot of type ggplot

See Also

calculateBsFoldChange

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])

# make testset
bds = makeBindingSites(bds, bsSize = 7)
bds = assignToGenes(bds, anno.genes = gns)
bds = imputeBsDifferencesForTestdata(bds)
bds = calculateBsBackground(bds, anno.genes = gns, use.offset = FALSE)

# use all filters and remove binding sites that fail (default settings)
bds = filterBsBackground(bds)

# calculate fold-changes
bds = calculateBsFoldChange(bds)

# make MA plot
plotBsMA(bds)

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