TEQC (version 3.12.0)

coverage.density: Coverage density plot

Description

Visualization of target coverage density for one or more samples.

Usage

coverage.density(coveragelist, normalized = TRUE, legend, main, xlab, col, lwd, lty, xlim, ylim, ...)

Arguments

coveragelist

Output of function coverage.target, where option perBase had to be set to TRUE, i.e. a list with elements coverageTarget and avgTargetCoverage. Or, when density of several samples shall be visualized, a list with respective outputs of coverage.target.

normalized

if TRUE, densities of normalized coverages will be shown; original coverages otherwise

legend

legend text. If missing, names of coveragelist will be taken. If NULL, no legend will be drawn.

main

main title

xlab

x-axis label

col

line color(s)

lwd

line width(s)

lty

line style(s)

xlim, ylim

x- and y-axis coordinate ranges

...

further graphical parameters passed to plot

Value

Details

If normalized = TRUE, the function calculates normalized coverages: per-base coverages divided by average coverage over all targeted bases. Normalized coverages are not dependent on the absolute quantity of reads and are hence better comparable between different samples or even different experiments.

See Also

coverage.target, covered.k, coverage.hist, coverage.uniformity, coverage.correlation, coverage.plot

Examples

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## calculate per-base coverages
Coverage <- coverage.target(reads, targets, perBase=TRUE)

## coverage density
coverage.density(Coverage)