coverage.targetlength.plot: Number of reads or average coverage versus target length...
In hummelma/TEQC: Quality control for target capture experiments

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/coverage.targetlength.plot.R

Plots either numbers of on-target reads or average per-target coverage (or potentially other per-target values) against respective target lengths. A smoothing spline is added to the scatter plot.

1	coverage.targetlength.plot(targets, plotcolumn, linecol = 2, xlab, ylab, lwd, pch, cex, ...)

`targets`	`RangedData` table containing positions of target regions and further 'values' columns that should be plotted, i.e. output from `coverage.target` or `readsPerTarget`
`plotcolumn`	name or index of column to plot (of the 'values' DataFrame within `targets`)
`linecol`	color of spline curve
`xlab, ylab`	x- and y-axis labels
`lwd`	line width of spline curve
`pch`	plotting character
`cex`	size of plotting character
`...`	further graphical parameters, passed to `plot`

coverage.target and readsPerTarget can be used to calculate average per-target coverages and numbers of reads overlapping each target. The values are added to the RangedData table containing the target positions. Such RangedData table can then be used for plotting the calculated values against the respecitve target lengths.

A scatterplot with the given per-target values on the y-axis and corresponding target lengths on the x-axis. A smoothing spline is added to the plot.

Manuela Hummel m.hummel@dkfz.de

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

## 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)

## get average per-target coverage
Coverage <- coverage.target(reads, targets, perTarget=TRUE)
targets2 <- Coverage$targetCoverages

## get numbers of reads per target
targets2 <- readsPerTarget(reads, targets2)

## coverage vs target length
coverage.targetlength.plot(targets2, plotcolumn="avgCoverage", pch="o")

## coverage vs number of reads per target
coverage.targetlength.plot(targets2, plotcolumn="nReads", pch="o")