coverage.uniformity: Coverage uniformity plot
In hummelma/TEQC: Quality control for target capture experiments

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

Visualization of target coverage uniformity. A line shows the cumulative fraction of targeted bases that reach at least a certain normalized coverage.

1	coverage.uniformity(coveragelist, addlines = TRUE, add = FALSE, xlab, ylab, xlim, ylim, col, lwd, ...)

`coveragelist`	output of function `coverage.target`, where option `perBase` had to be set to `TRUE`, i.e. a list with elements `coverageTarget` and `avgTargetCoverage`
`addlines`	if `TRUE`, dashed lines are added to the plot that indicate the fractions of bases achieving at least the average or at least half the average coverage
`add`	if `TRUE`, the coverage uniformity line of a new sample is added to an already existing plot
`xlab, ylab`	x- and y-axis labels
`xlim, ylim`	x- and y-axis coordinate ranges
`col`	line color
`lwd`	line width
`...`	further graphical parameters passed to `plot`

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.

Line plot showing the fraction of targeted bases (y-axis) achieving a normalized coverage of at least x. The x-axis by default is truncated at 1, which corresponds to the average normalized coverage. The steeper the curve is falling, the less uniform is the coverage. If addlines = TRUE, dashed lines indicate the fractions of bases achieving at least the average (=1) or at least half (=0.5) the average coverage.

Manuela Hummel m.hummel@dkfz.de

Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009; 27(2): 182-9.

coverage.target, covered.k, coverage.hist, coverage.density, coverage.plot, coverage.targetlength.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)

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

## coverage uniformity plot
coverage.uniformity(Coverage)