Coverage uniformity plot

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Description

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

Usage

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

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

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

Details

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.

Value

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.

Author(s)

Manuela Hummel m.hummel@dkfz.de

References

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.

See Also

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

Examples

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## 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)