coverage.plot: Coverage versus base position plot
In TEQC: Quality control for target capture experiments

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

Line plot of per-base coverages along a genomic region. Position of target regions can be shown.

1	coverage.plot(coverageAll, targets, chr, Start, End, Offset = 0, add = FALSE, col.line = 1, col.target = "orange", col.offset = "yellow", xlab, ylab, ylim, ...)

`coverageAll`	`RleList` containing `Rle` vectors of per-base coverages for each chromosome, i.e. `coverageAll` output from `coverage.target`
`targets`	optional; `RangedData` table containing positions of target regions, i.e. output from `get.targets`; if missing no genomic regions are highlighted
`chr`	on which chromosome the region to plot is located (string, e.g. "chr1")
`Start`	genomic position where to start the plot
`End`	genomic position where to end the plot
`Offset`	integer; highlight `Offset` bases on both sides of each targeted region; defaults to 0
`add`	if `TRUE`, the coverage line of a new sample is added to an already existing plot
`col.line`	color of the coverage line
`col.target`	color of the bar indicating target regions
`col.offset`	color for highlighting `Offset` on the sides of target regions
`xlab, ylab`	x- and y-axis labels
`ylim`	y-axis coordinate ranges
`...`	further graphical parameters, passed to `plot`

If coverage of a new sample is added to an existing plot with add = TRUE, parameters chr, Start, End still have to be specified and should be the same as in the previous call in order to make sense. Parameters targets and Offset can but do not have to be given again. They can also differ from the previous ones, if for the additional sample a different target was captured.

Line plot showing per-base read coverages for a specified genomic region. When positions of target regions are provided, a bar on the bottom indicates their location such that coverage can be related to the captured targets.

Manuela Hummel m.hummel@dkfz.de

coverage.target, make.wigfiles, covered.k, coverage.hist, coverage.uniformity, 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 plot
coverage.plot(Coverage$coverageAll, targets, Offset=100, chr="chr1", Start=11157524, End=11158764)

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[1] "read 19546 sequenced reads"
[1] "read 50 (non-overlapping) target regions"