chrom.barplot: Reads per chromosome barplot
In TEQC: Quality control for target capture experiments

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

Barplot of numbers (or fractions) of reads (and targets) falling on each chromosome

1	chrom.barplot(reads, targets, plotchroms, col = c("darkgreen", "orange"), ylab, legendpos = "topright", ...)

`reads`	`RangedData` table containing read positions, i.e. output from `get.reads`. To ensure a useful ordering of the bars, the chromosome information ('spaces' of `reads`) should be given as "chr" plus a number/letter [plus further specification], e.g. "chr1", "chrX", "chr17_ctg5_hap1", "chrUn_gl000211".
`targets`	Optional `RangedData` table containing positions of target regions, i.e. output from `get.targets`. The chromosome information should match the one of `reads`. If `targets` is missing, only numbers of reads will be displayed.
`plotchroms`	character vector specifying the chromosomes that shall be included in the plot (and their desired order)
`col`	color(s) of the bars
`ylab`	y-axis label
`legendpos`	Position of the legend. String from the list "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center". Ignored if `targets` is missing.
`...`	graphical parameters passed to `barplot`

If targets is not specified, absolute read counts per chromosome are shown in the barplot. If targets is provided, fractions of reads and targets are shown. For reads, this is the fraction within the total number of reads (since reads are expected to have all the same length). In contrast, for the targets, the fraction of targeted bases on each chromosome is calculated. Since targets might vary in length it is reasonable to account for the actual target sizes instead of considering merely numbers of targets per chromosome.

Barplot of reads and optionally targets per chromosome.

Manuela Hummel m.hummel@dkfz.de

get.reads

## 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)

chrom.barplot(reads, targets)

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