insert.size.hist: Insert sizes histogram
In hummelma/TEQC: Quality control for target capture experiments

Description Usage Arguments Value Author(s) See Also Examples

Computes read pair insert sizes, i.e. distance from first base of first read to last base of second read of a read pair, and plots a histogram for all insert sizes.

1	insert.size.hist(readpairs, returnInserts = FALSE, legendpos="topleft", outline=FALSE, main, xlab, ylab, breaks, col, ...)

`readpairs`	`RangedData` table containing positions of read pairs, i.e. output of `reads2pairs` (or the element `readpairs` from the `reads2pairs` output in case single reads without matching pair were found).
`returnInserts`	if `TRUE`, the vector of read pair insert sizes is returned
`legendpos`	position of the legend, e.g. 'topleft' or 'topright'
`outline`	if `FALSE`, outliers (according to `boxplot.stats`) are removed before plotting. If `returnInserts=TRUE`, those outliers are still included in the output.
`main`	plot title
`xlab, ylab`	x- and y-axis labels
`breaks`	e.g. integer specifying the number of cells for the histogram, see `?hist`
`col`	histogram color
`...`	further graphical parameters passed to `hist`

Histogram of read pair insert sizes. Average, standard deviation and median insert size are given in the legend and indicated by lines.

If returnInserts = TRUE, a named vector of insert sizes is returned.

Manuela Hummel m.hummel@dkfz.de

get.reads, reads2pairs, duplicates.barplot

## get reads
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)

## merge to read pairs
readpairs <- reads2pairs(reads)

## insert size histogram
insert.size.hist(readpairs, breaks=10)