insert.size.hist: Insert sizes histogram
In 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)

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: hwriter
[1] "read 19546 sequenced reads"