insert.size.hist: Insert sizes histogram

Description Usage Arguments Value Author(s) See Also Examples

Description

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.

Usage

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

Arguments

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

Value

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.

Author(s)

Manuela Hummel [email protected]

See Also

get.reads, reads2pairs, duplicates.barplot

Examples

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## 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)

Example output

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"

TEQC documentation built on Nov. 17, 2017, 8:57 a.m.