coverage.GC: Bait coverage versus GC content plot

In TEQC: Quality control for target capture experiments

Description

Calculates and plots average normalized coverage per hybridization probe versus GC content of the respective probe. A smoothing spline is added to the scatter plot.

Usage

coverage.GC(coverageAll, baits, returnBaitValues = FALSE, linecol = "darkred", lwd, xlab, ylab, pch, col, cex, ...)

Arguments

coverageAll	RleList containing Rle vectors of per-base coverages for each chromosome, i.e. coverageAll output of coverage.target
baits	A RangedData table holding the hybridization probe ("bait") positions and sequences, i.e. output ofget.baits
returnBaitValues	if TRUE, average coverage, average normalized coverage and GC content per bait are returned
linecol, lwd	color and width of spline curve
xlab, ylab	x- and y-axis labels
pch	plotting character
col, cex	color and size of plotting character
...	further graphical parameters passed to plot

Details

The function calculates average normalized coverages for each bait: the average coverage over all bases within a bait is divided by the average coverage over all bait-covered bases. Normalized coverages are not dependent on the absolute quantity of reads and are hence better comparable between different samples or even different experiments.

Value

A scatterplot with normalized per-bait coverages on the y-axis and GC content of respective baits on the x-axis. A smoothing spline is added to the plot.

If returnBaitValues = TRUE average coverage, average normalized coverage and GC content per bait are returned as 'values' columns of the baits input RangedData table

Author(s)

Manuela Hummel [e-mail]

References

Tewhey R, Nakano M, Wang X, Pabon-Pena C, Novak B, Giuffre A, Lin E, Happe S, Roberts DN, LeProust EM, Topol EJ, Harismendy O, Frazer KA. Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol. 2009; 10(10): R116.

See Also

coverage.target, covered.k, coverage.hist, coverage.plot, coverage.uniformity, coverage.targetlength.plot

Examples

## 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)

## get bait positions and sequences
baitsfile <- file.path(exptPath, "ExampleSet_Baits.txt")
baits <- get.baits(baitsfile, chrcol=3, startcol=4, endcol=5, seqcol=2)

## do coverage vs GC plot
coverage.GC(Coverage$coverageAll, baits)

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"
[1] "read 50 (non-overlapping) target regions"
[1] "read 108 hybridization probes"

TEQC documentation built on Nov. 8, 2020, 8:07 p.m.