coverage.uniformity: Coverage uniformity plot

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

View source: R/coverage.uniformity.R

Description

Visualization of target coverage uniformity. A line shows the cumulative fraction of targeted bases that reach at least a certain normalized coverage.

Usage

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coverage.uniformity(coveragelist, addlines = TRUE, add = FALSE, xlab, ylab, xlim, ylim, col, lwd, ...)

Arguments

coveragelist

output of function coverage.target, where option perBase had to be set to TRUE, i.e. a list with elements coverageTarget and avgTargetCoverage

addlines

if TRUE, dashed lines are added to the plot that indicate the fractions of bases achieving at least the average or at least half the average coverage

add

if TRUE, the coverage uniformity line of a new sample is added to an already existing plot

xlab, ylab

x- and y-axis labels

xlim, ylim

x- and y-axis coordinate ranges

col

line color

lwd

line width

...

further graphical parameters passed to plot

Details

The function calculates normalized coverages: per-base coverages divided by average coverage over all targeted 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

Line plot showing the fraction of targeted bases (y-axis) achieving a normalized coverage of at least x. The x-axis by default is truncated at 1, which corresponds to the average normalized coverage. The steeper the curve is falling, the less uniform is the coverage. If addlines = TRUE, dashed lines indicate the fractions of bases achieving at least the average (=1) or at least half (=0.5) the average coverage.

Author(s)

Manuela Hummel [email protected]

References

Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009; 27(2): 182-9.

See Also

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

Examples

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## 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)

## coverage uniformity plot
coverage.uniformity(Coverage)

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"

TEQC documentation built on May 2, 2018, 4:04 a.m.