coverage.hist {TEQC} | R Documentation |
Histogram and cumulative density of target base coverages
coverage.hist(coverageTarget, col.hist = "lightblue", col.line = "orange", covthreshold, outline = FALSE, breaks = "Sturges", xlab, ylab, main, lwd, ...)
coverageTarget |
|
col.hist |
histogram color |
col.line |
color of the cumulative density line |
covthreshold |
indicates with dashed vertical and horizontal lines, which fraction of bases
has a coverage of at least |
outline |
if |
breaks |
number of cells for the histogram, or string naming an algorithm to compute
the number of cells, or function to compute the number of cells,
or vector giving the breakpoints between histogram cells (see |
xlab, ylab |
x- and y-axis labels |
main |
plot title |
lwd |
line width |
... |
further graphical parameters, passed to |
Histogram of read coverages for bases within the target. Additionally, a line and the right
axis indicate the cumulative fraction of target bases with coverage of at least x.
If option covthreshold
is specified, red dashed lines highlight the cumulative fraction
of target bases with at least the specified coverage.
Manuela Hummel m.hummel@dkfz.de
coverage.target
, coverage.uniformity
, coverage.density
, coverage.plot
,
coverage.targetlength.plot
## 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 histogram coverage.hist(Coverage$coverageTarget, covthreshold=8)