coverage.density {TEQC} | R Documentation |
Visualization of target coverage density for one or more samples.
coverage.density(coveragelist, normalized = TRUE, legend, main, xlab, col, lwd, lty, xlim, ylim, ...)
coveragelist |
Output of function |
normalized |
if |
legend |
legend text. If missing, names of |
main |
main title |
xlab |
x-axis label |
col |
line color(s) |
lwd |
line width(s) |
lty |
line style(s) |
xlim, ylim |
x- and y-axis coordinate ranges |
... |
further graphical parameters passed to |
If normalized = TRUE
, 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.
Line plot(s) showing densities.
Manuela Hummel m.hummel@dkfz.de
coverage.target
, covered.k
, coverage.hist
,
coverage.uniformity
, coverage.correlation
, coverage.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 density coverage.density(Coverage)