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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(TEQC)
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, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: hwriter
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TEQC/coverage.uniformity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: coverage.uniformity
> ### Title: Coverage uniformity plot
> ### Aliases: coverage.uniformity
> ### Keywords: hplot
>
> ### ** 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)
[1] "read 19546 sequenced reads"
> targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
> targets <- get.targets(targetsfile, skip=0)
[1] "read 50 (non-overlapping) target regions"
Warning message:
the "reduce" method for RangedData object is deprecated
>
> ## calculate per-base coverages
> Coverage <- coverage.target(reads, targets, perBase=TRUE)
>
> ## coverage uniformity plot
> coverage.uniformity(Coverage)
>
>
>
>
>
> dev.off()
null device
1
>