phredDist {seqTools} | R Documentation |
The phredDist
function returns a named vector with
relative Phred content from the whole Fastqq
object or a subset
which is denoted by a index i
.
The plotPhredDist
function produces a plot of the
phredDist
values.
phredDist(object, i) plotPhredDist(object, i, maxp=45, col, ...)
object |
|
i |
|
maxp |
|
col |
Colour encoding for plotted lines. |
... |
Additional values passed to plot function. |
i must be a numerical vector with values in {1,...,nFiles}. The
plotPhredDist
function is also prepared for additional arguments:
The maxp value denotes the maximal Phred value until which the Phred values
are plotted (possibly shrinks the x-Axis). The standard line color is
topo.colors(10)[3]
. Additional arguments (e.g. main="") can be
passed to the plot function.
phredDist
returns numeric
. plotPhredDist
returns nothing.
Wolfgang Kaisers
Ewing B, Green P Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 1998 Vol. 8 No. 3 186-194
basedir <- system.file("extdata", package="seqTools") setwd(basedir) fq <- fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4, probeLabel=c("g4","g5")) # phredDist(fq) plotPhredDist(fq, main="g4 and g5") #