seqTools (version 1.6.0)

phredDist: phredDist: Global relative content of Phred values in Fastqq objects (or subsets).

Description

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.

Usage

phredDist(object, i)
plotPhredDist(object, i, maxp=45, col, ...)

Arguments

object

Fastqq: Object which contains collected values from nFiles FASTQ files.

i

integer(optional): Index of FASTQ file(s) from which Phred values are counted. When value is missing, Phred counts for all contained data is returned.

maxp

numeric(optional): Value of maximal plotted phred value (right limit of x-axis).

col

Colour encoding for plotted lines.

...

Additional values passed to plot function.

Value

returns numeric. plotPhredDist returns nothing.

Details

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.

References

Ewing B, Green P Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 1998 Vol. 8 No. 3 186-194

Examples

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")
#