phredDist: phredDist: Global relative content of Phred values in Fastqq...
In seqTools: Analysis of nucleotide, sequence and quality content on fastq files

Description Usage Arguments Details Value Author(s) References Examples

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.

1 2	phredDist(object, i) plotPhredDist(object, i, maxp=45, col, ...)

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.

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")
#