seqTools (version 1.6.0)

plotKmerCount: plotKmerCount: Creation of plots DNA for k-mer counts from Fastqq objects.

Description

The function creates plots from counted DNA k-mers from Fastqq objects.

Usage

plotKmerCount(object,index,mxey,main="K-mer count",...)

Arguments

object

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

index

integer(optional): Index of FASTQ file(s) for which data is plotted. When value is missing, k-mer counts for all contained data is plotted.

mxey

integer(optional): Maximal value for y axis, given by power of 2 (when mxey=4, then maximal ylim value is 2^4 = 16). Allows overriding of automatic calculated values.

main

character(optional): Caption text which printed into the output.

...

Additional parameters which are passed down to the plot function.

Value

Details

Values for i must be in {1,...,nFiles}. The function shrinks the k-mer count table down to size of 4096 (k = 6) when k > 6 in order to limit the complexity of the plot.

References

Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM The sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants. Nucleic Acids Research 2010 Vol.38 No.6 1767-1771

See Also

Fastqq-class

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"))
#
plotKmerCount(fq)
plotKmerCount(fq,1)
plotKmerCount(fq, 1:2)
#