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

In wokai/seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

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.

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.

Value

None.

Note

The static size of the retured k-mer array is 4^k.

Author(s)

Wolfgang Kaisers

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)
#

wokai/seqTools documentation built on May 4, 2019, 9:46 a.m.