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
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> library(seqTools)
Loading required package: zlibbioc
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqTools/plotKmerCount.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotKmerCount
> ### Title: plotKmerCount: Creation of plots DNA for k-mer counts from
> ### Fastqq objects.
> ### Aliases: plotKmerCount plotKmerCount-methods
> ### plotKmerCount,Fastqq-method
> ### Keywords: plotKmerCount kmer
>
> ### ** 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"))
[fastqq] File ( 1/2) 'g4_l101_n100.fq.gz' done.
[fastqq] File ( 2/2) 'g5_l101_n100.fq.gz' done.
> #
> plotKmerCount(fq)
> plotKmerCount(fq,1)
> plotKmerCount(fq, 1:2)
> #
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
