fastqKmerLocs function: Counts DNA k-mers position wise from FASTQ files.

Description

Reads (compressed) FASTQ files and counts for DNA k-mers for each position in sequence.

Usage

fastqKmerLocs(filenames, k=4)

Arguments

Details

Maximal allowed value for k is 12.

Value

list. The length of the list equals the number of given filenames. Contains for each given file a matrix with 4^k rows and (maxSeqLen - k + 1) columns (maxSeqLen= maximum read length). The matrix contains for each k-mer and k-mer-start position the counted values.

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

Examples

basedir <- system.file("extdata", package="seqTools")
setwd(basedir)
res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
res <- fastqKmerLocs("test_l10_atcg.fq", k=2)
res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
res <- fastqKmerLocs("test_l6_multi_line.fq", k=2)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(seqTools)
Loading required package: zlibbioc
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqTools/fastqKmerLocs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fastqKmerLocs
> ### Title: fastqKmerLocs function: Counts DNA k-mers position wise from
> ###   FASTQ files.
> ### Aliases: fastqKmerLocs
> ### Keywords: fastqKmerLocs kmer
> 
> ### ** Examples
> 
> basedir <- system.file("extdata", package="seqTools")
> setwd(basedir)
> res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
[fastq_Klocs] File ( 1/1) 'test_l10_ATCGN.fq' 	done.
> res <- fastqKmerLocs("test_l10_atcg.fq", k=2)
[fastq_Klocs] File ( 1/1) 'test_l10_atcg.fq' 	done.
> res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
[fastq_Klocs] File ( 1/1) 'test_l10_ATCGN.fq' 	done.
> res <- fastqKmerLocs("test_l6_multi_line.fq", k=2)
[fastq_Klocs] File ( 1/1) 'test_l6_multi_line.fq' 	done.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>