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+\name{fastqKmerLocs}

+%

+\alias{fastqKmerLocs}

+%

+\title{

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

+}

+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %

+% Description

+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %

+\description{Reads (compressed) FASTQ files and counts for DNA k-mers

+    for each position in sequence.}

+%

+\usage{fastqKmerLocs(filenames, k=4)}

+%

+\arguments{

+    \item{filenames}{Vector of FASTQ file names. Files can be gz compressed.}

+    %

+    \item{k}{Length of counted DNA k-mers.}

+}

+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %

+% Details

+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %

+\details{Maximal allowed value for k is 12.}

+\value{\code{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.}

+%

+\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

+}

+\author{

+Wolfgang Kaisers

+}

+\note{The static size of the retured k-mer array is 4^k.}

+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %

+% Examples

+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %

+\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)

+}

+\keyword{fastqKmerLocs}

+\keyword{kmer}