man/fastqKmerLocs.Rd
e46f15e6
 \name{fastqKmerLocs}
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 \alias{fastqKmerLocs}
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 \title{
 fastqKmerLocs function: Counts DNA k-mers position wise from FASTQ files.
 }
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 % Description
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 \description{Reads (compressed) FASTQ files and counts for DNA k-mers
     for each position in sequence.}
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 \usage{fastqKmerLocs(filenames, k=4)}
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 \arguments{
     \item{filenames}{Vector of FASTQ file names. Files can be gz compressed.}
     %
     \item{k}{Length of counted DNA k-mers.}
 }
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 % Details
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 \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.}
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 \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.}
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 % Examples
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 \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}