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add seqTools package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@95415 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 13/10/2014 19:02:34
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+\name{fastqKmerLocs}
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+%
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+\alias{fastqKmerLocs}
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+%
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+\title{
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+fastqKmerLocs function: Counts DNA k-mers position wise from FASTQ files.
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+}
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+% Description
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+\description{Reads (compressed) FASTQ files and counts for DNA k-mers
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+    for each position in sequence.}
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+%
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+\usage{fastqKmerLocs(filenames, k=4)}
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+%
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+\arguments{
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+    \item{filenames}{Vector of FASTQ file names. Files can be gz compressed.}
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+    %
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+    \item{k}{Length of counted DNA k-mers.}
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+}
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+% Details
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+\details{Maximal allowed value for k is 12.}
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+\value{\code{list}. The length of the list equals the number of given
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+    filenames. 
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+    Contains for each given file a matrix with 4^k rows and 
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+    (maxSeqLen - k + 1) columns (maxSeqLen= maximum read length).
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+    The matrix contains for each k-mer and 
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+    k-mer-start position the counted values.}
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+%
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+\references{
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+Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM
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+The sanger FASTQ file format for sequences with quality scores and 
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+    the Solexa/Illumina FASTQ variants.
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+Nucleic Acids Research 2010 Vol.38 No.6 1767-1771
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+}
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+\author{
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+Wolfgang Kaisers
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+}
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+\note{The static size of the retured k-mer array is 4^k.}
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+% Examples
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+% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - %
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+\examples{
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+basedir <- system.file("extdata", package="seqTools")
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+setwd(basedir)
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+res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
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+res <- fastqKmerLocs("test_l10_atcg.fq", k=2)
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+res <- fastqKmerLocs("test_l10_ATCGN.fq", k=2)
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+res <- fastqKmerLocs("test_l6_multi_line.fq", k=2)
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+}
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+\keyword{fastqKmerLocs}
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+\keyword{kmer}