\name{gcContentMatrix}
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% Alias
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\alias{gcContentMatrix}
\alias{gcContentMatrix-methods}
\alias{gcContentMatrix,Fastqq-method}
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\title{
gcContentMatrix: Returns matrix with read counts for GC content.
}
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% Description
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\description{Returns a matrix with read counts.}
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\usage{
gcContentMatrix(object)
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\arguments{
  \item{object}{\code{Fastqq}: Object from wich data is copied.}
}
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% Details
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\details{The matrix contains one column for each FASTQ file. Rows labeled 
    from 0 to 100 which represents percent (\%) GC content. The matrix contains
    numbers of reads with the respective proportion of GC (Row 2 contains
    number of reads with 2\% GC content).}
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\value{\code{matrix}.}
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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}
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% Examples
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\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"))
fqm<-gcContentMatrix(fq)
}
\seealso{gcContent}
\keyword{gcContentMatrix}
\keyword{kmer}
\keyword{fastqq}