\name{propPhred}
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% Alias
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\alias{propPhred}
\alias{propPhred-methods}
\alias{propPhred,Fastqq-method}
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\title{ propPhred:
    Lane specific proportion of reads in a specified Phred-region.}
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\description{ The \code{propPhred} function returns a named vector
    with relative Phred content for all contained lanes.}
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\usage{propPhred(object, greater = 30, less = 93)}
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\arguments{
    \item{object}{\code{Fastqq}: Object which contains collected values from 
        FASTQ files.}
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    \item{greater}{\code{numeric}: Limits the counted proportion of phred
        to values which are greater than the given value (default: 30).}
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    \item{less}{\code{numeric}: Limits the counted proportion of phred to 
        values which are less than the given value (default: 93).}
}
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\details{The \code{greater} and \code{less} arguments must be numeric, have
    length 1 and be >0 and < 94. \code{greater} must be less than \code{less}.
    With the default settings the reported proportions should be >50 \% for
    all lanes in order to be acceptable (see 't Hoen et. al.).}
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\value{Numeric.}
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\references{
't Hoen et.al
Reproducibility of high-throughput mRNA and small RNA sequencing 
    across laboratories
Nature Biotechnology 2013 Vol. 31  1015 - 1022 (doi:10.1038/nbt.2702)
}
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\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"))
# Proportion of phred Values >30
propPhred(fq)
# Proportion of phred Values >10 and < 30
propPhred(fq, greater=10, less=30)
}
\keyword{propPhred}