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getMCQual-methods.Rd
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getMCQual-methods.Rd
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\name{getMCQual-methods}
\docType{methods}
\alias{getMCQual}
\alias{getMCQual-methods}
\alias{getMCQual,FASTQSummary-method}
\title{Get a Data Frame of Simulated Qualitied from a \code{FASTQSummary} object}
\description{
An object that inherits from class \code{\link[=FASTQSummary-class]{FASTQSummary}} contains
base quality data by position gathered by
\code{\link{readSeqFile}}. \code{\link{getMCQual}} generates simulated
quality data for each base from this binned quality data that can be
used for adding smoothed lines via lowess.
This accessor function is useful if you want to map variables to
custom \code{ggplot2} aesthetics.
}
\usage{
getMCQual(x, n=100)
}
\arguments{
\item{x}{an S4 object that inherits from \code{FASTQSummary} from
\code{readSeqFile}.}
\item{n}{a numeric value indicating the number of quality values to
draw per base.}
}
\value{
\code{getMCQual} returns a \code{data.frame} with columns:
\item{position}{the position in the read.}
\item{quality}{simulated quality scores.}
}
\section{Methods}{
\describe{
\item{\code{signature(x = "FASTQSummary")}}{
\code{getMCQual} is a function that works on any object with class
\code{FASTQSummary} read in with \code{readSeqFile}.
}
}}
\author{Vince Buffalo <vsbuffalo@ucdavis.edu>}
\examples{
## Load a FASTQ file, with sequence hashing.
s.fastq <- readSeqFile(system.file('extdata', 'test.fastq',
package='qrqc'))
# A custom quality plot
ggplot(getQual(s.fastq)) + geom_linerange(aes(x=position, ymin=lower,
ymax=upper), color="grey") + geom_smooth(aes(x=position, y=quality),
data=getMCQual(s.fastq), color="blue", se=FALSE)
}
\seealso{\code{\link{getGC}}, \code{\link{getSeqlen}}, \code{\link{getBase}}, \code{\link{getBaseProp}}, \code{\link{getQual}}, \code{\link{qualPlot}}}
\keyword{methods}
\keyword{accessor}