\name{getBase-methods}
\docType{methods}
\alias{getBase}
\alias{getBase-methods}
\alias{getBase,SequenceSummary-method}
\title{Get a Data Frame of Base Frequency Data from a \code{SequenceSummary} Object}
\description{
  An object that inherits from class \code{\link[=SequenceSummary-class]{SequenceSummary}} contains
  base frequency data by position gathered by \code{\link{readSeqFile}}. \code{\link{getBase}}
  is an accessor function that reshapes the base frequency data by position
  into a data frame.

  This accessor function is useful if you want to map variables to
  custom \code{ggplot2} aesthetics. Base proportions can be accessed
  with \code{\link{getBaseProp}}.
}


\usage{
  getBase(x, drop=TRUE)
}

\arguments{
  \item{x}{an S4 object that inherits from \code{SequenceSummary} from
    \code{readSeqFile}.}
  \item{drop}{a logical value indicating whether to drop bases that
  don't have any counts.}
}


\value{
  \code{getBase} returns a \code{data.frame} with columns:

  \item{position}{the position in the read.}
  \item{base}{the base.}
  \item{frequency}{the number of a base found per position in the read.}
}

\section{Methods}{
  \describe{
    \item{\code{signature(x = "SequenceSummary")}}{
      \code{getBase} is an accessor function that works on any object read
      in with \code{readSeqFile}; that is, objects that inherit from
      \code{SequenceSummary}.
    }
}}

\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 base plot
  ggplot(getBase(s.fastq)) + geom_line(aes(x=position, y=frequency,
    color=base)) + facet_grid(. ~ base) + scale_color_dna()
}


\seealso{\code{\link{getGC}}, \code{\link{getSeqlen}}, \code{\link{getBaseProp}}, \code{\link{getQual}}, \code{\link{getMCQual}}, \code{\link{basePlot}}}
\keyword{methods}
\keyword{accessor}