\name{BowtieQA-class}
\docType{class}
\alias{BowtieQA-class}
\alias{report,BowtieQA-method}
\alias{report_html,BowtieQA-method}

\title{Quality assessment summaries from Bowtie files}

\description{

  This class contains a list-like structure with summary descriptions
  derived from visiting one or more Bowtie files. 

}

\section{Objects from the Class}{
  
  Objects of the class are usually produced by a \code{\link{qa}}
  method, with the argument \code{type="Bowtie"}.

}
\section{Slots}{
  \describe{
    \item{\code{.srlist}:}{Object of class \code{"list"}, containing
      data frames or lists of data frames summarizing the results of
      qa.}
  }
}
\section{Extends}{
Class \code{"\linkS4class{SRList}"}, directly.
Class \code{"\linkS4class{.QA}"}, directly.
Class \code{"\linkS4class{.SRUtil}"}, by class "SRList", distance 2.
Class \code{"\linkS4class{.ShortReadBase}"}, by class ".QA", distance 2.
}

\section{Methods}{
  Accessor methods are inherited from the \code{\linkS4class{SRList}}
  class. 
  \describe{
    \item{report}{\code{signature(x="BowtieQA", ...,
        dest=tempfile(), type="html")}: produces an
      html file summarizing the QA results.}
  }
}
\author{Martin Morgan <mtmorgan@fhcrc.org>}

\seealso{
  \code{\link{qa}}.
}
\examples{
showClass("BowtieQA")
}
\keyword{classes}