File: SolexaExportQA-class.Rd

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\name{SolexaExportQA-class}
\docType{class}
\alias{SolexaExportQA}
\alias{SolexaExportQA-class}
\alias{SolexaRealignQA-class}
\alias{report,SolexaExportQA-method}
\alias{report_html,SolexaExportQA-method}
\alias{report_html,SolexaRealignQA-method}
\alias{show,SolexaExportQA-method}

\title{(Legacy) Quality assessment summaries from Solexa export and
  realign files}

\description{

  This class contains a list-like structure with summary descriptions
  derived from visiting one or more Solexa \sQuote{export} or
  \sQuote{realign} files.

}

\section{Objects from the Class}{
  
  Objects of the class are usually produced by a \code{\link{qa}}
  method.

}
\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.

  Additional methods defined on this class are:
  \describe{

    \item{report}{\code{signature(x="SolexaExportQA", ..., dest=tempfile(), type="html")}:
	  produces HTML files summarizing QA results. \code{dest} should be
	  a directory.}

    \item{report}{\code{signature(x="SolexaExportQA", ..., dest=tempfile(), type="pdf")}:
	  (deprecated; use \code{type="html"} instead) produces a pdf file
	  summarizing QA results. \code{dest} should be a file.}

    \item{report}{\code{signature(x="SolexaRealignQA", ..., dest=tempfile(), type="html")}:
	  produces HTML files summarizing QA results. \code{dest} should be
	  a directory.}
  }
}
\author{Martin Morgan <mtmorgan@fhcrc.org>}

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