Browse code

mark readAligned and other early functions 'legacy'

- revise vignette to reflect working with short reads, not alignments
- update example data


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@82095 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 24/10/2013 04:05:22
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@@ -7,7 +7,7 @@
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 \alias{show,ExperimentPath-method}
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 \alias{detail,ExperimentPath-method}
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-\title{"ExperimentPath" class representing a file hierarchy of data
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+\title{(Legacy) "ExperimentPath" class representing a file hierarchy of data
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   files}
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 \description{
Browse code

The detail function and generic have moved to Biostrings.

This changes the manual pages etc. so that the detail function and
generic can be moved to the Biostrings package.


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@49981 bc3139a8-67e5-0310-9ffc-ced21a209358

Marc Carlson authored on 06/10/2010 20:27:30
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@@ -51,8 +51,8 @@
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     \item{show}{\code{signature(object = "ExperimentPath")}: briefly
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       summarize the file paths of \code{object}.}
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-    \item{detail}{\code{signature(object = "ExperimentPath")}: summarize
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-      file paths of \code{object}.}
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+    \item{detail}{\code{signature(x = "ExperimentPath")}: summarize
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+      file paths of \code{x}.}
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   }
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 }
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Browse code

Fully deprecate basePath in favor of experimentPath Work on SRSet - readInd (class definition) readInds(undefined function call) replaced by readIndex - readIndex, readCount initialized to integer(0) so new("SRSet") creates valid objects - experimentPath method to directly access sourcePath - add implied sampleNames,ExperimentPath-method for non-RochePath ExperimentPath Misc code tidy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@33714 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 14/09/2008 01:26:21
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@@ -39,7 +39,7 @@
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   \describe{
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     \item{\code{basePath}}{See above.}
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   }
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-  The slot is accessed with \code{basePath} or \code{experimentPath}.
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+  The slot is accessed with \code{experimentPath}.
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 }
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 \section{Extends}{
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   Class \code{"\linkS4class{.ShortReadBase}"}, directly.
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Derive SolexaPath from ExperimentPath - allow for use of experimentPath rather than basePath, to avoid confusion between DNA 'base' and file system 'base' Additional code tidy - document ExperimentPath class - document additional methods - show,ExperimentPath and detail,ExperimentPath deal only with it's slot

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead@33712 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 13/09/2008 15:11:44
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new file mode 100644
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+\name{ExperimentPath-class}
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+\docType{class}
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+\alias{ExperimentPath-class}
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+% constructors
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+\alias{ExperimentPath}
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+% etc
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+\alias{show,ExperimentPath-method}
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+\alias{detail,ExperimentPath-method}
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+
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+\title{"ExperimentPath" class representing a file hierarchy of data
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+  files}
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+
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+\description{
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+
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+  Short read technologies often produce a hierarchy of output files. The
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+  content of the hierarchy varies. This class represents the root of the
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+  file hierarchy. Specific classes (e.g.,
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+  \code{\linkS4class{SolexaPath}}) represent different technologies.
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+
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+}
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+\section{Objects from the Class}{
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+
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+  Objects from the class are created by calls to the constructor:
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+  
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+  \code{ExperimentPath(experimentPath)}
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+
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+  \describe{
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+    \item{experimentPath}{\code{character(1)} object pointing to the
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+      top-level directory of the experiment; see specific technology
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+      classes for additional detail.}
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+    \item{verbose=FALSE}{(optional) logical vector which, when
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+      \code{TRUE} results in warnings if paths do not exist.}
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+  }
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+  All paths must be fully-specified.
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+}
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+\section{Slots}{
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+  \code{ExperimentPath} has one slot, containing a fully
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+  specified path to the corresponding directory (described above).
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+  \describe{
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+    \item{\code{basePath}}{See above.}
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+  }
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+  The slot is accessed with \code{basePath} or \code{experimentPath}.
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+}
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+\section{Extends}{
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+  Class \code{"\linkS4class{.ShortReadBase}"}, directly.
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+}
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+\section{Methods}{
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+  Methods include:
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+  \describe{
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+
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+    \item{show}{\code{signature(object = "ExperimentPath")}: briefly
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+      summarize the file paths of \code{object}.}
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+
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+    \item{detail}{\code{signature(object = "ExperimentPath")}: summarize
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+      file paths of \code{object}.}
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+  }
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+}
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+
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+\author{Michael Lawrence}
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+\examples{
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+showClass("ExperimentPath")
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+}
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+\keyword{classes}