1. gmapR
  2. man
  3. GmapSnps-class.Rd
Browse code

*drop passing of ... arg to method snps<- eventually dispatches on

*doc'ed ... arg to GmapSnps constructor

*added aliases for snps<- when first arg is a GmapGenomeDirectory

*test case for creating a GmapGenome via a DNAStringSet was
broken. Example sequence was too short for gmap_build to work


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69386 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 12/09/2012 22:29:42
Showing 1 changed files
man/GmapSnps-class.Rd
History View file @ 15766c6
... ... 
@@ -25,8 +25,10 @@ Objects can be created by calls of the form \code{GmapSnps(snps,
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   \item{name}{If provided, the name to give the database of SNPs. If not
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   provided, defauts to the \code{snps} argument.}
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   \item{create}{If the directory provided in the \code{directory}
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-  argument does not exist, create it.}
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-  }
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+    argument does not exist, create it.}
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+  \item{...}{Additional arguments to be passed to the SNPs
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+    replacement method.}
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+}
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 \section{Accessors}{
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     \describe{
... ... 
@@ -36,8 +38,7 @@ Objects can be created by calls of the form \code{GmapSnps(snps,
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 	this \code{GmapSnps} object.}
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     }
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 }
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-
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-
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+
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 \section{Methods}{
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   \describe{
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     \item{directory}{\code{signature(x = "GmapSnps")}: ... }
Browse code

exporting GmapSnps and GmapSnpDirectory

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68698 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 21/08/2012 23:52:09
Showing 1 changed files
man/GmapSnps-class.Rd
History View file @ 0a4b811
... ... 
@@ -3,6 +3,7 @@
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 \docType{class}
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 \alias{GmapSnps-class}
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 \alias{directory,GmapSnps-method}
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+\alias{GmapSnps}
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 \title{Class \code{"GmapSnps"}}
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 \description{
... ... 
@@ -14,6 +15,29 @@
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 Objects can be created by calls of the form \code{GmapSnps(snps,
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   directory, name, create)}.
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 }
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+
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+\usage{GmapSnps(snps, directory, name = snps, create = FALSE, ...)}
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+
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+\arguments{
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+  \item{snps}{A path to a VCF file}
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+  \item{directory}{The directory to create the IIT files used by GMAP
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+  and GSNAP}
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+  \item{name}{If provided, the name to give the database of SNPs. If not
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+  provided, defauts to the \code{snps} argument.}
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+  \item{create}{If the directory provided in the \code{directory}
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+  argument does not exist, create it.}
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+  }
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+
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+\section{Accessors}{
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+    \describe{
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+      \item{}{\code{name(x)}: returns the name of the \code{GmapSnps} object}
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+      \item{}{\code{directory(x)}: returns the \code{GmapGenomeDirectory}
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+	that is the parent of the directory containing the index files for
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+	this \code{GmapSnps} object.}
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+    }
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+}
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+
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+
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 \section{Methods}{
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   \describe{
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     \item{directory}{\code{signature(x = "GmapSnps")}: ... }
Browse code

renaming gmapR2 to gmapR: it lives again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/08/2012 22:24:24
Showing 1 changed files
man/GmapSnps-class.Rd
History View file @ b22faf0
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,25 @@
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+\name{GmapSnps-class}
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+\Rdversion{1.1}
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+\docType{class}
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+\alias{GmapSnps-class}
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+\alias{directory,GmapSnps-method}
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+
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+\title{Class \code{"GmapSnps"}}
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+\description{
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+  This class represents a set of SNPs (single nucleotide polymorphisms)
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+  for use with GMAP and GSNAP (typically for SNP-tolerant alignment.)
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+}
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+\section{Objects from the Class}{
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+  ##TODO: doc these args
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+Objects can be created by calls of the form \code{GmapSnps(snps,
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+  directory, name, create)}.
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+}
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+\section{Methods}{
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+  \describe{
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+    \item{directory}{\code{signature(x = "GmapSnps")}: ... }
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+  }
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+}
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+\author{
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+  Michael Lawrence
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+}
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+\keyword{classes}