1. crlmm
  2. man
  3. methods-eSet.Rd
Browse code

cleaned up a few of the classes. defined new class called CNSet to take the place of CrlmmSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43144 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2009 14:59:04
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man/methods-eSet.Rd
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-\name{methods-eSet}
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-\alias{chromosome}
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-\alias{chromosome,eSet-method}
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-\alias{cnIndex}
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-\alias{cnIndex,eSet-method}
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-\alias{position}
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-\alias{position,eSet-method}
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-\alias{snpIndex}
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-\alias{snpIndex,eSet-method}
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-
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-\title{Methods for eSet derivatives}
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-
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-\description{
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-  \code{chromosome} return the chromosome number for SNP and NP probes.
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-
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-  \code{cnIndex, ...} return the row indices of copy number probes.
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-
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-  \code{position} return the physical position of the SNP or the
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-  physical position for the first index of the NP probe.
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-
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-  \code{snpIndex, ...} return the row indices of polymorphic loci.
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-
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-}
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-
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-\usage{
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-
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-  chromosome(object)
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-  cnIndex(object, ...)
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-  position(object)
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-  snpIndex(object, ...)
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-
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-}
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-
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-\arguments{
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-
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-  \item{object}{Any object extending eSet (ABset, CopyNumberSet,
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-    CrlmmSetList, SnpSet}
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-
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-  \item{\dots}{Usually the character string indicating annotation package.}
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-
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-}
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-
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-\value{
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-
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-  Vector of indices.
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-
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-}
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-
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-\seealso{
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-
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-  \code{"\linkS4class{ABset}"}
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-  \code{"\linkS4class{CopyNumberSet}"}
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-  \code{"\linkS4class{CrlmmSetList}"}
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-
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-}
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-
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-
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-\keyword{manip}
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\ No newline at end of file
Browse code

changes to crlmmWrapper. updated vignettes in inst/scripts.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@42144 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 04/10/2009 02:37:32
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man/methods-eSet.Rd
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@@ -1,24 +1,32 @@
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 \name{methods-eSet}
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+\alias{chromosome}
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+\alias{chromosome,eSet-method}
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 \alias{cnIndex}
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 \alias{cnIndex,eSet-method}
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+\alias{position}
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+\alias{position,eSet-method}
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 \alias{snpIndex}
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 \alias{snpIndex,eSet-method}
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-
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 \title{Methods for eSet derivatives}
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 \description{
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+  \code{chromosome} return the chromosome number for SNP and NP probes.
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+
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+  \code{cnIndex, ...} return the row indices of copy number probes.
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+  \code{position} return the physical position of the SNP or the
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+  physical position for the first index of the NP probe.
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+
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   \code{snpIndex, ...} return the row indices of polymorphic loci.
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-  \code{cnIndex, ...} return the row indices of copy number probes.
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-
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 }
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 \usage{
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+  chromosome(object)
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   cnIndex(object, ...)
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-
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+  position(object)
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   snpIndex(object, ...)
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 }
Browse code

changes to vignette. removed crlmmIlluminaWrapper function. added boxplot method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@41178 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/08/2009 14:14:25
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man/methods-eSet.Rd
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 \usage{
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-  cnIndex(object, cdfName)
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+  cnIndex(object, ...)
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-  snpIndex(object, cdfName)
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+  snpIndex(object, ...)
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 }
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@@ -28,7 +28,7 @@
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   \item{object}{Any object extending eSet (ABset, CopyNumberSet,
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     CrlmmSetList, SnpSet}
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-  \item{cdfName}{Character string indicating annotation package.}
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+  \item{\dots}{Usually the character string indicating annotation package.}
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 }
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Browse code

several updates to vignette, documentation, and copy number for illumina.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@41171 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 13/08/2009 19:47:13
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man/methods-eSet.Rd
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 \description{
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-  \code{snpIndex} return the row indices of polymorphic loci.
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+  \code{snpIndex, ...} return the row indices of polymorphic loci.
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-  \code{cnIndex} return the row indices of copy number probes.
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+  \code{cnIndex, ...} return the row indices of copy number probes.
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 }
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 \usage{
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-  cnIndex(object)
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+  cnIndex(object, cdfName)
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-  snpIndex(object)
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+  snpIndex(object, cdfName)
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 }
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   \item{object}{Any object extending eSet (ABset, CopyNumberSet,
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     CrlmmSetList, SnpSet}
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+  \item{cdfName}{Character string indicating annotation package.}
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+
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 }
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 \value{
Browse code

beginning of copy number methods for illumina. some work on copy number estimation for chromosome X

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@40527 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 06/07/2009 19:24:27
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man/methods-eSet.Rd
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+\name{methods-eSet}
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+\alias{cnIndex}
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+\alias{cnIndex,eSet-method}
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+\alias{snpIndex}
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+\alias{snpIndex,eSet-method}
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+
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+
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+\title{Methods for eSet derivatives}
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+
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+\description{
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+
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+  \code{snpIndex} return the row indices of polymorphic loci.
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+
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+  \code{cnIndex} return the row indices of copy number probes.
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+
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+}
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+
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+\usage{
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+
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+  cnIndex(object)
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+
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+  snpIndex(object)
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+
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+}
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+
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+\arguments{
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+
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+  \item{object}{Any object extending eSet (ABset, CopyNumberSet,
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+    CrlmmSetList, SnpSet}
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+
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+}
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+
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+\value{
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+
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+  Vector of indices.
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+
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+}
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+
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+\seealso{
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+
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+  \code{"\linkS4class{ABset}"}
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+  \code{"\linkS4class{CopyNumberSet}"}
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+  \code{"\linkS4class{CrlmmSetList}"}
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+
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+}
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+
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+
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+\keyword{manip}
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\ No newline at end of file