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Create the function rawCopynumber that aliases totalCopynumber

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53577 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2011 19:30:54
Showing4 changed files

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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.9.17
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+Version: 1.9.18
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 Date: 2010-12-10
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 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -68,7 +68,7 @@ export(crlmm,
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        genotype.Illumina,
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        crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
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 export(constructIlluminaCNSet)
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-export(totalCopynumber)
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+export(totalCopynumber, rawCopynumber)
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 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
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 ## for posterior means
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@@ -569,6 +569,7 @@ setMethod("totalCopynumber", signature=signature(object="CNSet"),
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 		  cb <- CB(object, ...)
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 		  return(ca+cb)
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 	  })
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+rawCopynumber <- totalCopynumber
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 ##setReplaceMethod("snpCall", c("CNSet", "ff_or_matrix"),
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 ##                 function(object, ..., value){
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 \alias{CB,CNSet-method}
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 \alias{lines,CNSet-method}
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 \alias{totalCopynumber,CNSet-method}
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+\alias{rawCopynumber,CNSet-method}
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 \alias{nuA,CNSet-method}
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 \alias{nuB,CNSet-method}
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 \alias{Ns,CNSet-method}
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@@ -36,6 +37,7 @@
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     \item{CB}{\code{signature(object="CNSet")}: ...}
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     \item{lines}{\code{signature(x="CNSet")}: ...}
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     \item{totalCopynumber}{\code{signature(object="CNSet")}: ...}
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+    \item{rawCopynumber}{\code{signature(object="CNSet")}: ...}
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     \item{nuA}{\code{signature(object="CNSet")}: ...}
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     \item{nuB}{\code{signature(object="CNSet")}: ...}
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     \item{phiA}{\code{signature(object="CNSet")}: ...}
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@@ -49,6 +51,7 @@
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 }
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 \seealso{
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-  \code{\link{CNSet-class}}, \code{\link{CA}}, \code{\link{CB}}, \code{\link{totalCopynumber}}
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+  \code{\link{CNSet-class}}, \code{\link{CA}}, \code{\link{CB}},
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+  \code{\link{totalCopynumber}}, \code{\link{rawCopynumber}}
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 }
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 \keyword{methods}