1. crlmm
  2. man
  3. cnrma.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
Showing 1 changed files
man/cnrma.Rd
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-\name{cnrma}
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-\alias{cnrma}
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-\title{Quantile normalizes the intensities for the nonpolymorphic probe
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-  to a HapMap reference distribution.}
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-\description{Quantile normalizes the intensities for the nonpolymorphic probe
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-  to a HapMap reference distribution.
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-}
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-\usage{
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-cnrma(filenames, cdfName, sns, seed = 1, verbose=FALSE)
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-}
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-\arguments{
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-  \item{filenames}{filenames with complete path}
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-  \item{cdfName}{Only 'genomewidesnp6' allowed}
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-  \item{sns}{the sample names. If missing, the basename of the filenames is used.}
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-  \item{seed}{seed for sampling the intensities to calculate skewness}
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-  \item{verbose}{logical}
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-}
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-\value{
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-  A list.  First element is the matrix of quantile-normalized
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-  intensities.  The second element is the skew.
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-}
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-\author{Rob Scharpf}
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-\note{Not tested}
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-\examples{
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-	library(genomewidesnp6Crlmm)
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-	library(hapmapsnp6)
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-	path <- system.file("celFiles", package="hapmapsnp6")
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-	celFiles <- list.celfiles(path, full.names=TRUE)
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-	cnrmaResult <- cnrma(celFiles, cdfName="genomewidesnp6")
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-}
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-\keyword{robust}
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-
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/cnrma.Rd
History View file @ 2ae7850
... ... 
@@ -6,7 +6,7 @@
6 6 
   to a HapMap reference distribution.
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 }
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 \usage{
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-cnrma(filenames, cdfName="genomewidesnp6", sns, seed = 1, verbose=FALSE)
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+cnrma(filenames, cdfName, sns, seed = 1, verbose=FALSE)
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 }
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 \arguments{
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   \item{filenames}{filenames with complete path}
Browse code

updated cnrma function and the copy number vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@38290 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 29/03/2009 19:59:40
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man/cnrma.Rd
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... ... 
@@ -6,12 +6,12 @@
6 6 
   to a HapMap reference distribution.
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 }
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 \usage{
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-cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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+cnrma(filenames, cdfName="genomewidesnp6", sns, seed = 1, verbose=FALSE)
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 }
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 \arguments{
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   \item{filenames}{filenames with complete path}
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+  \item{cdfName}{Only 'genomewidesnp6' allowed}
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   \item{sns}{the sample names. If missing, the basename of the filenames is used.}
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-  \item{cdfName}{Should be 'genomewidesnp6Crlmm'}
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   \item{seed}{seed for sampling the intensities to calculate skewness}
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   \item{verbose}{logical}
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 }
... ... 
@@ -22,13 +22,11 @@ cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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 \author{Rob Scharpf}
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 \note{Not tested}
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 \examples{
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-	\dontrun{
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-		library(genomewidesnp6Crlmm)
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-		library(hapmapsnp6)
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-		path <- system.file("celFiles", package="hapmapsnp6")
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-		celFiles <- list.celfiles(path, full.names=TRUE)
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-		cnrmaResult <- cnrma(celFiles)
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-	}
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+	library(genomewidesnp6Crlmm)
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+	library(hapmapsnp6)
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+	path <- system.file("celFiles", package="hapmapsnp6")
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+	celFiles <- list.celfiles(path, full.names=TRUE)
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+	cnrmaResult <- cnrma(celFiles, cdfName="genomewidesnp6")
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 }
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 \keyword{robust}
34 32
Browse code

prep'ing to submit to peer review

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@37828 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 09/03/2009 00:19:46
Showing 1 changed files
man/cnrma.Rd
History View file @ 07cc385
... ... 
@@ -15,8 +15,6 @@ cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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   \item{seed}{seed for sampling the intensities to calculate skewness}
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   \item{verbose}{logical}
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 }
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-\details{
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-}
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 \value{
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   A list.  First element is the matrix of quantile-normalized
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   intensities.  The second element is the skew.
... ... 
@@ -27,7 +25,7 @@ cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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 	\dontrun{
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 		library(genomewidesnp6Crlmm)
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 		library(hapmapsnp6)
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-		path <- system.file("celFiles", package="hapmapsnp5")
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+		path <- system.file("celFiles", package="hapmapsnp6")
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 		celFiles <- list.celfiles(path, full.names=TRUE)
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 		cnrmaResult <- cnrma(celFiles)
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 	}
Browse code

fixed bug in cnrma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@37700 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/03/2009 21:19:51
Showing 1 changed files
man/cnrma.Rd
History View file @ 75e7ffb
... ... 
@@ -2,7 +2,8 @@
2 2 
 \alias{cnrma}
3 3 
 \title{Quantile normalizes the intensities for the nonpolymorphic probe
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   to a HapMap reference distribution.}
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-\description{
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+\description{Quantile normalizes the intensities for the nonpolymorphic probe
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+  to a HapMap reference distribution.
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 }
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 \usage{
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 cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
... ... 
@@ -12,6 +13,7 @@ cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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   \item{sns}{the sample names. If missing, the basename of the filenames is used.}
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   \item{cdfName}{Should be 'genomewidesnp6Crlmm'}
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   \item{seed}{seed for sampling the intensities to calculate skewness}
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+  \item{verbose}{logical}
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 }
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 \details{
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 }
... ... 
@@ -21,7 +23,6 @@ cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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 }
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 \author{Rob Scharpf}
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 \note{Not tested}
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-\seealso{\code{\link{snprma}}}
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 \examples{
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 	\dontrun{
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 		library(genomewidesnp6Crlmm)
Browse code

fixed bug in cnrma man file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@37699 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/03/2009 20:53:57
Showing 1 changed files
man/cnrma.Rd
History View file @ 0909ceb
... ... 
@@ -21,9 +21,10 @@ cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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 }
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 \author{Rob Scharpf}
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 \note{Not tested}
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-\seealso{}
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+\seealso{\code{\link{snprma}}}
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 \examples{
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 	\dontrun{
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+		library(genomewidesnp6Crlmm)
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 		library(hapmapsnp6)
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 		path <- system.file("celFiles", package="hapmapsnp5")
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 		celFiles <- list.celfiles(path, full.names=TRUE)
Browse code

added verbose argument to cnrma. added man pages for computeCopynumber and cnrma

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@37693 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/03/2009 14:32:33
Showing 1 changed files
man/cnrma.Rd
History View file @ 38d8707
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@@ -0,0 +1,34 @@
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+\name{cnrma}
2 
+\alias{cnrma}
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+\title{Quantile normalizes the intensities for the nonpolymorphic probe
4 
+  to a HapMap reference distribution.}
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+\description{
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+}
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+\usage{
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+cnrma(filenames, sns, cdfName, seed = 1, verbose=FALSE)
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+}
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+\arguments{
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+  \item{filenames}{filenames with complete path}
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+  \item{sns}{the sample names. If missing, the basename of the filenames is used.}
13 
+  \item{cdfName}{Should be 'genomewidesnp6Crlmm'}
14 
+  \item{seed}{seed for sampling the intensities to calculate skewness}
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+}
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+\details{
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+}
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+\value{
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+  A list.  First element is the matrix of quantile-normalized
20 
+  intensities.  The second element is the skew.
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+}
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+\author{Rob Scharpf}
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+\note{Not tested}
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+\seealso{}
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+\examples{
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+	\dontrun{
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+		library(hapmapsnp6)
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+		path <- system.file("celFiles", package="hapmapsnp5")
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+		celFiles <- list.celfiles(path, full.names=TRUE)
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+		cnrmaResult <- cnrma(celFiles)
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+	}
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+}
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+\keyword{robust}
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+