* mymac:
add AffyGW.pdf
update vignettes in inst/scripts
Change argument of validCEL to celfiles
Update constructInf to accommodate GenomeDataFrame class for featureData
bump version to 1.13.7
Add doRUnit.R
Add celfile-utils.Rd
Streamlne some of the Rd files
add validCEL function that checks whether all celfiles can be read
getFeatureData returns GenomeAnnotatedDataFrame
Remove imports from methods. Remove pdf of illumina_copynumber.pdf (large file) and copynumber.pdf
getFeatureDAta returns GenomeAnnotatedDataFrame
Remove separate vignette for copy number in inst/scripts. Include copynumber section in both affy and illumina pipelines.
update documentation files for genotype.Illumina, preprocessInf, and genotypeInf (cdfName added as argument. Indicate that 'batch' should be a character string)
pass cdfName to genotypeInf and preprocessInf
add unitTests and cn-functions for 'simple usage'
Combine AffyPreprocess and copynumber. Combine IlluminaPreprocess and copynumber
remove depency on ff to allow installation on my mac
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62108 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 17/01/2012 19:13:44
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@@ -35,9 +35,7 @@ ABpanel(x, y, predictRegion, copyNumber = 0:4, fill, ..., subscripts) |
| 35 | 35 |
See \code{xyplot} in the \pkg{lattice} package.
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} |
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} |
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-\details{
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-%% ~~ If necessary, more details than the description above ~~ |
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-} |
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+ |
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\value{
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Not applicable |
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} |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58644 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 01/10/2011 04:48:25
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@@ -29,7 +29,7 @@ ABpanel(x, y, predictRegion, copyNumber = 0:4, fill, ..., subscripts) |
| 29 | 29 |
certain point symbols. See \code{points}.
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} |
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\item{\dots}{
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- Additional arguments to \code{panel.xyplot} and \code{\lpolygon}.
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+ Additional arguments to \code{panel.xyplot} and \code{lpolygon}.
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} |
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\item{subscripts}{
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See \code{xyplot} in the \pkg{lattice} package.
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58638 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 01/10/2011 04:47:42
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new file mode 100644 |
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@@ -0,0 +1,64 @@ |
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+\name{ABpanel}
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+\alias{ABpanel}
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+\title{A panel function for plotting prediction regions and
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+ log-normalized intensities |
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+} |
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+\description{
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+ A panel function for plotting prediction regions and |
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+ log-normalized intensities |
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+} |
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+\usage{
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+ABpanel(x, y, predictRegion, copyNumber = 0:4, fill, ..., subscripts) |
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+} |
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+%- maybe also 'usage' for other objects documented here. |
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+\arguments{
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+ \item{x}{
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+ log-normalized intensities for the A or B allele |
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+} |
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+\item{y}{
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+ log-normalized intensities for the A or B allele |
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+} |
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+ \item{predictRegion}{
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+ A \code{list}. See \code{predictionRegion}.
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+} |
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+ \item{copyNumber}{
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+ Integer vector. Indicates which prediction regions are drawn. |
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+} |
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+ \item{fill}{
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+ Character or integer vector for coloring the points. Only valid for |
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+ certain point symbols. See \code{points}.
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+} |
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+ \item{\dots}{
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+ Additional arguments to \code{panel.xyplot} and \code{\lpolygon}.
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+} |
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+ \item{subscripts}{
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+ See \code{xyplot} in the \pkg{lattice} package.
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+} |
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+} |
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+\details{
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+%% ~~ If necessary, more details than the description above ~~ |
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+} |
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+\value{
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+ Not applicable |
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+} |
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+ |
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+\note{
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+ |
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+ \code{ABpanel} can be passed as the argument to panel in the
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+ \code{xyplot} method for \code{CNSet} objects. See the examples in
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+ \code{xyplot}.
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+ |
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+} |
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+ |
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+\author{
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+R. Scharpf |
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+} |
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+ |
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+\seealso{
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+ \code{\link[lattice]{xyplot}}, \code{\link[lattice]{panel.xyplot}}
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+ \code{\link[lattice]{lpolygon}}
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+} |
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+ |
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+% Add one or more standard keywords, see file 'KEYWORDS' in the |
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+% R documentation directory. |
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+\keyword{aplot}
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\ No newline at end of file |