Browse code

Merge branch 'collab'

* collab:
bump version
made cnSetExample smaller. Fix notes
Trying to revert bad commit
remove cn-functions. update description
comment most of cn-functions.r
Resaved rdas
update data/cnSetExample.rda and data/cnSetExample2.rda
bump version
coercion method from CNSet to oligoSnpSet makes integer matrices of BAFs and lrr's
import ff_or_matrix from oligoClasses. bump dependency on oligoClasses version. Use library(oligoClasses) in some of the crlmm examples.
Cleaning pkg loading process: work still required
move Biobase and methods to imports

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64324 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/03/2012 03:34:50
Showing1 changed files
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@@ -31,6 +31,7 @@ R. Scharpf
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 }
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 \examples{
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+library(oligoClasses)
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 if(require(hapmapsnp6)){
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   path <- system.file("celFiles", package="hapmapsnp6")
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   cels <- list.celfiles(path, full.names=TRUE)
Browse code

Merge branch 'mymac'

* 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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new file mode 100644
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@@ -0,0 +1,41 @@
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+\name{validCEL}
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+\alias{celDates}
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+\alias{validCEL}
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+\title{
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+  Reads cel files and return an error if a file is not read
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+}
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+\description{
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+  Reads cel files and return an error if a file is not read
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+}
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+\usage{
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+validCEL(celfiles)
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+celDates(celfiles)
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+}
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+\arguments{
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+  \item{celfiles}{
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+    vector of cel file names to read
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+}
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+}
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+\value{
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+  Returns a message that cel files were successfully read, or an error
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+  if there were problems reading the cel files.
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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{ \cite{\link[affyio]{read.celfile.header}},
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+  \cite{\link{POSIXt}},
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+  \code{\link{read.celfile}}
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+}
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+
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+\examples{
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+if(require(hapmapsnp6)){
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+  path <- system.file("celFiles", package="hapmapsnp6")
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+  cels <- list.celfiles(path, full.names=TRUE)
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+  validCEL(cels)
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+  celDates(cels)
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+}
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+}
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+\keyword{IO}
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\ No newline at end of file