1. crlmm
  2. man
  3. calculateRBaf.Rd
Browse code

Merge branch 'collab'

* collab:
update Rds
revert imputeGender to original api
bug fix for calculateRBafCNSet
update calculateRBafCNSet
Fix documentation for crlmmCopynumber -- added argument fitLinearModel
update crlmmGT2
Put rm(DD, ...) further down in crlmmGT2 function
remove message about cloning A and B
Open and close callsPr and callsGt in crlmmGT2 (when args not missing)
revert removed indices loaded in crlmmGT2
snprmaAffy no longer writes normalized intensities to calls and callProbability slots. crlmmGT2 takes arguments callsGt and callsPr. When present, crlmmGT2 will not overwrite A and B.
explicit coercion to matrix in imputeGender
Assign imputed gender to cnSet$gender within crlmmGT2 function.
Change sum(SNR > SNRmin) to sum(SNR[] > SNRmin) in imputeGender

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69450 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/09/2012 20:07:37
Showing 1 changed files
man/calculateRBaf.Rd
History View file @ 2bc2962
... ... 
@@ -58,10 +58,16 @@ calculateRBaf(object, batch.name, chrom)
58 58 
 \author{Lynn Mireless}
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 \examples{
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-data(cnSetExample)
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-baf.lrr <- calculateRBaf(cnSetExample, "SHELF")
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-hist(baf.lrr[["baf"]][[1]]/1000, breaks=100)
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-hist(baf.lrr[["lrr"]][[1]]/100, breaks=100)
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+	data(cnSetExample)
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+	baf.lrr <- suppressWarnings(calculateRBaf(cnSetExample, "SHELF"))
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+	hist(baf.lrr[["baf"]][[1]]/1000, breaks=100)
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+	hist(baf.lrr[["lrr"]][[1]]/100, breaks=100)
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+	\dontrun{
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+		library(ff)
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+		baf.lrr <- suppressWarnings(calculateRBaf(cnSetExample, "SHELF"))
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+		class(baf.lrr[["baf"]][[1]]) ## ff_matrix
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+		class(baf.lrr[["lrr"]][[1]]) ## ff_matrix
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+	}
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 }
66 72 
 \keyword{list}
67 73 
 \keyword{methods}
Browse code

Merge branch 'collab'

* collab: (34 commits)
revert change to IlluminaPreprocessCN
fix bug in isValidCdfName
print warning when all features in a batch of probes are flagged, but allow processing to continue
add utility cleancdfnames
Add validCdfNames.Rd
export validCdfNames
imputeGender fix when chromosome Y not available
Use splitIndicesByLength(index, ocSamples/getDoParWorkers())
Can not allocate vector of size XG with genotype.Illumina. Use splitIndicesByNode() only if the length of the list is greater than the split from splitIndicesByLength(). Otherwise, split by length using ocSamples()
update .gitignore
Add make.unique for sampleSheet$Sample_ID in readIdatFiles
bug in description
ensure sample ids stored in samplesheet are unique when constructing cnSet object
update oligoClasses dependency
update unit test for genotype.Illumina
revert change in constructInf call from genotype.Illumina
Update genotype.Rd
edit ACN function
1.15.6 use make.unique(basename(arrayNames)) to allow processing of Illumina samples with duplicated barcodes
check that sample identifies are unique in crlmm function
...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67435 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/07/2012 19:00:03
Showing 1 changed files
man/calculateRBaf.Rd
History View file @ 063b3d1
... ... 
@@ -5,45 +5,63 @@
5 5 
 \description{Calculate log R ratios and B allele frequencies from
6 6 
   a \code{CNSet} object}
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 \usage{
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-calculateRBaf(object, batch.name)
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+calculateRBaf(object, batch.name, chrom)
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 }
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 \arguments{
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+
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   \item{object}{A \code{CNSet} object.}
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-  \item{batch.name}{A character string.  See details.}
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+
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+  \item{batch.name}{A character string indicating the batch.  If
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+  missing, log R ratios and B allele frequencies are calculated for all
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+  batches in the \code{object}.}
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+
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+  \item{chrom}{Integer indicating which chromosome to process. If
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+  missing, B allele frequencies and log R ratios are calculated for all
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+  autosomal chromosomes and chromosome X that are included in
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+  \code{object}.}
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+
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 }
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-\details{\code{batch.name} must be a value in
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-  \code{batch(object)}. Currently, one must specify a single
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-  \code{batch.name}. If a character vector for \code{batch.name} is
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-  supplied, only the first is evaluated.
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+
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+\details{
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+
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+  \code{batch.name} must be a value in \code{batch(object)}. Currently,
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+  one must specify a single \code{batch.name}. If a character vector for
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+  \code{batch.name} is supplied, only the first is evaluated.
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   TODO: A description of how these values are calculated.
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 }
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 \value{
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-  A list.
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+  A named list.
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-  \code{baf}: A matrix of B allele frequencies.
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+  \code{baf}: Each element in the baf list is a matrix of B allele
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+  frequencies (one matrix for each chromosome).
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-  \code{lrr}: A matrix of log R ratios.
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+  \code{lrr}: Each element in the lrr list is a matrix of log R ratios
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+  (one matrix for each chromosome).
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+
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+  The log R ratios were scaled by a factor of 100 and stored as an
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+  integer.  B allele frequencies were scaled by a factor of 1000 and
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+  stored as an integer.
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 }
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 \references{
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-  Reference for BAFs, LRRs.
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+  Peiffer et al., High-resolution genomic profiling of chromosomal aberrations using
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+  Infinium whole-genome genotyping (2006), Genome Research
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 }
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+
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 \author{Lynn Mireless}
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 \examples{
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 data(cnSetExample)
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 baf.lrr <- calculateRBaf(cnSetExample, "SHELF")
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-hist(baf.lrr[["baf"]], breaks=100)
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-hist(baf.lrr[["lrr"]], breaks=100)
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+hist(baf.lrr[["baf"]][[1]]/1000, breaks=100)
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+hist(baf.lrr[["lrr"]][[1]]/100, breaks=100)
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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{list}
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-\keyword{methods}
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\ No newline at end of file
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+\keyword{methods}
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
Showing 1 changed files
man/calculateRBaf.Rd
History View file @ 7c0c9ac
... ... 
@@ -38,13 +38,10 @@ calculateRBaf(object, batch.name)
38 38 
 \author{Lynn Mireless}
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40 40 
 \examples{
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-
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 data(cnSetExample)
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 baf.lrr <- calculateRBaf(cnSetExample, "SHELF")
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 hist(baf.lrr[["baf"]], breaks=100)
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 hist(baf.lrr[["lrr"]], breaks=100)
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-
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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.
Browse code

Replace sample.CNSet and sample.CNSet2 with cnSetExample and cnSetExample2

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@59039 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 11/10/2011 12:17:42
Showing 1 changed files
man/calculateRBaf.Rd
History View file @ cceffc9
... ... 
@@ -39,8 +39,8 @@ calculateRBaf(object, batch.name)
39 39
40 40 
 \examples{
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-data(sample.CNSet)
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-baf.lrr <- calculateRBaf(sample.CNSet, "SHELF")
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+data(cnSetExample)
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+baf.lrr <- calculateRBaf(cnSetExample, "SHELF")
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 hist(baf.lrr[["baf"]], breaks=100)
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 hist(baf.lrr[["lrr"]], breaks=100)
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Browse code

bringing changes from GitHub; from now on, keeping code on BioC servers

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58710 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 03/10/2011 18:12:55
Showing 1 changed files
man/calculateRBaf.Rd
History View file @ b6f0c38
... ... 
@@ -43,6 +43,8 @@ data(sample.CNSet)
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 baf.lrr <- calculateRBaf(sample.CNSet, "SHELF")
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 hist(baf.lrr[["baf"]], breaks=100)
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 hist(baf.lrr[["lrr"]], breaks=100)
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+
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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.
Browse code

Add calculateRBaf.Rd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58667 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:50:44
Showing 1 changed files
man/calculateRBaf.Rd
History View file @ 4d0bba5
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,50 @@
1 
+\name{calculateRBaf}
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+\alias{calculateRBaf}
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+\alias{calculateRBaf,CNSet-method}
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+\title{Calculate log R ratios and B allele frequencies.}
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+\description{Calculate log R ratios and B allele frequencies from
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+  a \code{CNSet} object}
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+\usage{
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+calculateRBaf(object, batch.name)
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+}
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+
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+\arguments{
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+  \item{object}{A \code{CNSet} object.}
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+  \item{batch.name}{A character string.  See details.}
14 
+}
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+\details{\code{batch.name} must be a value in
16 
+  \code{batch(object)}. Currently, one must specify a single
17 
+  \code{batch.name}. If a character vector for \code{batch.name} is
18 
+  supplied, only the first is evaluated.
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+
20 
+  TODO: A description of how these values are calculated.
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+
22 
+}
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+
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+\value{
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+  A list.
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+
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+  \code{baf}: A matrix of B allele frequencies.
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+
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+  \code{lrr}: A matrix of log R ratios.
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+
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+}
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+
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+\references{
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+
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+  Reference for BAFs, LRRs.
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+
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+}
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+\author{Lynn Mireless}
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+
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+\examples{
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+
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+data(sample.CNSet)
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+baf.lrr <- calculateRBaf(sample.CNSet, "SHELF")
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+hist(baf.lrr[["baf"]], breaks=100)
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+hist(baf.lrr[["lrr"]], breaks=100)
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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{list}
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+\keyword{methods}
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\ No newline at end of file