Browse code

update sample.CNSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53580 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2011 19:31:11
Showing6 changed files

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@@ -1,3 +1,4 @@
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+.auto*
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 test/*
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 myCrlmmGT2.Rnw
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 ffobjs*
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new file mode 100644
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Binary files /dev/null and b/data/sample.CNSet.rda differ
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deleted file mode 100644
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Binary files a/data/sample.CNSetLM.rda and /dev/null differ
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@@ -77,10 +77,8 @@ log-scale the variance is rougly constant for CA, CB > 0).
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 }
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 \examples{
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-data(sample.CNSetLM)
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-## update to class CNSet
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-cnSet <- as(sample.CNSetLM, "CNSet")
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-## All NAs. Need to replace sample.CNSetLM with a HapMap example
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+data(sample.CNSet)
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+## All NAs. Need to replace sample.CNSet with a HapMap example
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 Ns(cnSet, i=1:5, j=1:2)
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 corr(cnSet, i=1:5, j=1:2)
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 medians(cnSet, i=1:5, j=1:2)
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@@ -78,10 +78,7 @@ rawCopynumber(object,...)
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 \examples{
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 ## Version 1.6* of crlmm used CNSetLM objects.
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-data(sample.CNSetLM)
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-
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-## To update to class CNSet, use
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-cnSet <- as(sample.CNSetLM, "CNSet")
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+data(sample.CNSet)
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 all(isCurrent(cnSet)) ## is the cnSet object current?
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 ## --------------------------------------------------
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similarity index 53%
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rename from man/sample.CNSetLM.Rd
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rename to man/sample.CNSet.Rd
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@@ -1,63 +1,34 @@
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-\name{sample.CNSetLM}
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-\alias{sample.CNSetLM}
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+\name{sample.CNSet}
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+\alias{sample.CNSet}
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 \docType{data}
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 \title{
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-	Dataset of class 'CNSetLM'
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+	Object of class 'CNSet'
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 }
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 \description{
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-	The data for 2119 polymorphic and nonpolymorphic markers on
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-	chromosome 1 for the CEPH and Yoruban HapMap samples.
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+	The data for the first 16 polymorphic markers in the HapMap analysis.
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 }
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-\usage{data(sample.CNSetLM)}
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+\details{
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+  This object was created from the copynumber vignette in inst/scripts.
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+}
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+\usage{data(sample.CNSet)}
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 \format{
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-
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-	This class has been deprecated.  See example below for how to
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-	update an existing 'CNSetLM' object to class 'CNSet'.
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-
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-	The data illustrates the \code{CNSetLM-class}, with
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+  The data illustrates the \code{CNSet-class}, with
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 	\code{assayData} containing the quantile-normalized
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 	intensities for the A and B alleles, genotype calls and
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-	confidence scores (call and callProbability), and
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-	allele-specific copy number (CA and CB). The parameters from
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-	the linear model are stored in the lM slot.
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+	confidence scores.  New slots that specific to copy number
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+	estimation are \code{batch} and \code{batchStatistics}.
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 }
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 \examples{
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-## class CNSetLM has been deprecated
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-data(sample.CNSetLM)
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-## update to class CNSet
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-cnSet <- as(sample.CNSetLM, "CNSet")
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-all(isCurrent(cnSet)) ## is the cnSet object current?
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-##subsetting
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-cnSet2 <- cnSet[, 1:5]
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-stopifnot(batchNames(cnSet2) == "C")
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-\dontrun{
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-	## updating class CNSetLM using ff objects
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-	## a bigger object with multiple batches
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-	if(require(ff)){
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-		outdir <- "/amber1/scratch/rscharpf/jss/hapmap2"
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-		load(file.path(outdir, "container.rda"))
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-		container <- object; rm(object); gc()
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-		container2 <- as(container, "CNSet")
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-		all(isCurrent(container2))
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-		## test replacement methods, subset methods
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-		table(batch(container2))
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-		##generates warning ... would need open, close in the '[' method
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-		invisible(open(nuA(container2)))
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-		xx <- nu(container2, "A")[1:5, ]
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-		nuA(container2)[1:5, ] <- xx
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-		invisible(close(nuA(container2)))
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-	}
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-}
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+data(sample.CNSet)
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 ## --------------------------------------------------
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 ## accessors for the feature-level info
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 ## --------------------------------------------------
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 chromosome(cnSet)[1:5]
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 position(cnSet)[1:5]
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 isSnp(cnSet)[1:5]
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-## 980 nonpolymorphic markers and 1139 polymoprhic markers
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 table(isSnp(cnSet))
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 ## --------------------------------------------------
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 ## sample-level statistics computed by crlmm
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@@ -71,14 +42,9 @@ cnSet$SKW[1:5]
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 ## the gender (gender is imputed unless specified in the call to crlmm)
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 table(cnSet$gender)  ## 1=male, 2=female
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 ## --------------------------------------------------
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-## --------------------------------------------------
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-##
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-## accessors for parameters estimated from the linear model for copy
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-## number (note that the parameters have dimension R x C, where R
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-## corresponds to the number of features and C corresponds to the
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-## number of batches)
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+## batchStatistics
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 ## -------------------------------------------------- estimate of
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-## background
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+## intercept from linear model
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 dim(nu(cnSet, "A"))
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 ## background for the A allele in the 2 batches for the
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 ## first 5 markers
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@@ -123,14 +89,5 @@ all.equal(cn4, cn2)
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 cn5 <- totalCopynumber(cnSet, i=1:5)
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 ## all markers, samples 1-5
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 cn6 <- totalCopynumber(cnSet, j=1:5)
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-
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-## NOTE: subsetting the object before extracting copy number
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-##       can be very inefficient when the data set is very large,
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-##       particularly if using ff objects.  IN particular, subsetting
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-##       the CNSet object will subset all of the assay data elements
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-##       and all of the elements in the LinearModelParameter slot
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-\dontrun{
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-	cnsubset <- cnSet[1:5, ]
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-}
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 }
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 \keyword{datasets}