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Update help files for posteriorProbability and calculatePosteriorMean

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58640 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:47:53
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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.11.19
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+Version: 1.11.20
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 Date: 2010-12-10
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 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -52,7 +52,15 @@ R. Scharpf
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 data(sample.CNSet)
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 pr <- predictionRegion(sample.CNSet, copyNumber=0:4)
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 pp <- posteriorProbability(sample.CNSet, predictRegion=pr)
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-pm <- calculatePosteriorMean(sample.CNSet, posteriorProb=pp, w=rep(1/5, 5))
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+pm <- calculatePosteriorMean(sample.CNSet, posteriorProb=pp)
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+
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+## multiple batches
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+data(sample.CNSet2)
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+pr <- predictionRegion(sample.CNSet2, copyNumber=0:4)
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+pp <- posteriorProbability(sample.CNSet2, predictRegion=pr)
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+## prediction regions not available for some batches
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+pm <- calculatePosteriorMean(sample.CNSet2, posteriorProb=pp)
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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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@@ -49,6 +49,11 @@ data(sample.CNSet)
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 pr <- predictionRegion(sample.CNSet, copyNumber=0:4)
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 pp <- posteriorProbability(sample.CNSet, predictRegion=pr)
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 dim(pp)
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+
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+## multiple batches
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+data(sample.CNSet2)
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+pr <- predictionRegion(sample.CNSet2, copyNumber=0:4)
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+pp <- posteriorProbability(sample.CNSet2, predictRegion=pr)
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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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@@ -36,10 +36,10 @@ predictionRegion(object, copyNumber)
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   A list named by the genotype.  `NULL' refers to copy number zero, `A'
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   is a hemizygous deletion, etc. Each element is a list of the means
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-  (mu) and covariance (cov) for each marker.  The covariance for each
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-  marker is stored as a vector in the order variance A, correlation,
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-  variance B. For nonpolymorphic markers, only the first mu and the
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-  first variance are used.
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+  (mu) and covariance (cov) for each marker stored as an array.  For
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+  `mu', the dimensions of the array are marker x allele (A or B) x
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+  batch.  For `cov', the dimensions of the array are marker x 3
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+  (varA, cor, and varB) x batch.
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 }
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