1. crlmm
  2. man
  3. batchStatisticAccessors.Rd
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/batchStatisticAccessors.Rd
History View file @ cceffc9
... ... 
@@ -73,11 +73,11 @@ 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.CNSet)
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-Ns(sample.CNSet)[1:5, , ]
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-corr(sample.CNSet)[1:5, , ]
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-meds <- medians(sample.CNSet)
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-mads(sample.CNSet)[1:5, , ,]
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-tau2(sample.CNSet)[1:5, , ,]
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+data(cnSetExample)
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+Ns(cnSetExample)[1:5, , ]
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+corr(cnSetExample)[1:5, , ]
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+meds <- medians(cnSetExample)
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+mads(cnSetExample)[1:5, , ,]
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+tau2(cnSetExample)[1:5, , ,]
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 }
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 \keyword{manip}
Browse code

Update batchStatisticAccessors.Rd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58647 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2011 04:48:44
Showing 1 changed files
man/batchStatisticAccessors.Rd
History View file @ 1f86c51
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@@ -28,16 +28,12 @@ Ns(object,...)
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 \arguments{
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   \item{object}{  An object of class \code{CNSet}.}
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-  \item{\dots}{
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-  An additional argument named 'i' can be passed to subset the markers
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-  and an argument 'j' can be passed to subset the batches.  Other
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-  arguments are ignored.
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-  }
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+  \item{\dots}{Ignored}
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 }
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 \value{
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-
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-An array with dimension R x A x G x C, or R x G x C.
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+
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+An array with dimension R x A x G x C, or R x G x C.
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 R: number of markers
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 A: number of alleles (2)
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@@ -78,11 +74,10 @@ log-scale the variance is rougly constant for CA, CB > 0).
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 \examples{
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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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-mads(cnSet, i=1:5, j=1:2)
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-tau2(cnSet, i=1:5, j=1:2)
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+Ns(sample.CNSet)[1:5, , ]
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+corr(sample.CNSet)[1:5, , ]
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+meds <- medians(sample.CNSet)
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+mads(sample.CNSet)[1:5, , ,]
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+tau2(sample.CNSet)[1:5, , ,]
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 }
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 \keyword{manip}
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
Showing 1 changed files
man/batchStatisticAccessors.Rd
History View file @ fd149ed
... ... 
@@ -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)
Browse code

changed copynumber vignette to call genotype, not genotypeLD.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@49145 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/08/2010 19:41:17
Showing 1 changed files
man/batchStatisticAccessors.Rd
History View file @ 46b837e
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new file mode 100644
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+\name{batchStatisticAccessors}
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+\alias{Ns}
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+\alias{corr}
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+\alias{tau2}
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+\alias{mads}
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+\alias{medians}
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+
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+\title{
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+
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+	Accessors for batch-specific summary statistics.
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+
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+}
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+
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+\description{
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+
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+	The summary statistics stored here are used by the tools for
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+	copy number estimation.
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+
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+}
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+
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+\usage{
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+corr(object, ...)
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+tau2(object, ...)
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+mads(object,...)
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+medians(object,...)
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+Ns(object,...)
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+}
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+
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+\arguments{
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+  \item{object}{  An object of class \code{CNSet}.}
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+  \item{\dots}{
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+  An additional argument named 'i' can be passed to subset the markers
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+  and an argument 'j' can be passed to subset the batches.  Other
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+  arguments are ignored.
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+  }
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+}
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+
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+\value{
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+
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+An array with dimension R x A x G x C, or R x G x C.
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+
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+R: number of markers
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+A: number of alleles (2)
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+G: number of biallelic genotypes (3)
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+C: number of batches
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+
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+\code{Ns} returns an array of genotype frequencies stratified by
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+batch.  Dimension R x G x C.
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+
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+\code{corr} returns an array of within-genotype correlations
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+(log2-scale) stratified by batch. Dimension R x G x C.
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+
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+\code{medians} returns an array of the within-genotype medians
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+(intensity-scale) stratified by batch and allele. Dimension R x A x G
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+x C.
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+
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+\code{mads} returns an array of the within-genotype median absolute
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+deviations (intensity-scale) stratified by batch and allele. Dimension
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+is the same as for \code{medians}.
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+
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+\code{tau2} returns an array of the squared within-genotype median
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+absolute deviation on the log-scale.  Only the mads for AA and BB
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+genotypes are stored.  Dimension is R x A x G x C, where G is AA or
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+BB.  Note that the mad for allele A/B for subjects with genotype BB/AA
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+is a robust estimate of the background variance, whereas the the mad
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+for allele A/B for subjects with genotype AA/BB is a robust estimate
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+of the variance for copy number greater than 0 (we assume that on the
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+log-scale the variance is rougly constant for CA, CB > 0).
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+
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+}
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+
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+
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+\seealso{
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+
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+	\code{\link{batchStatistics}}
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+
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+}
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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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+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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+mads(cnSet, i=1:5, j=1:2)
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+tau2(cnSet, i=1:5, j=1:2)
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+}
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+\keyword{manip}