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check that batch length is same as length of filenames in constructAffy. Add additional documentation for CNSet class man page.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@55178 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/04/2011 01:49:59
Showing4 changed files

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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: 1.11.0
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+Version: 1.11.1
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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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@@ -100,6 +100,7 @@ construct <- function(filenames,
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 }
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 constructAffy <- function(filenames, sns, cdfName, batch, verbose=TRUE){
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+	stopifnot(length(sns)==length(batch))
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 	is.lds <- ifelse(isPackageLoaded("ff"), TRUE, FALSE)
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 	if(!is.lds) stop("this function now requires that the ff package be loaded")
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 	if(missing(cdfName)) stop("must specify cdfName")
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@@ -21,12 +21,20 @@
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 \section{Methods}{
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   \describe{
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-    \item{Ns}{\code{signature(object="AssayData")}: ...}
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-    \item{corr}{\code{signature(object="AssayData")}: ...}
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-    \item{mads}{\code{signature(x="AssayData")}: ...}
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-    \item{medians}{\code{signature(object="AssayData")}: ...}
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-    \item{tau2}{\code{signature(object="AssayData")}: ...}
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-	 }
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+    \item{Ns}{\code{signature(object="AssayData")}:  Accessor for genotype
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+  frequencies}
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+    \item{corr}{\code{signature(object="AssayData")}: Accessor for the correlation of the
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+  log-transformed normalized intensities within the diallelic genotype clusters}
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+    \item{mads}{\code{signature(x="AssayData")}: Accessor for the median
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+  absolute deviation of the  normalized intensities within the
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+  diallelic genotype clusters }
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+    \item{medians}{\code{signature(object="AssayData")}: Accessor for
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+  the posterior mean of the normalized intensity within the diallelic genotype
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+  clusters.}
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+    \item{tau2}{\code{signature(object="AssayData")}: Accessor for the
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+  median absolute deviation of the log-transformed intensities within
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+  the diallelic genotype clusters}
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+  }
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 }
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 \seealso{
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@@ -33,17 +33,24 @@
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 \section{Methods}{
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   \describe{
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-    \item{CA}{\code{signature(object="CNSet")}: ...}
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-    \item{CB}{\code{signature(object="CNSet")}: ...}
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-    \item{lines}{\code{signature(x="CNSet")}: ...}
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-    \item{totalCopynumber}{\code{signature(object="CNSet")}: ...}
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-    \item{rawCopynumber}{\code{signature(object="CNSet")}: ...}
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-    \item{nuA}{\code{signature(object="CNSet")}: ...}
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-    \item{nuB}{\code{signature(object="CNSet")}: ...}
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-    \item{phiA}{\code{signature(object="CNSet")}: ...}
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-    \item{phiB}{\code{signature(object="CNSet")}: ...}
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-    \item{Ns}{\code{signature(object="CNSet")}: ...}
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-    \item{corr}{\code{signature(object="CNSet")}: ...}
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+    \item{CA}{\code{signature(object="CNSet")}: calculates raw copy number
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+  for allele A}
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+    \item{CB}{\code{signature(object="CNSet")}: calculates raw copy
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+  number for allele B}
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+    \item{lines}{\code{signature(x="CNSet")}: plot ellipses (95th
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+  percentile) for prediction regions}
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+    \item{totalCopynumber}{\code{signature(object="CNSet")}: calculates
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+  total raw copy number}
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+    \item{rawCopynumber}{\code{signature(object="CNSet")}: same as totalCopynumber}
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+    \item{nuA}{\code{signature(object="CNSet")}: estimate of mean
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+  background (intensity-scale) for allele A}
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+    \item{nuB}{\code{signature(object="CNSet")}: estimate of mean
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+  background (intensity-scale) for allele A}
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+    \item{phiA}{\code{signature(object="CNSet")}: estimate of slope coefficient (intensity-scale) for allele A}
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+    \item{phiB}{\code{signature(object="CNSet")}: estimate of slope coefficient (intensity-scale) for allele B}
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+    \item{Ns}{\code{signature(object="CNSet")}: genotype frequencies }
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+    \item{corr}{\code{signature(object="CNSet")}: correlation of
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+  log-transformed normalized intensities within the genotype clusters}
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     \item{mads}{\code{signature(x="CNSet")}: ...}
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     \item{medians}{\code{signature(object="CNSet")}: ...}
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     \item{tau2}{\code{signature(object="CNSet")}: ...}