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Fixing NEWS.Rd

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@51846 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 10/01/2011 12:08:42
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+\name{NEWS}
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+\title{News for Package 'crlmm'}
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+
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+\section{Changes in version 1.10}{
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+  \subsection{USER VISIBLE CHANGES}{
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+    \itemize{
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+      \item Using NEWS.Rd
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+    }
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+  }
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+}
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+
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+\section{Changes in version 1.3}{
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+  \subsection{USER VISIBLE CHANGES}{
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+    \itemize{
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+      \item 3 new classes created:
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+      \itemize{
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+	\item 'ABset': container for quantile-normalized A and B
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+       	intensities for both SNP and copy number probes.  Required
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+       	assay data elements are 'A' and 'B'.  Extends eSet
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+       	directly.
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+	\enumerate{
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+          \item For nonpolymorphic probes, the quantile normalized
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+          intensity is stored in the 'A' assay data element.
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+          The corresponding row in the 'B' assay data element
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+          is NA.  This is a bit inefficient, but greatly
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+          simplifies downstream analyses.  In particular, '['
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+          works.
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+	}
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+
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+        \item 'CrlmmSetList': container for results from preprocessing
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+	and genotyping.  This object is a list.  The first
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+	element of the list is an ABset.  The second element is a
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+	SnpSet containing genotype calls.  The two elements are
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+	required to have identical featureNames and sampleNames.
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+	\enumerate{
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+       	  \item added several methods for subsetting and accessing
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+ 	  elements of this object, including featureNames,
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+ 	  sampleNames, and '['.
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+	}
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+	
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+        \item 'CopyNumberSet': contains locus-level estimates of copy
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+  	number for SNPs and polymorphic probes.
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+	\enumerate{
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+	  \item Required assay data elements are 'CA' and 'CB',
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+          corresponding to the absolute copy number for allele
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+          A and B, respectively.
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+
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+	  \item For nonpolymorphic probes, the total copy number is
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+          stored in the 'CA' slot and a NA is recorded for the
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+          corresponding row in the CB matrix. 
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+
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+	  \item Useful methods: 'copyNumber', 'ellipse', 'points'
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+	}
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+      }
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+      \item 'crlmmWrapper' function does preprocessing
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+      (quantile-normalization) and genotyping, saving an object of
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+      class CrlmmSetList for each chromosome
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+
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+     \item 'computeCopynumber' now requires an object of class
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+     'CrlmmSetList' and returns an object of class 'CopyNumberSet'.
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+    }
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+  }
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+}