#### Update to NEWS

Benilton Carvalho authored on 31/03/2011 10:24:57
Showing 1 changed files
 ... ... @@ -1,8 +1,7 @@ 1 1  \name{NEWS} 2 2  \title{News for Package 'crlmm'} 3 3   4 - 5 -\section{Changes in version 1.9}{ 4 +\section{Changes in version 1.10}{ 6 5  \subsection{USER VISIBLE CHANGES}{ 7 6  \itemize{ 8 7  \item Using NEWS.Rd

#### provide some news for v1.8 of crlmm

Rob Scharp authored on 31/03/2011 00:40:56
Showing 1 changed files
 ... ... @@ -37,6 +37,27 @@ 37 37  } 38 38  } 39 39   40 +\section{Changes in version 1.8}{ 41 + \subsection{USER VISIBLE CHANGES}{ 42 + \itemize{ 43 + 44 + \item define CNSet class with batch and batchStatistics slots 45 + 46 + \item deprecate CNSetList class 47 + 48 + \item deprecate crlmmWrapper, genotype2, and crlmmCopynumber2. 49 + Use crlmmCopynumber in place of crlmmWrapper and crlmmCopynumber2. 50 + Use genotype instead of genotype2. 51 + 52 + \item raw copy number estimates no longer stored in container. CA 53 + and CB methods are no longer simple accessors to data stored in 54 + the eset-extension. These functions compute raw copy number 55 + estimates from the linear model parameters. 56 + 57 + } 58 + } 59 +} 60 + 40 61  \section{Changes in version 1.3}{ 41 62  \subsection{USER VISIBLE CHANGES}{ 42 63  \itemize{

#### update news

Rob Scharp authored on 30/03/2011 19:27:43
Showing 1 changed files
 ... ... @@ -16,15 +16,19 @@ 16 16  \item We have added several vignettes pertaining to copy number 17 17  analyses in the crlmm package: CopyNumberOverview, 18 18  AffymetrixPreprocessCN, IlluminaPreprocessCN, and Infrastructure. 19 + The AffymetrixPreprocessCN and IlluminaPreprocessCN vignettes 20 + provide instructions for preprocessing and genotyping the raw 21 + intensities for Affymetrix and Illumina platforms, respectively. 19 22  The 'copynumber' and 'Infrastructure' vignettes are applicable to 20 23  both the Illumina and Affymetrix platforms. The CopyNumberOverview 21 - vignette gives a brief summary of the available vignettes for copy 22 - number analyses. 24 + vignette provides a brief summary of the available vignettes for 25 + copy number analysis. 23 26   24 - \item Exporting function constructInf, preprocessInf, and 25 - genotypeInf for preprocessing and genotyping Illumina files prior 26 - to copy number analyses. The genotype.Illumina function is now a 27 - wrapper for these functions. 27 + \item For those interested in copy number analysis of Illumina 28 + platforms, we added functions that break-down the preprocessing 29 + and genotyping steps: constructInf, preprocessInf, and 30 + genotypeInf. The genotype.Illumina function is now a wrapper for 31 + these functions. 28 32   29 33  \item additional documentation for crlmm is provided in a 30 34  compendium: http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html

#### genotype function is a wrapper for constructAffy, snprmaAffy, cnrmaAffy, and genotypeAffy. the *Affy functions are not currently exported.

 ... ... @@ -1,10 +1,34 @@ 1 1  \name{NEWS} 2 2  \title{News for Package 'crlmm'} 3 3   4 -\section{Changes in version 1.10}{ 4 + 5 +\section{Changes in version 1.9}{ 5 6  \subsection{USER VISIBLE CHANGES}{ 6 7  \itemize{ 7 8  \item Using NEWS.Rd 9 + 10 + \item batch slot in CNSet objects is class 'character' 11 + (previously, class was 'factor') 12 + 13 + \item the ff package is required for preprocessing and genotyping 14 + prior to copy number analyses with the crlmmCopynumber function. 15 + 16 + \item We have added several vignettes pertaining to copy number 17 + analyses in the crlmm package: CopyNumberOverview, 18 + AffymetrixPreprocessCN, IlluminaPreprocessCN, and Infrastructure. 19 + The 'copynumber' and 'Infrastructure' vignettes are applicable to 20 + both the Illumina and Affymetrix platforms. The CopyNumberOverview 21 + vignette gives a brief summary of the available vignettes for copy 22 + number analyses. 23 + 24 + \item Exporting function constructInf, preprocessInf, and 25 + genotypeInf for preprocessing and genotyping Illumina files prior 26 + to copy number analyses. The genotype.Illumina function is now a 27 + wrapper for these functions. 28 + 29 + \item additional documentation for crlmm is provided in a 30 + compendium: http://www.biostat.jhsph.edu/~rscharpf/crlmmCompendium/index.html 31 + 8 32  } 9 33  } 10 34  } ... ... @@ -37,7 +61,7 @@ 37 61  elements of this object, including featureNames, 38 62  sampleNames, and '['. 39 63  } 40 -  64 + 41 65  \item 'CopyNumberSet': contains locus-level estimates of copy 42 66  number for SNPs and polymorphic probes. 43 67  \enumerate{ ... ... @@ -47,7 +71,7 @@ 47 71   48 72  \item For nonpolymorphic probes, the total copy number is 49 73  stored in the 'CA' slot and a NA is recorded for the 50 - corresponding row in the CB matrix.  74 + corresponding row in the CB matrix. 51 75   52 76  \item Useful methods: 'copyNumber', 'ellipse', 'points' 53 77  } ... ... @@ -60,4 +84,5 @@ 60 84  'CrlmmSetList' and returns an object of class 'CopyNumberSet'. 61 85  } 62 86  } 87 + 63 88  }
 1 1 new file mode 100644 ... ... @@ -0,0 +1,63 @@ 1 +\name{NEWS} 2 +\title{News for Package 'crlmm'} 3 + 4 +\section{Changes in version 1.10}{ 5 + \subsection{USER VISIBLE CHANGES}{ 6 + \itemize{ 7 + \item Using NEWS.Rd 8 + } 9 + } 10 +} 11 + 12 +\section{Changes in version 1.3}{ 13 + \subsection{USER VISIBLE CHANGES}{ 14 + \itemize{ 15 + \item 3 new classes created: 16 + \itemize{ 17 + \item 'ABset': container for quantile-normalized A and B 18 + intensities for both SNP and copy number probes. Required 19 + assay data elements are 'A' and 'B'. Extends eSet 20 + directly. 21 + \enumerate{ 22 + \item For nonpolymorphic probes, the quantile normalized 23 + intensity is stored in the 'A' assay data element. 24 + The corresponding row in the 'B' assay data element 25 + is NA. This is a bit inefficient, but greatly 26 + simplifies downstream analyses. In particular, '[' 27 + works. 28 + } 29 + 30 + \item 'CrlmmSetList': container for results from preprocessing 31 + and genotyping. This object is a list. The first 32 + element of the list is an ABset. The second element is a 33 + SnpSet containing genotype calls. The two elements are 34 + required to have identical featureNames and sampleNames. 35 + \enumerate{ 36 + \item added several methods for subsetting and accessing 37 + elements of this object, including featureNames, 38 + sampleNames, and '['. 39 + } 40 +  41 + \item 'CopyNumberSet': contains locus-level estimates of copy 42 + number for SNPs and polymorphic probes. 43 + \enumerate{ 44 + \item Required assay data elements are 'CA' and 'CB', 45 + corresponding to the absolute copy number for allele 46 + A and B, respectively. 47 + 48 + \item For nonpolymorphic probes, the total copy number is 49 + stored in the 'CA' slot and a NA is recorded for the 50 + corresponding row in the CB matrix.  51 + 52 + \item Useful methods: 'copyNumber', 'ellipse', 'points' 53 + } 54 + } 55 + \item 'crlmmWrapper' function does preprocessing 56 + (quantile-normalization) and genotyping, saving an object of 57 + class CrlmmSetList for each chromosome 58 + 59 + \item 'computeCopynumber' now requires an object of class 60 + 'CrlmmSetList' and returns an object of class 'CopyNumberSet'. 61 + } 62 + } 63 +}