@@ -346,3 +346,7 @@ is decoded and scanned

       removed inadvertantly in version 1.3.7, put back]

  * removed header checking from readIdatFiles() (seems to fail often).  

       Instead check that the number of SNPs agrees (to within +/- 10K SNPs)

+

+2009-12-04 B. Carvalho - committed version 1.5.11

+

+ * moved IRanges and oligoClasses to Depends (DESCRIPTION)

@@ -1,20 +1,20 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

-Version: 1.5.10

+Version: 1.5.11

 Date: 2009-12-03

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms

 License: Artistic-2.0

-Depends: methods, Biobase (>= 2.5.5), R (>= 2.10.0)

-Imports: affyio, preprocessCore, utils, stats, genefilter, splines, mvtnorm, oligoClasses (>= 1.9.9), ellipse, methods, SNPchip, oligoClasses, VanillaICE (>= 1.9.1), IRanges

+Depends: methods, Biobase (>= 2.5.5), R (>= 2.10.0), oligoClasses (>= 1.9.14), IRanges

+Imports: affyio, preprocessCore, utils, stats, genefilter, splines, mvtnorm, ellipse, methods, SNPchip, oligoClasses, VanillaICE (>= 1.9.1)

 Suggests: hapmapsnp5, hapmapsnp6, genomewidesnp5Crlmm (>= 1.0.2),genomewidesnp6Crlmm (>= 1.0.2), snpMatrix

 Collate: AllGenerics.R

+         methods-AlleleSet.R

 	 methods-CNSet.R

 	 methods-eSet.R

          methods-SnpSuperSet.R

-        methods-AlleleSet.R

          cnrma-functions.R

          crlmm-functions.R

          crlmm-illumina.R

@@ -5,33 +5,30 @@ useDynLib("crlmm", .registration=TRUE)

 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet,

 		  SnpSet, NChannelSet, MIAME, Versioned, VersionedBiobase, Versions)

-importMethodsFrom(Biobase, annotation, "annotation<-", annotatedDataFrameFrom,

-                  assayData, "assayData<-", combine, dims,

-                  experimentData, "experimentData<-",

+importMethodsFrom(Biobase, annotation, "annotation<-",

+                  annotatedDataFrameFrom, assayData, "assayData<-",

+                  combine, dims, experimentData, "experimentData<-",

                   fData, featureData, "featureData<-", featureNames,

-                  fvarMetadata, fvarLabels,

-                  pData, phenoData, "phenoData<-", protocolData, "protocolData<-",

-                  pubMedIds, rowMedians, sampleNames,

-                  storageMode, "storageMode<-", updateObject, varLabels)

+                  fvarMetadata, fvarLabels, pData, phenoData,

+                  "phenoData<-", protocolData, "protocolData<-",

+                  pubMedIds, rowMedians, sampleNames, storageMode,

+                  "storageMode<-", updateObject, varLabels)

 importFrom(Biobase, assayDataElement, assayDataElementNames,

            assayDataElementReplace, assayDataNew, classVersion, validMsg)

 ## oligoClasses

+importFrom(oligoClasses, position, chromosome)

 importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet)

-importMethodsFrom(oligoClasses, 

-				 allele,

-                                 calls, "calls<-",  

-          			 confs, "confs<-",

-				 cnConfidence, "cnConfidence<-", 

-				 copyNumber)

-importFrom("oligoClasses", "position")

-importFrom("oligoClasses", "chromosome")

+

+importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,

+                  "confs<-", cnConfidence, "cnConfidence<-", copyNumber)

+

 ## IRanges

-importClassesFrom(IRanges, "RangedData", "IRanges")

-importMethodsFrom(IRanges, Rle, start, end, width, runValue)

-importFrom(IRanges, IRanges, RleList, RangedData)

+importClassesFrom(IRanges, RangedData, IRanges)

+importFrom(IRanges, IRanges, RleList, RangedData, width)

+importMethodsFrom(IRanges, Rle, start, end, runValue)

 ##importMethodsFrom(methods, initialize, show)

@@ -72,7 +69,9 @@ exportMethods(chromosome, position)

 export(

        celDates, 

       crlmm, 

-       cnOptions, 

+       cnOptions,

+       calls,

+       "calls<-",

        confs,

        "confs<-",

        copyNumber, 

@@ -1,3 +1,7 @@

+## IMPORTANT 

+- move IRanges and oligoClasses back to Suggests? BC moved them to

+Depends just to get rid of annoying warnings while transitioning.

+

 #####################################

 ### FOR CRLMM

 #####################################

similarity index 59%

rename from man/SnpQSet-methods.Rd

rename to man/AlleleSet-methods.Rd

@@ -1,18 +1,19 @@

-\name{SnpQSet-methods}

+\name{AlleleSet-methods}

+\docType{methods}

 \alias{A}

-\alias{A,SnpQSet-method}

+\alias{A,AlleleSet-method}

 \alias{A<-}

-\alias{A<-,SnpQSet,matrix-method}

+\alias{A<-,AlleleSet,matrix-method}

 \alias{B}

-\alias{B,SnpQSet-method}

+\alias{B,AlleleSet-method}

 \alias{B<-}

-\alias{B<-,SnpQSet,matrix-method}

+\alias{B<-,AlleleSet,matrix-method}

 \alias{isSnp}

-\alias{isSnp,SnpQSet-method}

+\alias{isSnp,AlleleSet-method}

 \title{Indicator for polymorphic probes}

 \description{

-  This functions uses the annotation slot of the SnpQSet object to load

+  This functions uses the annotation slot of the AlleleSet object to load

   the corresponding annotation package and determine whether each probe

   in the object interrogates a polymorphic or nonpolymorphic allele. For

   instance, in the Affy 6.0 platform roughly 900,000 of the 1.8 million

@@ -20,10 +21,12 @@

 }

 \usage{

+A(object)

+B(object)

 isSnp(object)

 }

 \arguments{

-  \item{object}{SnpQSet object}

+  \item{object}{AlleleSet object}

 }

 \value{

   an indicator: 0=nonpolymorphic, 1=polymorphic

@@ -63,10 +63,6 @@ Class \code{"\linkS4class{Versioned}"}, by class "SnpCallSetPlus", distance 6.

 	 }

 }

 \author{R. Scharpf}

-\seealso{

-%	~~objects to See Also as \code{\link{~~fun~~}}, ~~~

-%	or \code{\linkS4class{CLASSNAME}} for links to other classes

-}

 \examples{

 showClass("CNSet")

 }

@@ -3,9 +3,9 @@

 %\alias{calls}

 \alias{calls,SnpSet-method}

 \alias{calls<-,SnpSet,matrix-method}

-\alias{confs}

+%\alias{confs}

 \alias{confs,SnpSet-method}

-\alias{confs<-}

+%\alias{confs<-}

 \alias{confs<-,SnpSet,matrix-method}

 \title{Accessors for Calls and Confidences on a SnpSet object}

@@ -1,7 +1,7 @@

 \name{methods-eSet}

-\alias{chromosome}

+%%\alias{chromosome}

 \alias{chromosome,eSet-method}

-\alias{position}

+%%\alias{position}

 \alias{position,eSet-method}

 \title{Methods for eSet derivatives}