@@ -319,4 +319,10 @@ is decoded and scanned

  - ABset and CrlmmSetList classes are gone. Using SnpCallSetPlus and CrlmmSet

  - Added class SegmentSet that extends CrlmmSet directly.

+2009-11-15 B Carvalho - committed version 1.5.4

+

+ * removed references to old C code

+ * added the missing files to the Collate field

+ * fixed classes imported from oligoClasses in NAMESPACE

+ * imported 'calls<-' from oligoClasses

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

 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: 1.5.3

+Version: 1.5.4

 Date: 2009-11-15

 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>

@@ -12,11 +12,14 @@ Imports: affyio, preprocessCore, utils, stats, genefilter, splines, mvtnorm, oli

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

 Collate: AllClasses.R

 	 AllGenerics.R

-	 methods-ABset.R

 	 methods-CopyNumberSet.R

-	 methods-CrlmmSetList.R

+         methods-CrlmmSet.R

+         methods-CrlmmSetFF.R

 	 methods-eSet.R

+         methods-SnpCallSetPlus.R

+         methods-SnpCallSetPlusFF.R

          methods-SnpSet.R

+         methods-SnpQSet.R

          cnrma-functions.R

          crlmm-functions.R

          crlmm-illumina.R

@@ -5,7 +5,7 @@ useDynLib("crlmm", .registration=TRUE)

 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet,

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

-importClassesFrom(oligoClasses, SnpLevelSet)

+importClassesFrom(oligoClasses, SnpLevelSet, SnpQSet, SnpCallSet, SnpCallSetPlus, QuantificationSet)

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

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

@@ -16,9 +16,7 @@ importMethodsFrom(Biobase, annotation, "annotation<-", annotatedDataFrameFrom,

                   pubMedIds, rowMedians, sampleNames,

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

-

-##importMethodsFrom(oligoClasses, chromosome, copyNumber, position)

-importMethodsFrom(oligoClasses, chromosome, copyNumber, position, calls)

+importMethodsFrom(oligoClasses, chromosome, copyNumber, position, calls, "calls<-")

 ##importMethodsFrom(methods, initialize, show)

@@ -3,20 +3,11 @@

 #include "crlmm.h"

 static const R_CallMethodDef CallEntries[] = {

-    {"test", (DL_FUNC)&test, 1},

-    {"gtypeCallerPart1nm", (DL_FUNC)&gtypeCallerPart1nm, 17},

-    {"gtypeCallerPart2nm", (DL_FUNC)&gtypeCallerPart2nm, 19},

-    {"gtypeCallerPart1NormalNoN", (DL_FUNC)&gtypeCallerPart1NormalNoN, 17},

     {"gtypeCallerPart1", (DL_FUNC)&gtypeCallerPart1, 17},

     {"gtypeCallerPart2", (DL_FUNC)&gtypeCallerPart2, 19},

-    {"gtypeCallerPart1TNoN", (DL_FUNC)&gtypeCallerPart1TNoN, 17},

-    {"gtypeCallerPart2TNoN", (DL_FUNC)&gtypeCallerPart2TNoN, 19},

     {NULL, NULL, 0}

 };

 void R_init_crlmm(DllInfo *dll){

     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);    

 }

-

-

-