@@ -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: 1.5.13

+Version: 1.5.14

 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>

@@ -1,8 +1,9 @@

 useDynLib("crlmm", .registration=TRUE)

 ## Biobase

-importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet,

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

+importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,

+		  NChannelSet, MIAME, Versioned, VersionedBiobase,

+		  Versions)

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

                   annotatedDataFrameFrom, assayData, "assayData<-",

@@ -12,25 +13,25 @@ importMethodsFrom(Biobase, annotation, "annotation<-",

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

                   pubMedIds, rowMedians, sampleNames, storageMode,

                   "storageMode<-", updateObject, varLabels)

+

 importFrom(Biobase, assayDataElement, assayDataElementNames,

-           assayDataElementReplace, assayDataNew, classVersion, validMsg)

+           assayDataElementReplace, assayDataNew, classVersion,

+           validMsg)

 ## oligoClasses

 importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet)

-importMethodsFrom(oligoClasses, 

-		  allele,

-                  calls, "calls<-",  

-          	  confs, "confs<-",

-	          cnConfidence, "cnConfidence<-", 

-		  copyNumber, isSnp, chromosome, position, CA, "CA<-", CB, "CB<-",

-		  rangedData, segmentData, "rangedData<-", "segmentData<-")

-importFrom(oligoClasses, chromosome2integer, celfileDate)

+

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

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

+		  isSnp, chromosome, position, CA, "CA<-", CB, "CB<-",

+		  rangedData, segmentData, "rangedData<-",

+		  "segmentData<-")

+

+importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles)

 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,

            polygon, rect, segments, text, points, boxplot)

-importFrom(stats, update)

-

 importFrom(grDevices, grey)

 importFrom(affyio, read.celfile.header, read.celfile)

@@ -39,7 +40,7 @@ importFrom(preprocessCore, normalize.quantiles.use.target, normalize.quantiles)

 importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)

-importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd)

+importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd, update)

 importFrom(genefilter, rowSds)

@@ -47,12 +48,8 @@ importFrom(mvtnorm, dmvnorm)

 importFrom(ellipse, ellipse)

-export(celDates,  ##move to oligoClasses

-       crlmm, 

-       cnOptions,

-       calls,

-       "calls<-",

-     snprma)

+## move to oligoClasses

+export(celDates, crlmm, cnOptions, calls, "calls<-", snprma)

 ##exportMethods(computeHmm) ##move to VanillaICE

 exportMethods(A, B, copyNumber)

@@ -66,6 +63,3 @@ export(##viterbi.CNSet, ##move to VanillaICE

 	readIdatFiles,

         withinGenotypeMoments,  

 	locationAndScale, getParam.SnpSuperSet)

-

-

-