Browse code

Fixed NAMESPACE

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43637 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 19/12/2009 01:07:55
Showing 2 changed files

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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.5.13
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+Version: 1.5.14
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 Date: 2009-12-03
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 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>
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 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -1,8 +1,9 @@
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 useDynLib("crlmm", .registration=TRUE)
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 ## Biobase
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-importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet,
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-		  SnpSet, NChannelSet, MIAME, Versioned, VersionedBiobase, Versions)
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+importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
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+		  NChannelSet, MIAME, Versioned, VersionedBiobase,
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+		  Versions)
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 importMethodsFrom(Biobase, annotation, "annotation<-",
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                   annotatedDataFrameFrom, assayData, "assayData<-",
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@@ -12,25 +13,25 @@ importMethodsFrom(Biobase, annotation, "annotation<-",
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                   "phenoData<-", protocolData, "protocolData<-",
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                   pubMedIds, rowMedians, sampleNames, storageMode,
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                   "storageMode<-", updateObject, varLabels)
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+
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 importFrom(Biobase, assayDataElement, assayDataElementNames,
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-           assayDataElementReplace, assayDataNew, classVersion, validMsg)
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+           assayDataElementReplace, assayDataNew, classVersion,
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+           validMsg)
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 ## oligoClasses
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 importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet)
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-importMethodsFrom(oligoClasses, 
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-		  allele,
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-                  calls, "calls<-",  
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-          	  confs, "confs<-",
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-	          cnConfidence, "cnConfidence<-", 
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-		  copyNumber, isSnp, chromosome, position, CA, "CA<-", CB, "CB<-",
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-		  rangedData, segmentData, "rangedData<-", "segmentData<-")
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-importFrom(oligoClasses, chromosome2integer, celfileDate)
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+
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+importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
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+		  "confs<-", cnConfidence, "cnConfidence<-", copyNumber,
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+		  isSnp, chromosome, position, CA, "CA<-", CB, "CB<-",
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+		  rangedData, segmentData, "rangedData<-",
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+		  "segmentData<-")
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+
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+importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles)
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 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
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            polygon, rect, segments, text, points, boxplot)
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-importFrom(stats, update)
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-
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 importFrom(grDevices, grey)
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 importFrom(affyio, read.celfile.header, read.celfile)
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@@ -39,7 +40,7 @@ importFrom(preprocessCore, normalize.quantiles.use.target, normalize.quantiles)
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 importFrom(utils, data, packageDescription, setTxtProgressBar, txtProgressBar)
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-importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd)
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+importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile, sd, update)
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 importFrom(genefilter, rowSds)
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@@ -47,12 +48,8 @@ importFrom(mvtnorm, dmvnorm)
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 importFrom(ellipse, ellipse)
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-export(celDates,  ##move to oligoClasses
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-       crlmm, 
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-       cnOptions,
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-       calls,
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-       "calls<-",
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-     snprma)
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+## move to oligoClasses
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+export(celDates, crlmm, cnOptions, calls, "calls<-", snprma)
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 ##exportMethods(computeHmm) ##move to VanillaICE
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 exportMethods(A, B, copyNumber)
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@@ -66,6 +63,3 @@ export(##viterbi.CNSet, ##move to VanillaICE
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 	readIdatFiles,
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         withinGenotypeMoments,  
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 	locationAndScale, getParam.SnpSuperSet)
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-
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-
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-