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