| 687883a0 |
useDynLib("crlmm", .registration=TRUE)
|
| a3335242 |
## this is temporary
|
| 1507ac0c |
## exportPattern("^[^\\.]")
|
| a3335242 |
|
| 6a6b67c5 |
##---------------------------------------------------------------------------
|
| 96d10c6e |
## Biobase
|
| 6a6b67c5 |
##---------------------------------------------------------------------------
|
| 115ec6a8 |
importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet, SnpSet,
NChannelSet, MIAME, Versioned, VersionedBiobase,
Versions)
|
| 824cfde4 |
importMethodsFrom(Biobase, annotation, "annotation<-",
annotatedDataFrameFrom, assayData, "assayData<-",
combine, dims, experimentData, "experimentData<-",
|
| 38fb1b80 |
fData, featureData, "featureData<-", featureNames,
|
| d5bc779e |
fvarMetadata, fvarLabels, pData, "pData<-", phenoData,
|
| 824cfde4 |
"phenoData<-", protocolData, "protocolData<-",
|
| afb508f9 |
pubMedIds, rowMedians, sampleNames, snpCall,
snpCallProbability,
"snpCall<-", "snpCallProbability<-", storageMode,
|
| 824cfde4 |
"storageMode<-", updateObject, varLabels)
|
| 96d10c6e |
importFrom(Biobase, assayDataElement, assayDataElementNames,
|
| 115ec6a8 |
assayDataElementReplace, assayDataNew, classVersion,
validMsg)
|
| 96d10c6e |
|
| 6a6b67c5 |
##---------------------------------------------------------------------------
|
| 96d10c6e |
## oligoClasses
|
| 6a6b67c5 |
##---------------------------------------------------------------------------
|
| 1c2a3f47 |
importClassesFrom(oligoClasses, SnpSuperSet, AlleleSet, CNSet)
|
| 5fcfed7d |
importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
|
| 9ac2da3a |
"confs<-", cnConfidence, "cnConfidence<-", isSnp,
|
| 481f4705 |
chromosome, position, A, B,
|
| 66900fea |
"A<-", "B<-", open, close, flags,
|
| 6846d583 |
batchStatistics, "batchStatistics<-", updateObject)
|
| 9ac2da3a |
importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
|
| 4c729c33 |
copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
|
| 7ae22f52 |
|
| 69ec8644 |
|
| 38fb1b80 |
importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
|
| b9ad9e2b |
polygon, rect, segments, text, points, boxplot, lines)
|
| 38fb1b80 |
importFrom(grDevices, grey)
|
| 04bd5f4c |
importFrom(affyio, read.celfile.header, read.celfile)
|
| 5fcfed7d |
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, update)
|
| eb5b9c72 |
importFrom(genefilter, rowSds)
|
| c255087e |
importFrom(mvtnorm, dmvnorm)
|
| 38fb1b80 |
importFrom(ellipse, ellipse)
|
| 56b783ec |
importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)
|
| 0198a9ad |
## It is important not to import these classes from oligoClasses
## Doing so causes the following errors:
## N.AA(container)[index, ] <- someMatrix
##Error in function (classes, fdef, mtable) :
## unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"
##importClassesFrom(oligoClasses, ffdf, ff_matrix)
|
| 94bdc2e6 |
importClassesFrom(oligoClasses, ff_matrix, ffdf)
|
| 0198a9ad |
## Important to export these classes
|
| 56b783ec |
##exportClasses(ff_or_matrix, ff_matrix, ffdf)
|
| 7799caf6 |
##exportClasses(ff_or_matrix)
|
| 0198a9ad |
exportMethods(lines)
exportMethods(CA, CB)
export(crlmm,
crlmmIllumina,
crlmmIlluminaV2,
genotype,
readIdatFiles,
|
| f0da6921 |
snprma,
snprma2,
|
| d5bc779e |
crlmm2,
|
| 3e4db4b1 |
genotype2, genotypeLD,
|
| 137e5619 |
genotype.Illumina,
|
| 3e4db4b1 |
crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
export(constructIlluminaCNSet)
export(totalCopynumber)
exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)
|
| 73fd7374 |
##export(summarizeNps, genotypeSummary, fit.lm2)
|
