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NAMESPACE
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NAMESPACE
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useDynLib("crlmm", .registration=TRUE)
importClassesFrom(Biobase, AssayData, eSet)
##importClassesFrom(methods, ANY, character, formula, integer, list,
## matrix, oldClass)
##importMethodsFrom(methods, initialize, show)
import(methods)
##importFrom(methods, setOldClass)
##importFrom(methods, as, callNextMethod, is, new, validObject)
##importFrom(methods, callNextMethod, new, validObject, coerce)
importFrom(RcppEigen, fastLmPure)
## importClassesFrom(oligoClasses, CNSet, CNSetLM, ff_matrix,
## ff_or_matrix, oligoSnpSet)
importClassesFrom(oligoClasses, CNSet, oligoSnpSet, ff_or_matrix, GenomeAnnotatedDataFrame)
##setOldClass(ff_or_matrix)
import(matrixStats)
importMethodsFrom(Biobase, annotatedDataFrameFrom, annotation,
AnnotatedDataFrame, assayData, experimentData, featureData,
"featureData<-", featureNames, "featureNames<-",
pData, "pData<-", phenoData, "phenoData<-",
protocolData, "protocolData<-",
sampleNames, snpCall, "snpCall<-",
snpCallProbability, "snpCallProbability<-",
storageMode, "storageMode<-", varLabels)
importMethodsFrom(BiocGenerics, cbind, colnames, Filter, get,
intersect, lapply, ncol, NCOL, nrow, NROW, order,
paste, pmax, pmin, rbind, rownames, sapply, setdiff,
table, union, unique)
##importMethodsFrom(genefilter, show)
importMethodsFrom(oligoClasses, A, "A<-", B, batch, batchNames,
batchStatistics, "batchStatistics<-", calls,
chromosome, close, confs, flags, isSnp, mean, nu,
open, phi, "sampleNames<-")
importFrom(affyio, read.celfile, read.celfile.header)
importFrom(illuminaio, readIDAT)
importFrom(Biobase, assayDataElement, assayDataElementReplace,
assayDataNew, copyEnv)
importFrom(ellipse, ellipse)
##importFrom(genefilter, rowSds)
importFrom(lattice, lpolygon, panel.grid, panel.number, panel.xyplot,
xyplot)
##importFrom(methods, as, callNextMethod, is, new, validObject)
importFrom(mvtnorm, rmvnorm)
importFrom(oligoClasses, celfileDate, chromosome2integer, i2p,
initializeBigMatrix, initializeBigVector, integerMatrix,
isPackageLoaded, ldPath, ocLapply, ocProbesets, ocSamples,
parStatus, splitIndicesByLength, splitIndicesByNode,
AssayDataList, genomeBuild, celfileName)
importFrom(preprocessCore, normalize.quantiles, normalize.quantiles.determine.target,
normalize.quantiles.use.target, subColSummarizeMedian)
importFrom(stats, coef, cov, dnorm, kmeans, lm, mad, median, quantile,
sd)
importFrom(utils, packageDescription, setTxtProgressBar,
txtProgressBar)
importFrom(graphics, plot, smoothScatter, abline)
importFrom(beanplot, beanplot)
## foreach
import(foreach)
importFrom(VGAM, vglm, multinomial, coefficients)
importFrom(parallel, makeCluster, detectCores, parRapply, stopCluster, clusterEvalQ, parCapply)
importFrom(limma, loessFit)
importFrom(ff, delete)
##----------------------------------------------------------------------------
## export
##----------------------------------------------------------------------------
exportClasses(PredictionRegion)
exportMethods(CA, CB,
A, B, corr, nuA, nuB, phiA, phiB,
predictionRegion, posteriorProbability,
tau2, Ns, medians, mads,
xyplot, calculateRBaf, OligoSetList,
BafLrrSetList)
export(crlmm,
crlmmIllumina,
constructAffyCNSet,
genotype,
genotypeAffy,
readIdatFiles,
readGenCallOutput,
snprma,
snprma2,
cnrmaAffy,
snprmaAffy,
crlmm2,
genotype2, genotypeLD,
genotypeAffy,
genotype.Illumina,
plotSamples, plotSNPs,
crlmmCopynumber2, crlmmCopynumberLD, crlmmCopynumber)
export(genotypes, totalCopynumber, rawCopynumber, xyplot)
export(ABpanel, validCEL, celDates, validCdfNames)
##export(constructOligoSetListFrom, constructBafLrrSetListFrom)