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# methods-ChIPseqSet.R
setGeneric("ChIPseqSet", function(chipVals, rowRanges,
colData = DataFrame(row.names=colnames(chipVals)),
metadata = list(), ...)
standardGeneric("ChIPseqSet"),
signature=c("chipVals", "rowRanges"))
setGeneric("chipVals", function(object)
standardGeneric("chipVals"))
setGeneric("chipVals<-", function(object, value)
standardGeneric("chipVals<-"))
setGeneric("cpm", function(object, libSize, log2=FALSE, priorCount=0.1)
standardGeneric("cpm"),
signature="object")
# methods-MixModel.R
setGeneric("acceptanceRate", function(object)
standardGeneric("acceptanceRate"))
setGeneric("chains", function(object)
standardGeneric("chains"))
setGeneric("classification", function(object, method)
standardGeneric("classification"))
setGeneric("components", function(object)
standardGeneric("components"))
setGeneric("convergence", function(object)
standardGeneric("convergence"))
setGeneric("mmData", function(object)
standardGeneric("mmData"))
setGeneric("listClassificationMethods", function(object)
standardGeneric("listClassificationMethods"))
setGeneric("weights", function(object)
standardGeneric("weights"))
# other methods
setGeneric("calculateCrossCorrelation", function(object, shift=c(200, 250, 300), bin=10,
mode="none", minReads=10000, chrs=NA, mc.cores=1)
standardGeneric("calculateCrossCorrelation"),
signature="object")
setGeneric("bayesMixModel", function(z, normNull=c(), expNeg=c(), expPos=c(), gamNeg=c(), gamPos=c(),
sdNormNullInit=c(), rateExpNegInit=c(), rateExpPosInit=c(),
shapeGamNegInit=c(), scaleGamNegInit=c(), shapeGamPosInit=c(), scaleGamPosInit=c(),
piInit, classificationsInit, dirichletParInit=1, shapeDir=1, scaleDir=1, weightsPrior="FDD", sdAlpha,
shapeNorm0=c(), scaleNorm0=c(), shapeExpNeg0=c(), scaleExpNeg0=c(), shapeExpPos0=c(), scaleExpPos0=c(),
shapeGamNegAlpha0=c(), shapeGamNegBeta0=c(), scaleGamNegAlpha0=c(), scaleGamNegBeta0=c(),
shapeGamPosAlpha0=c(), shapeGamPosBeta0=c(), scaleGamPosAlpha0=c(), scaleGamPosBeta0=c(),
itb, nmc, thin, average="mean", sdShape)
standardGeneric("bayesMixModel"),
signature="z")
setGeneric("getAlignmentQuality", function(bamFile, verbose=FALSE, mc.cores=1)
standardGeneric("getAlignmentQuality"),
signature="bamFile")
setGeneric("integrateData", function(expr, chipseq, factor, reference)
standardGeneric("integrateData"))
setGeneric("matchProbeToPromoter", function(probeToTranscript, transcriptToTSS,
promWidth=4000, mode="union", fix="center")
standardGeneric("matchProbeToPromoter"))
setGeneric("mlMixModel", function(z, normNull=c(), expNeg=c(), expPos=c(),
sdNormNullInit=c(), rateExpNegInit=c(), rateExpPosInit=c(),
piInit=c(), maxIter=500, tol=0.001)
standardGeneric("mlMixModel"),
signature="z")
setGeneric("normalizeChIP", function(object, method)
standardGeneric("normalizeChIP"))
setGeneric("plotChains", function(object, chain, component, itb=1, thin=1, cols, ...)
standardGeneric("plotChains"))
setGeneric("plotClassification", function(object, method, ...)
standardGeneric("plotClassification"),
signature="object")
setGeneric("plotComponents", function(object, density=FALSE, ...)
standardGeneric("plotComponents"),
signature="object")
setGeneric("summarizeReads", function(object, regions, summarize)
standardGeneric("summarizeReads"))
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