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## GENERIC ACCESSOR METHODS:
## SMAPObservations
if (!isGeneric("name"))
setGeneric("name", function(object) standardGeneric("name"))
if (!isGeneric("value"))
setGeneric("value", function(object) standardGeneric("value"))
if (!isGeneric("noObservations"))
setGeneric("noObservations", function(object)
standardGeneric("noObservations"))
if (!isGeneric("chromosome"))
setGeneric("chromosome", function(object) standardGeneric("chromosome"))
if (!isGeneric("chroms"))
setGeneric("chroms", function(object) standardGeneric("chroms"))
if (!isGeneric("chrom.start"))
setGeneric("chrom.start", function(object) standardGeneric("chrom.start"))
if (!isGeneric("startPosition"))
setGeneric("startPosition", function(object)
standardGeneric("startPosition"))
if (!isGeneric("endPosition"))
setGeneric("endPosition", function(object) standardGeneric("endPosition"))
if (!isGeneric("reporterId"))
setGeneric("reporterId", function(object) standardGeneric("reporterId"))
if (!isGeneric("distance"))
setGeneric("distance", function(object) standardGeneric("distance"))
if (!isGeneric("overlapIds"))
setGeneric("overlapIds", function(object) standardGeneric("overlapIds"))
if (!isGeneric("overlaps"))
setGeneric("overlaps", function(object) standardGeneric("overlaps"))
if (!isGeneric("startOverlaps"))
setGeneric("startOverlaps", function(object) standardGeneric("startOverlaps"))
if (!isGeneric("noOverlaps"))
setGeneric("noOverlaps", function(object) standardGeneric("noOverlaps"))
## SMAPHMM
if (!isGeneric("A"))
setGeneric("A", function(object) standardGeneric("A"))
if (!isGeneric("Pi"))
setGeneric("Pi", function(object) standardGeneric("Pi"))
if (!isGeneric("Phi"))
setGeneric("Phi", function(object) standardGeneric("Phi"))
if (!isGeneric(".Phi"))
setGeneric(".Phi", function(object) standardGeneric(".Phi"))
if (!isGeneric("noStates"))
setGeneric("noStates", function(object) standardGeneric("noStates"))
if (!isGeneric(".Z"))
setGeneric(".Z", function(object) standardGeneric(".Z"))
if (!isGeneric(".Y"))
setGeneric(".Y", function(object) standardGeneric(".Y"))
if (!isGeneric(".eta"))
setGeneric(".eta", function(object) standardGeneric(".eta"))
if (!isGeneric(".grad"))
setGeneric(".grad", function(object) standardGeneric(".grad"))
## SMAPProfile
if (!isGeneric("HMM"))
setGeneric("HMM", function(object) standardGeneric("HMM"))
if (!isGeneric("observations"))
setGeneric("observations", function(object)
standardGeneric("observations"))
if (!isGeneric("P"))
setGeneric("P", function(object) standardGeneric("P"))
if (!isGeneric("Q"))
setGeneric("Q", function(object) standardGeneric("Q"))
## gaussparam
if (!isGeneric("gaussMean"))
setGeneric("gaussMean", function(object) standardGeneric("gaussMean"))
if (!isGeneric("gaussSd"))
setGeneric("gaussSd", function(object) standardGeneric("gaussSd"))
## GENERIC REPLACEMENT METHODS:
## SMAPObservations
if (!isGeneric("value<-"))
setGeneric("value<-", function(x, value) standardGeneric("value<-"))
if (!isGeneric("overlaps<-"))
setGeneric("overlaps<-", function(x, value) standardGeneric("overlaps<-"))
if (!isGeneric("overlapIds<-"))
setGeneric("overlapIds<-", function(x, value)
standardGeneric("overlapIds<-"))
if (!isGeneric("startOverlaps<-"))
setGeneric("startOverlaps<-", function(x, value)
standardGeneric("startOverlaps<-"))
if (!isGeneric("noOverlaps<-"))
setGeneric("noOverlaps<-", function(x, value) standardGeneric("noOverlaps<-"))
## SMAPHMM
if (!isGeneric("A<-"))
setGeneric("A<-", function(x, value) standardGeneric("A<-"))
if (!isGeneric("Pi<-"))
setGeneric("Pi<-", function(x, value) standardGeneric("Pi<-"))
if (!isGeneric("Phi<-"))
setGeneric("Phi<-", function(x, value) standardGeneric("Phi<-"))
if (!isGeneric(".Phi<-"))
setGeneric(".Phi<-", function(x, value) standardGeneric(".Phi<-"))
if (!isGeneric(".Z<-"))
setGeneric(".Z<-", function(x, value) standardGeneric(".Z<-"))
if (!isGeneric(".Y<-"))
setGeneric(".Y<-", function(x, value) standardGeneric(".Y<-"))
if (!isGeneric(".eta<-"))
setGeneric(".eta<-", function(x, value) standardGeneric(".eta<-"))
if (!isGeneric(".grad<-"))
setGeneric(".grad<-", function(x, value) standardGeneric(".grad<-"))
## gaussparam
if (!isGeneric("gaussMean<-"))
setGeneric("gaussMean<-", function(x, value) standardGeneric("gaussMean<-"))
if (!isGeneric("gaussSd<-"))
setGeneric("gaussSd<-", function(x, value) standardGeneric("gaussSd<-"))
## GENERIC METHODS:
if (!isGeneric(".split.on.chrom"))
setGeneric(".split.on.chrom", function(Obs)
standardGeneric(".split.on.chrom"))
if (!isGeneric("getChromObs"))
setGeneric("getChromObs", function(Obs, c) standardGeneric("getChromObs"))
if (!isGeneric(".viterbi"))
setGeneric(".viterbi", function(x, Obs, mean.ref, sd.min, mean.sd,
W.A, W.Pi,
overlap=TRUE, distance=TRUE, L=2000000)
standardGeneric(".viterbi"))
if (!isGeneric(".calc.overlaps"))
setGeneric(".calc.overlaps", function(Obs, overlap=TRUE)
standardGeneric(".calc.overlaps"))
if (!isGeneric(".gradient.descent"))
setGeneric(".gradient.descent", function(x, Obs, Q, P, mean.ref,
sd.min, mean.sd,
W.A, W.Pi,
max.iters=Inf, tau=0.05,
eta=0.005, e.change=0.5,
e.same=1.2,
e.min=0.0001, e.max=0.5,
adaptive=TRUE,
overlap=TRUE, distance=TRUE,
verbose=1, L=2000000)
standardGeneric(".gradient.descent"))
if (!isGeneric("smap"))
setGeneric("smap", function(x, Obs, sd.min=0.05, mean.sd=0.05,
max.iters=Inf, gd.max.iters=Inf, tau=0.05,
eta=0.01, e.change=0.5, e.same=1.2,
e.min=0.0001, e.max=0.5, adaptive=TRUE,
overlap=TRUE, distance=TRUE,
chrom.wise=FALSE, verbose=1,
L=5000000)
standardGeneric("smap"))
if (!isGeneric(".draw.dist"))
setGeneric(".draw.dist", function(x,col) standardGeneric(".draw.dist"))
if (!isGeneric("profilePlot"))
setGeneric("profilePlot", function(profile, ...)
standardGeneric("profilePlot"))
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