Nothing
famMix <- function (x, R, id.U, id.V = NULL,partialmarker=NULL,theta=0,mutationRateFemale = 0, mutationRateMale = 0, mutationModelFemale = "stable", mutationModelMale = "stable", mutationRangeFemale = 0.1, mutationRangeMale = 0.1, silentFrequency = 0,check=TRUE) {
if(silentFrequency==0) silentFrequency=NULL
stopifnot(x$nMark==0)
if (is.null(partialmarker)) m = stop("Partialmarker must be supplied") else m = partialmarker
allgenos = paramlink:::.allGenotypes(attr(m, 'nalleles'))
allgenos_in_R = which(allgenos[, 1] %in% R & allgenos[, 2] %in% R)
all_typed = which(m[,1] != 0 | m[,2] != 0)
contrib_typed = setdiff(all_typed, id.V)
contrib_untyped = id.U
K = unique(c(m[contrib_typed, ]))
R_not_masked = setdiff(R, K)
if(check) stopp=euroMix:::.checkInput(x,R,id.U,id.V,partialmarker=m,all_typed,K,R_not_masked)
set=generate(R,K,length(contrib_untyped))
if(is.null(set)) x=addMarker(x,m)
else {
dd=dim(set)[2]/2
for (i in 1:dd) x=addMarker(x,m)
x=modifyMarkerMatrix(x, contrib_untyped, set)
}
m2=x$markerdata[[1]]
x$available=which(m2[,1] != 0 | m2[,2] != 0)
x=relabel(x,1:x$nInd,x$orig.ids)
euroMix:::.preFamilias2(x,new=TRUE,mutationRateFemale = mutationRateFemale, mutationRateMale = mutationRateMale , mutationModelFemale = mutationModelFemale, mutationModelMale = mutationModelMale, mutationRangeFemale = mutationRangeFemale, mutationRangeMale = mutationRangeMale, silentFrequency = silentFrequency )
PE=GetProbabilities(kinship=theta)$likelihoodsPerSystem
list(x=x,likelihood = sum(PE), allLikelihoods = PE[PE>0])
}
.preFamilias2=function (x, new = TRUE, mutationRateFemale = 0, mutationRateMale = 0,
mutationModelFemale = "stable", mutationModelMale = "stable",
mutationRangeFemale = 0.1, mutationRangeMale = 0.1, silentFrequency = NULL)
{
if(is.null(silentFrequency)) hack=0 else hack=silentFrequency
if (new) {
NewFamilias()
for (i in x$orig.ids) AddPerson(x$pedigree[i, 4] == 1)
for (i in 1:x$nMark) {
afreq=attr(x$markerdata[i][[1]], which = "afreq")
afreq=(1-hack)*afreq
AddAlleleSystem(afreq, mutationRateFemale = mutationRateFemale,
mutationRateMale = mutationRateMale, mutationModelFemale = mutationModelFemale,
mutationModelMale = mutationModelMale, mutationRangeFemale = mutationRangeFemale,
mutationRangeMale = mutationRangeMale, silentFrequency = silentFrequency)
}
for (i in 1:x$nMark) for (j in x$available) AddDNAObservation(j,
i, x$markerdata[[i]][j, 1], x$markerdata[[i]][j,
2])
}
ped = AddPedigree()
if (max(x$ped[, 2:3]) > 0) {
for (i in x$orig.ids) {
Father = x$pedigree[i, 2]
Mother = x$pedigree[i, 3]
Child = x$pedigree[i, 1]
if (Father > 0)
AddRelation(Father, Child, ped)
if (Mother > 0)
AddRelation(Mother, Child, ped)
}
}
ped
}
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