Description Usage Arguments Examples
correct genotype by Hidden Markov Model
1 2 | hmm.vitFUN.rils(geno, position, geno.probability, transitionFUN =
phy2get.haldane.rils, emissionFUN = makeEmissionFUN(errorRate = 0.01), ...)
|
geno |
a numeric matrix of SNP genotype formatted |
position |
vector of SNP positions |
geno.probability |
vector of start probability |
transitionFUN |
a function about transition |
emissionFUN |
a function about emission |
... |
arguments to be passed to other methods. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | O <- c(1,1,1,1,1,1,1,2,1,1,1,1,1,1,2,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,1,2,2,2,2,2,2,2,2,1,2,2,2,2,
2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,2,1,1,2,2,1,2,1,2,1,2,1,2,1,2,1,1,1,1,1,1,1,2,1,1,1,1,
1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,2,1,1,1,1,1)
O.pos <- 30e3*1:length(O)
O.cr <- hmm.vitFUN.rils(geno=O,position=O.pos,geno.probability=c(0.4975, 0.4975,0.005),
transitionFUN = phy2get.haldane.rils,
emissionFUN = makeEmissionFUN(errorRate = 0.01))
rbind(raw=paste(O,collapse=''),correct=paste(O.cr,collapse=''))
## [,1]
## raw "11111112111111211111112222222212222222212222212222222222
## 22221211221212121212111111121111111111121111111211111"
## correct "11111111111111111111112222222222222222222222222222222222
## 22223333333333333333111111111111111111111111111111111"
|
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