MPR.genotyping (version 0.8)

hmm.vitFUN.rils: Genotyping by HMM

Description

correct genotype by Hidden Markov Model

Usage

hmm.vitFUN.rils(geno, position, geno.probability, transitionFUN = 
	phy2get.haldane.rils, emissionFUN = makeEmissionFUN(errorRate = 0.01), ...)

Arguments

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.

Examples

# NOT RUN {
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"
# }