haplo {SHARE}R Documentation

Haplotype Estimation

Description

Estimate haplotype sequences and frequencies from genotype sequences by EM algorithm

Usage

haplo(.Object, ...)

Arguments

.Object A object of calss "genoSet".
... Other arguments used in haplo.em from haplo.stats package.

Details

By using the haplo.em function in haplo.stats package, haplo convert unphased genotype sequences into phased haplotype sequences by EM algorithm. Haplotype frequencies are also estimated by haplp.em function.

Value

haplo returns an object of class "haplo" which results in the following slots:

haploSeq unique haplotypes. This is from the "haplotype" component in the result of haplo.em funciton.
haploFreq MLE's of haplotype probabilities. This is from the "hap.prob" component in the result of haplo.em funciton.
hap1 the code of first haplotype of each subject. This is from the "hap1code" component in the result of haplo.em funciton.
hap2 the code of first haplotype of each subject. This is from the "hap2code" component in the result of haplo.em funciton.
poolHapPair Subject IDs. This is from the "subj.id" component in the result of haplo.em funciton.
nPosHapPair vector for the count of haplotype pairs that map to each subject's marker genotypes. This is from the "nreps" component in the result of haplo.em funciton.
post vector of posterior probabilities of pairs of haplotypes for a person, given their marker phenotypes. This is from the "post" component in the result of haplo.em funciton.

Author(s)

James Y. Dai

References

haplo.em

See Also

genoSet, haplo-class

Examples

## See vignette for more details
## Not run: 
unphasedHaplo <- haplo(unphasedGeno)
unphasedHaplo
## End(Not run)


[Package SHARE version 1.0.4 Index]