haplo {SHARE} | R Documentation |
Estimate haplotype sequences and frequencies from genotype sequences by EM algorithm
haplo(.Object, ...)
.Object |
A object of calss "genoSet". |
... |
Other arguments used in haplo.em from haplo.stats package. |
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.
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. |
James Y. Dai
haplo.em
## See vignette for more details ## Not run: unphasedHaplo <- haplo(unphasedGeno) unphasedHaplo ## End(Not run)