HapEstXXR (version 0.1-8)

itegeppXXR: Haplotype estimation routine for single individual data

Description

itegeppXXR is haplotype estimation routine for samples of independent individual genotypes (EM-algorithm).

Usage

itegeppXXR(geno, des = 0, lim = 0.05)

Arguments

geno

(n,m)-Matrix; n=No of Individuals, m=No of SNPs; R-Code: 1-column genotype matrix - code 1 = 1/1, 3 = 1/2, 2 = 2/2

des

des=1 haplotype pairs, des=0 single haplotypes

lim

Threshold for combining rare haplotypes

Value

hap.id

Id. of haplotypes

hap

estimated haplotypes

freq

haplotype frequencies

hapres

individual haplotypes

likres

Likelihood value

desres

Design matrix for the model (des=1 => Haplotype pairs, des=0 => single haplotypes)

Details

Inferring haplotypes by EM-Algorithm

References

Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12:921-927

Examples

  set.seed(123456)
  ns <- 4  # Number of SNPs
  N <- 2000   # Number of individuals
  patid <- N:1
  geno <- matrix(sample(c(1, 2, 3), ns * N, replace = TRUE), ncol = ns)
  iteHAP <- itegeppXXR(geno, des = 1, lim = 0.01)