reconstruct.haps: Perform (simplistic) haplotype reconstruction, given parental...

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Perform (simplistic) haplotype reconstruction, given parental genotypes

Usage

reconstruct.haps(geno, parents, scale = 10, err = 0.001, ...)

Arguments

geno	a genotypes object
parents	a matrix of parental genotypes
scale	scaling parameter for expected recombination fraciton (see Details)
err	genotyping error rate
...	ignored

Details

This function attempts to reconstruct haplotypes of target individuals (in geno) in terms of the founder genotypes given in parents. It expects founders to be inbred; markers at which any founder has a heterozygous genotype are dropped. (TODO: relax that assumption.)

Transition probabilities in the HMM are proportional to expected recombination fractions, calculated with the Haldane map function from genetic positions of markers. The scale parameter is a multiplier for these fractions when the target individuals are >1 generation removed from the founders. Tuning the transition probabilities will be a matter of trial and error, and optimal values will probably vary by dataset.

Haplotype segments are pseudo-phased in the result: phase is set to greedily minimize the number of haplotype transitions between adjacent segments. (There is no look-ahead, so in some cases the result may be less than optimal.) Real phasing is beyond the scope of this package at present.

The model is constrained to only the homozygous states when a sample should really be hemizygous: this is true for males on chrX and everybody on chrM.

Value

a dataframe of haplotype segments

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.