genotype: Genotype calculator

In Alethere/SmoothDescent: Application of map-based genotype correction algorithm Smooth Descent

Genotype calculator

Description

Given a set of IBD probabilities, genotypes are calculated. Can take as input a single matrix containing all homologue probabilities of a single individual; or a list of matrices, where each element contains the probabilities of all individuals for one homologue (same as output of 'calc_IBD.list')

Usage

genotype(IBD, homologue, threshold = 0.8, ploidy = 2)

## S3 method for class 'matrix'
genotype(IBD, homologue, threshold = 0.8, ploidy = 2)

## S3 method for class 'list'
genotype(IBD, homologue, threshold = 0.8, ploidy = 2)

Arguments

IBD	numeric matrix or list of matrices.
homologue	homologue matrix for both parents. The first 'ploidy' columns from parent 1 and the second 'ploidy' columns from parent 2.
threshold	probability threshold to assign a homologue to an individual ( if IBD probability for hom 1 > threshold, it is considered that that individual has inherited hom 1).
ploidy	numeric

Details

Genotypes can be though of as a multiplication between a set of homologue probabilites and homologue genotypes. For example, in a diploid we have the following IBD probabilities: p(h1) = 0.9, p(h2) = 0.1, p(h3) = 1, p(h4) = 0; and genotypes g(h1) = 1, g(h2) = 0, g(h3) = 0, g(h4) = 1. The resulting genotype using a simple multiplication would be \sum{p(hi)*g(hi)}, 0.9 in this case.
We are more interested in imputing integer genotypes, so probabilities must be turned into integers. For that reason we use a threshold, default 0.8. All probabilities above 0.8 are turned to 1, and all probabilities below 0.8 are turned to 0. If not enough homologues are assigned this way, that is, an individual cannot be assigned at least 'ploidy' homologues, no genotype can be calculated and NA is returned.

Value

A vector or matrix of imputed genotypes. If not enough IBD probabilities are above the threshold for one individual, NA is returned.

Methods (by class)

• matrix: Method for a single individual

• list: Method for a list of IBD matrices

Examples

data("smooth_descent")
data("homologue")
IBD <- sdescent$predIBD

#For all individuals at once
gen <- genotype(IBD, hom)
#Or one single individual
#Note this is a matrix where each column is one homologue
ind <- sapply(IBD,'[',,1)
gen <- genotype(ind, hom)

Alethere/SmoothDescent documentation built on Oct. 21, 2023, 7:11 a.m.