get_GP_bayesian: Infer posterior genotype probabilities based on the Bayesian...

In Yi-Jiang/MethyGenotyper: MethylGenotyper: Accurate estimation of SNP genotypes from DNA methylation data

Infer posterior genotype probabilities based on the Bayesian approach

Description

Prior genotype probabilities were inferred from AFs. The AFs can be in population level or individual-specific level. For population level AFs, they can be extracted from the matched population in the 1000 Genomes Project (1KGP). For individual-specific AFs, they can be calculated according to the top four PCs.

Usage

get_GP_bayesian(pD_AA, pD_AB, pD_BB, AF)

Arguments

pD_AA	A MxN matrix of AA genotype probabilities. Provide SNPs as rows and samples as columns.
pD_AB	A MxN matrix of AB genotype probabilities. Provide SNPs as rows and samples as columns.
pD_BB	A MxN matrix of BB genotype probabilities. Provide SNPs as rows and samples as columns.
AF	A MxN matrix of AFs. Provide SNPs as rows and samples as columns.

Value

A list containing

pAA	Posterior genotype probability of AA
pAB	Posterior genotype probability of AB
pBB	Posterior genotype probability of BB

Yi-Jiang/MethyGenotyper documentation built on Sept. 4, 2024, 12:47 p.m.