MultiLociPOE.input: Inputs for the function MultiLociPOE

In zhanghfd/CCMO: Case-Control Mother-Offspring Pair Genetic Association Studies

Description

This function can be used to obtain required inputs for the function MultiLociPOE: all possible haplotypes in the population of interest and the corresponding haplotype frequencies.

Usage

MultiLociPOE.input(gmm, gcc, type)

Arguments

gmm	a n x m matrix of genotypes for mothers (n: number of mothers; m: number of SNPs). The possible values should be 0, 1, 2.
gcc	a n x m matrix of genotypes for offspring (n: number of offspring; m: number of SNPs). The possible values should be 0, 1, 2.
type	an indicator for the genotype data format. (0 for genotype coded as 0, 1, 2; 1 for normalized genotype coded as 0, 1/2, 1; 2 for genotype coded like "A/A", "A/B", "B/B")

Value

a list with the following elements

gmm	matrix of genotypes for mothers (n: number of mothers; m: number of SNPs)
gcc	matrix of genotypes for offspring (n: number of offspring; m: number of SNPs)
hap	a l x m matrix of possible haplotypes in the cohort (l: number of possible haplotypes; m: number of SNPs)
ppi	a l-vector of the corresponding haplotype frequencies (l: number of possible haplotypes)

zhanghfd/CCMO documentation built on March 18, 2021, 12:18 a.m.