MultiLociPOE: POEs analysis using multi-locus genotype data from...

Description Usage Arguments Value Examples

View source: R/CCMO.R

Description

This function implements the statistical method M-HAP for detecting POEs using genotype data from case-control mother-offspring pairs by adjusting for covariates. M-HAP utilizes available information such as Medelian inheritance law, Hardy-Weinberg equilibrium, and conditional independence between offspring genotypes and maternal covariates given maternal genotypes.

Usage

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MultiLociPOE(Y, gmm, gcc, X, loci, hap, f, ppi)

Arguments

Y

a n-vector of disease statuses for n offspring (1 for case and 0 for control).

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.

X

a n-vector of maternal covariates for main effects (n: number of mothers).

loci

an indicator for the test locus. The possible values could be 1,...,m (m: number of SNPs).

hap

a l x m matrix of possible haplotypes in the population of interest (l: number of possible haplotypes; m: number of SNPs).

f

specified disease prevalence.

ppi

a l-vector of the corresponding haplotype frequencies (m: number of possible haplotypes).

Value

a list with the following elements

new

estimation and significance test results for the new method M-HAP

log

estimation and significance test results for the standard logistic regression method

cov.new

covariance matrix of the estimated parameters by the new method M-HAP

cov.log

covariance matrix of the estimated parameters by the standard logistic regression method)

Examples

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## Not run: 
data(POESampleData)
Y = POESampleData[,1]
gmm = POESampleData[,2:6]
gcc = POESampleData[,7:11]
X = POESampleData[,12]
loci = 1
f = 0.01
data = MultiLociPOE.input(gmm,gcc,0)
gmm = data$gmm
gcc = data$gcc
hap = data$hap
ppi = data$ppi
fit = MultiLociPOE(Y,gmm,gcc,X,loci,hap,f,ppi)

## End(Not run)

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