SNP: Functions for single nucleotide polymorphisms
In gap: Genetic Analysis Package

snpHWE

R Documentation

Functions for single nucleotide polymorphisms

Description

These are a set of functions specifically for single nucleotide polymorphisms (SNPs), which are biallelic markers. This is particularly relevant to the genomewide association studies (GWAS) using GeneChips and in line with the classic generalised single-locus model. snpHWE is from Abecasis's website and yet to be adapted for chromosome X.

Usage

snpHWE(g)

PARn(p, RRlist)

snpPVE(beta, se, N)

snpPAR(RR, MAF, unit = 2)

Arguments

`g`	Observed genotype vector.
`p`	genotype frequencies.
`RRlist`	A list of RRs.
`beta`	Regression coefficient.
`se`	Standard error for beta.
`N`	Sample size.
`RR`	Relative risk.
`MAF`	Minar allele frequency.
`unit`	Unit to exponentiate for homozygote.

Details

snpHWE gives an exact Hardy-Weinberg Equilibrium (HWE) test and it return -1 in the case of misspecification of genotype counts.

snpPAR calculates the the population attributable risk (PAR) for a particular SNP. Internally, it calls for an internal function PARn, given a set of frequencies and associate relative risks (RR). Other 2x2 table statistics familiar to epidemiologists can be added when necessary.

snpPVE provides proportion of variance explained (PVE) estimate based on the linear regression coefficient and standard error. For logistic regression, we can have similar idea for log(OR) and log(SE(OR)).