snp_test: Calculate genotype-phhenotype associations

In hclimente/martini: GWAS Incorporating Networks

Calculate genotype-phhenotype associations

Description

Calculate the association between genotypes and a phenotype, adjusting by covariates.

Usage

snp_test(gwas, covars, score, family, link)

Arguments

gwas	A SnpMatrix object with the GWAS information.
covars	A data frame with the covariates. It must contain a column 'sample' containing the sample IDs, and an additional columns for each covariate.
score	Association score to measure association between genotype and phenotype. Possible values: chi2 (default), glm.
family	A string defining the generalized linear model family. This should match one of "binomial", "poisson", "gaussian" or "gamma". See snp.rhs.tests for details.
link	A string defining the link function for the GLM. This should match one of "logit", "log", "identity" or "inverse". See snp.rhs.tests for details.

Value

A named vector with the association scores.

hclimente/martini documentation built on Feb. 26, 2024, 6:23 p.m.