snp_test {martini} | R Documentation

## 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.

[Package martini version 1.12.0 Index]