mvtests {snpStats} | R Documentation

## Multivariate SNP tests

### Description

This function calculates multivariate score tests between a multivariate (or multinomial) phenotype and sets of SNPs

### Usage

    mvtests(phenotype, sets, stratum, data = sys.parent(), snp.data, rules = NULL, complete = TRUE, uncertain = FALSE, score = FALSE)

### Arguments

`phenotype` | Either a factor (for a multinomial phenotype) or a matrix (for a multivariate phenotype)
`sets` | A list of sets of SNPs to be tested against the phenotype
`stratum` | (Optional) a stratifying variable
`data` | A data frame in which `phenotype` and `stratum` reside. If absent these are assumed to be in the parent frame and correctly aligned with the rows of `snp.data`
`snp.data` | An object of class `SnpMatrix` containing the SNP data
`rules` | (Optional) A set of imputation rules. The function then carries out tess on imputed SNPs
`complete` | If `TRUE` each test will use only subjects who have complete data for the phenotype and all SNPs in the set to be tested. If `FALSE`, then complete data for the phenotype is required, but tests are based upon complete pairs of SNPs
`uncertain` | If `TRUE`, uncertain genotype calls will be used in the tests (scored by their posterior expectations). Otherwise such calls are treated as missing
`score` | If `TRUE`, the score vectors and their variance-covariance matrices are saved in the output object for further processing

### Details

Currently `complete=FALSE` is not implemented

### Value

An object of class `snp.tests.glm` or `GlmTests.score` depending on whether `score` is set to `FALSE` or `TRUE` in the call

### Note

This is an experimental version

### Author(s)

David Clayton dc208@cam.ac.uk

### Examples

    ## No example yet

[Package snpStats version 1.30.0 Index]