snpStats: mvtests – R documentation

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mvtests

Multivariate SNP tests

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

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

`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

Currently complete=FALSE is not implemented

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

This is an experimental version

## No example yet

SnpMatrix and XSnpMatrix classes and methods

v1.40.0

GPL-3

Authors

David Clayton <dc208@cam.ac.uk>

Initial release

2019-10-08