GWASDS: Genome-wide association analysis (GWAS) on the server-side

In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

Genome-wide association analysis (GWAS) on the server-side

Description

Performs GWAS using GENESIS Bioconductor package

Usage

GWASDS(genoData, outcome, covars = NULL, family = "binomial", snpBlock, ...)

Arguments

genoData	a GenotypeData object which is a container for storing genotype data from a GWAS toghether with the metadata associated with the subjects (i.e. phenotypes and/or covariates) and SNPs
outcome	A character string specifying the name of the outcome variable in genoData
covars	A vector of character strings specifying the names of the fixed effect covariates in genoData; an intercept term is automatically included. If NULL (default) the only fixed effect covariate is the intercept term
family	A description of the generalized linear model used. The defatul is "binomial" that is defined for case/control studies. Quantitative traits can be analyzed by using "gaussian". Other values are accepted.
snpBlock	an integer specifying the number of SNPs in an iteration block. See GenotypeIterator function in GWASTools package.
...	other arguments of fitNullModel function in GENESIS package

Value

a matrix with SNPs ordered by p-values

Author(s)

Gonzalez, JR.

isglobal-brge/dsOmics documentation built on Nov. 6, 2024, 1:28 a.m.