ds.metaGWAS: Genome-wide association analysis (GWAS)

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

Genome-wide association analysis (GWAS)

Description

Performs GWAS using GENESIS

Usage

ds.metaGWAS(
  genoData,
  model,
  family = "binomial",
  snpBlock = 10000,
  datasources = NULL,
  ...
)

Arguments

genoData	character vector of objects on the server side 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)
model	formula indicating the condition (left side) and other covariates to be adjusted for (i.e. condition ~ covar1 + ... + covar2). The fitted model is: snp ~ condition + covar1 + ... + covarN
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/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.