Genome-wide association analysis (GWAS) — ds.metaGWAS • dsOmicsClient

Performs GWAS using GENESIS

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

a matrix with SNPs ordered by p-values

Gonzalez, JR.