ds.glmSNP: Logistic regression analysis of pooled data for each SNP site...
In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

ds.glmSNP

R Documentation

Logistic regression analysis of pooled data for each SNP site in study

Description

Fits a generalized linear model to gentic data for each SNP in the data sets considered, using user specified outcome and phenotypic variabes as covariates Outputs a matrix containing a beta value, standard error and p-value for each SNP

Usage

ds.glmSNP(
  snps.fit = NULL,
  model,
  genoData,
  datasources = NULL,
  type.p.adj = "fdr",
  mc.cores = 1,
  family = "binomial",
  strata = NULL
)

Arguments

`snps.fit`	an optional parameter input as a character vector of SNPs (rs numbers) that should be analysed. If missing all SNPs are analysed
`model`	list of phenotypic variables to use as covariates in the regression analysis in the form: "outcome ~ covar1 + covar2 + ... + covarN"
`genoData`	name of the DataSHIELD object to which the genotype (snpMatrix) and phenotypic data (data.frame) has been assigned
`datasources`	Opal object or list of opal objects denoting the opal server(s) information
`mc.cores`	optional parameter that allows the user to specify the number of CPU cores to use
`strata`	`character` Categorical variable to perform a stratified glm