GWAS: Conducts an association study (GWAS) using a 'genData'...

In gdlc/dMatrix: Memory Mapped Matrices and Data Structures for Genomic Data

Description

This function conducts an association test using the formula provided by the user (formula) plus one column of @geno, one column at a time. The data from the association tests is obtained from a genData object.

Usage

GWAS(formula, data, method, plot = FALSE, verbose = FALSE,
  min.pValue = 1e-10, chunkSize = 10, ...)

Arguments

formula	A formula (e.g. weight~sex+age) with the response on the left-hand side and predictors (all the covariates except the markers) on the right-hand side. The variables included in the formula must be in the @pheno object of the genData.
data	A genData object.
method	The regression method to be used. Currently, the following methods are implemented: lm, lm.fit, lsfit, glm and lmer.
plot	If TRUE a Manhattan plot is produced and filled with points as the association tests are run.
verbose	If TRUE more messages are printed.
min.pValue	Numeric, the minimum p-value expected, used to determine the limits of the vertical axis of the Manhattan plot.
chunkSize	Represents the number of columns of @geno that are brought into RAM for processing (10 by default).

Value

Returns a matrix with estimates, SE, p-value, etc.

gdlc/dMatrix documentation built on May 17, 2019, 12:12 a.m.