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

Description Usage Arguments Value

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

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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.