MultiABEL (version 1.1-6)

Multivariate: Multivariate genome-wide association scan

Description

The function imports GenABEL (gwaa.data class) or DatABEL (.fv*) data formats and performs multivariate test for each genetic variant using multivariate analysis of variance (MANOVA).

Usage

Multivariate(x, trait.idx = NULL, ...)

Arguments

x

An object created by MultiLoad.

trait.idx

A vector giving the indices of traits to be analyzed.

...

not used.

Value

The function returns a data frame containing the multi-trait GWAS results, where the row names are the variants names. The column names are: variant name (Marker), allele frequency (Freq), the smallest sample size of the traits (N), effect on the phenotype score (Beta.S, see reference), standard error (SE), p-value (P), and the rest the coefficients to construct the phenotype score (see reference).

References

Xia Shen, ..., Jim Wilson, Gordan Lauc, Yurii Aulchenko (2015). Multi-omic-variate analysis identified novel loci associated with compound N-Glycosylation of human Immunoglobulin G. Submitted.

See Also

MultiLoad

Examples

## loading example gwaa.data in GenABEL
require(GenABEL)
data(ge03d2ex.clean)

## running multivariate GWAS for 3 traits: height, weight, bmi
loaded <- MultiLoad(gwaa.data = ge03d2ex.clean, trait.cols = c(5, 6, 8), 
                    covariate.cols = c(2, 3))

## running the multivariate GWAS 
res <- Multivariate(loaded)