Multivariate: Multivariate genome-wide association scan

In MultiABEL: Multi-Trait Genome-Wide Association Analysis

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).

Note

Either gwaa.data (for GenABEL data format) or the combination of phenofile and genofile (for DatABEL data format) has to be provided. If all are provided, only phenofile and genofile will be used. When using DatABEL format input, individual IDs in phenofile and genofile have to match!

Author(s)

Xia Shen

References

Shen X, Klaric L, Sharapov S, Mangino M, Ning Z, Wu D, Trbojevic-Akmacic I, Pucic-Bakovic M, Rudan I, Polasek O, Hayward C, Spector TD, Wilson JF, Lauc G, Aulchenko YS (2017): Multivariate discovery and replication of five novel loci associated with Immunoglobulin G N-glycosylation. Nature Communications, 8, 447; doi: 10.1038/s41467-017-00453-3.

See Also

MultiLoad

Examples

## Not run: 
## 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)

## End(Not run)

MultiABEL documentation built on May 2, 2019, 5:57 p.m.