MultiLoad: Load individual-level data for multivariate GWA analysis

In MultiABEL: Multi-Trait Genome-Wide Association Analysis

Description

The function imports GenABEL (gwaa.data class) or DatABEL (.fv*) data formats to perform multivariate test for each genetic variant.

Usage

MultiLoad(gwaa.data = NULL, phenofile = NULL, genofile = NULL,
  trait.cols, covariate.cols = NULL, cuts = 20, impute = TRUE,
  gaussianize = TRUE, ...)

Arguments

gwaa.data	An (optional) object of {gwaa.data-class}.
phenofile	An (optional) plain text file contains phenotypic outcomes and covariates.
genofile	An (optional) object of {databel-class} containing genotype data.
trait.cols	A vector (length > 1) giving the column indices of the phenotypes to be analyzed.
covariate.cols	An (optional) vector giving the column indices of the covariates to be included.
cuts	An integer telling how many pieces the genotype data matrix will be splitted for analyze. The value can be set depending on the memory size. The smaller the value is, potentially the faster the analysis will be.
impute	An (optional) logical argument telling whether missing genotypes should be imputed.
gaussianize	An (optional) logical argument telling whether the phenotypes should be gaussianized via inverse-Gaussian transformation.
...	not used.

Value

The function returns a list of cleaned statistics for subsequent, with class multi.loaded.

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

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

Multivariate

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))

## converting the same dataset into DatABEL format files
require(DatABEL)
write.table(phdata(ge03d2ex.clean), 'pheno.txt', col.names = TRUE, row.names = TRUE, 
            quote = FALSE, sep = '\t')
geno <- as.double(ge03d2ex.clean)
matrix2databel(geno, 'geno')

## running the multivariate GWAS again
loaded <- MultiLoad(phenofile = 'pheno.txt', genofile = 'geno', trait.cols = c(5, 6, 8), 
                    covariate.cols = c(2, 3))

## End(Not run)

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