GWAS_GenABEL: GWAS using GenAbel functions
In vincentgarin/GWASToolBox: GWAS analysis

Description Usage Arguments Details Value Author(s) References Examples

Perform a SNP genome wide association study using optional principal components terms or a kinship matrix to correct for the genetic background. The function is a wrapper for the GenAbel package functions (Covarrubias-Pazaran, 2016).

1 2	GWAS_GenABEL(gwaa, trait = 1, model = "kinship", nPC = NULL, K_i = TRUE, verbose = FALSE)

`gwaa`	`gwaa.data` object.
`trait`	`Numerical` or `character` indicator to specify which trait of the gp object should be used. Default = 1.
`model`	`Character` argument specifying the type of model that is used to perform the GWAS analysis: 1) 'null' for a simple model with only the QTL position; 2) 'PC' model with genetic background correction using the `nPC` first principal components; 3) 'kinship', model with kinship genetic background correction. Default = 'kinship'.
`nPC`	Optional matrix of principal components for genetic background correction. Default = NULL.
`K_i`	`Logical` specifying if the kinship correction should be done by removing the markers of the scanned chromosome. Default = TRUE.
`verbose`	`Logical` indicating if function outputs should be printed. Default = FALSE.

The model can be fitted using the kinship containing all markers or removing the markers of the scanned chromosome (K_i = TRUE).

Return:

G_res

Object of class G_res representing a data.frame with four columns: marker identifier, chromosome, position in cM or bp and -log10(p-value).

Vincent Garin

Aulchenko, Y. S., Ripke, S., Isaacs, A., & Van Duijn, C. M. (2007). GenABEL: an R library for genome-wide association analysis. Bioinformatics, 23(10), 1294-1296.

Aulchenko, Y. S., De Koning, D. J., & Haley, C. (2007). Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics, 177(1), 577-585.