ltgwas: Association Teste using Linear Transformation of Genomic Evaluations

Description

Standardized test of association where genomic breeding values from a mixed model including fixed effects and a genomic information are linearly transformed to estimate marker effects and pvalues.

Usage

ltgwas(file = NULL, varG = NULL, varE = NULL, gebv = NULL)

Arguments

Argument	Description
file	name of all plink files (.bed, bim and .fam)
varG	genetic variance
varE	residual variance
gebv	genomic estimated breeding value

Value

Returns SNP effects, SNP variance and p-values using t test, Z score and Wald test.

Author

Fernando Brito Lopes

References

VanRaden, Paul M. Efficient methods to compute genomic predictions. Journal of dairy science 91.11 (2008): 4414-4423.

Gualdron Duarte JL, Cantet RJ, Bates RO, Ernst CW, Raney NE, Steibel JP. Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations. BMC Bioinformatics (2014). 19;15:246. doi: 10.1186/1471-2105-15-246.

Examples

 
 # GWAS <- ltgwas(file = "filename",
 #                varG=10,
 #                varE=20,
 #                gebv=gebv)