mas-package {mas}

Marker Association Studies

Description

Genome-wide association analysis that accommodate membership information, variance adjustment, and correlated responses.

Details

The DESCRIPTION file:

Package:	mas
Type:	Package
Title:	Marker Association Studies
Version:	0.3
Date:	2024-04-08
Authors@R:	c(person("Alencar", "Xavier", role=c("aut", "cre"), email = "[e-mail]"),person("Shizhong", "Xu", role=c("aut", "ctb")))
Author:	Alencar Xavier [aut, cre], Shizhong Xu [aut, ctb]
Maintainer:	Alencar Xavier <[e-mail]>
Description:	Genome-wide association analysis that accommodate membership information, variance adjustment, and correlated responses.
License:	GPL-3
Imports:	Rcpp, truncdist
LinkingTo:	Rcpp, RcppEigen
Depends:	R (>= 3.2.0), methods (>= 3.2.0)
Archs:	x64

Index of help topics:

gwas                    Genome-Wide Association Studies
mas-package             Marker Association Studies
y                       Soybean dataset

Author(s)

Alencar Xavier [aut, cre], Shizhong Xu [aut, ctb] Maintainer: Alencar Xavier <[e-mail]>

References

Wei, J. and Xu, S., 2016. A random-model approach to QTL mapping in multiparent advanced generation intercross (MAGIC) populations. Genetics, 202(2), pp.471-486.

Xavier, A. and Habier, D., 2022. A new approach fits multivariate genomic prediction models efficiently. Genetics Selection Evolution, 54(1), pp.1-15.

Examples

## Not run: 
# load the toy dataset
data( soy ) 

# run gwas
fit1 = gwas(y[w], Z[w,], pop[w]) 
# adjust variances
fit2 = CorrectBeavis( fit1 ) 

# Compare before and after correction
plot( fit1, h2=TRUE, col=8, pch=20) # display QTL h2
plot( fit2, h2=TRUE, add=TRUE, pch=20, type='o') # adjusted QTL h2
legend('topleft',pch=16,col=c(8,1),c('Before correction','After Beavis correction'))

## End(Not run)