emmax_group: Modification of Emmax to be used for Genome Wide Association...

In petrikemppainen/LDna: Linkage disequilibrum network analysis (LDna)

Modification of Emmax to be used for Genome Wide Association (GWA) analyses using Groups of SNPs connected by high LD.

Description

This function is not meant to be a part of LDna but is provided here to show an example of how output from LDnClusteringEL can be used for GWA studies. Potentially there will be a separate R-package in the future that focuses on GWA. For now we refer to code provided with the reference, see below.

Usage

emmax_group(Y, X, Grp, K, B = NULL)

Arguments

Y	Phenotypic value
X	Original SNP data used for by LDnClusteringEL (matrix with SNPs as columns and individuals as rows)
Grp	Index indicating which LD-cluster SNPs belong to. Produced by LDnClusteringEL.
K	Kinship matrix, as produced e.g by A.mat, package rrBLUP
B	Number of permutations. If NULL, permutation is not performed

Details

See reference

Value

See reference

Author(s)

Petri Kemppainen [e-mail], zitong.li [e-mail]

References

Li, Z., Kemppainen, P., Rastas, P., Merila, J. Linkage disequilibrium clustering-based approach for association mapping with tightly linked genome-wide data. Accepted to Molecular Ecology Resources.

See Also

LDnClusteringEL

Examples

## see \code{\link{LDnClusteringEL}}

petrikemppainen/LDna documentation built on April 14, 2024, 6:37 p.m.