create_refset: Create a set of weakly linked reference SNPs.

In bcm-uga/NaturalGWAS: Simulating Phenotypes and Evaluating GWAS Methods

Description

This function creates a reference set for causal variants in the simulation based on a LD window.

Usage

create_refset(window = 101, chr.pos)

Arguments

window	an integer for the spacing of SNPs in the reference set (should be based on LD information).
chr.pos	a p by 2 matrix where p is the number of SNPs (rows) that contains the genetic map for the genotype matrix. The first column must contain chromosome number (numeric) and the second column must contain the SNP positions for each chromosome.

Value

A vector of reference SNP spaced by window size.

Author(s)

Olivier François

See Also

simu_pheno

Examples

library(naturalgwas)

## Load A. thaliana example
data(A.thaliana)
ref.set <- create_refset(A.thaliana$chrpos, window = 101)

bcm-uga/NaturalGWAS documentation built on Dec. 18, 2019, 12:36 a.m.