README.md

In MathieuEmily/EpiTag: TagSNP selection for epistasis

EpiTag

The aim of this package is to propose a method for selecting TagSNPs to optimize power for detecting epistasis.

Installation

To install and load the package in R

library(devtools)
install_github("MathieuEmily/EpiTag")
library(EpiTag)

Function EpiTag can take as input two data.frame Region1 and Region2, where Region1 has n rows (individuals) and p1 columns (number of SNPs) and Region2 has n rows (individuals) and p2 columns (number of SNPs). Cell (i,j) of the input matrices contains the allele or the genotype of the individual i for the SNP j.

Example:

data(RegionA)
data(RegionB)

By typing

res.EpiTag <- EpiTag(Region1=RegionA,Region2=RegionB,threshold=0.81,allelic=TRUE)

you can get the set of tag SNPs selected in each genomic region:

> res.EpiTag$tagSNPs.R1
[1] "SNPA.4"
> res.EpiTag$tagSNPs.R2
[1] "SNPB.3"

MathieuEmily/EpiTag documentation built on May 8, 2019, 9:48 a.m.