outerSnpListInteraction: Pairwise Interaction Test Outer The SNP Lists

In FRGEpistasis: Epistasis Analysis for Quantitative Traits by Functional Regression Model

Description

Test the SNP-SNP interaction. And the SNPs are organized into two different SNP Lists.

Usage

outerSnpListInteraction(pheno, snpList1, snpList2)

Arguments

pheno	Vector of phenotype data.
snpList1	Matrix of the genotypes of all the SNPs on the first SNP list for testing the pairwise interactions.
snpList2	Matrix of the genotypes of all the SNPs on the second SNP list for testing the pairwise interactions.

Details

This function aims to test the pairwise interactions between the SNPs organized into different data structures. It takes phenotype and genotypes of the SNPs as the input. And output all the p values for the interactions of SNP pairs.

Value

Return a frame contains names of all the SNPs pairs and p values for interactions of these pairs.

Author(s)

Futao Zhang

Examples

snp_list_1 <- as.data.frame(matrix(round(runif(3000,0,2)),1000,3))
snp_list_2 <- as.data.frame(matrix(round(runif(5000,0,2)),1000,5))
colnames(snp_list_1 )<-c("rs10","rs11","rs12")
colnames(snp_list_2 )<-c("rs20","rs21","rs22","rs23","rs24")
pheno<- round(runif(1000,40,60))
outerSnpListInteraction(pheno,snp_list_1,snp_list_2)

Example output

Loading required package: MASS
Loading required package: fda
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

The following object is masked from 'package:graphics':

    matplot

   snp1 snp2       pval
1  rs10 rs20 0.49230423
2  rs10 rs21 0.19595688
3  rs10 rs22 0.51305321
4  rs10 rs23 0.44934658
5  rs10 rs24 0.15068855
6  rs11 rs20 0.18181302
7  rs11 rs21 0.67590924
8  rs11 rs22 0.13996027
9  rs11 rs23 0.57738850
10 rs11 rs24 0.77921465
11 rs12 rs20 0.66654538
12 rs12 rs21 0.41549860
13 rs12 rs22 0.08124968
14 rs12 rs23 0.44049944
15 rs12 rs24 0.03967868

FRGEpistasis documentation built on Nov. 8, 2020, 5:51 p.m.