WriteSnpPairs

is the Z score matrix (non-symmetric matrix).

Zmatrix

is the index of Zmarix whose z score is over the given <code>zpthres</code>.

indexArr

is the SNP pairs file for the second stage.

outfile

Write out the result of epistasis analysis. Z score matrix is not a symmetric matrix.

Searching genomic interactions with linear/logistic regression in a high-dimensional dataset is a time-consuming task. This package provides some efficient ways to scan epistasis in genome-wide interaction studies (GWIS). Both case-control status (binary outcome) and quantitative phenotype (continuous outcome) are supported (the main references: 1. Kam-Thong, T., D. Czamara, K. Tsuda, K. Borgwardt, C. M. Lewis, A. Erhardt-Lehmann, B. Hemmer, et al. (2011). <doi:10.1038/ejhg.2010.196>. 2. Kam-Thong, T., B. P<c3><bc>tz, N. Karbalai, B. M<c3><bc>ller-Myhsok, and K. Borgwardt. (2011). <doi:10.1093/bioinformatics/btr218>.)

WriteSnpPairs: Write out epistasis result (normal matrix)

Description

Usage

Arguments

Value