Scan Pairwise Epistasis
Check chunk size
Parallelized calculation of the difference of correlation coefficients...
Parallelized calculattion of the difference of correlation coefficient...
Calculate HSIC values
Calculate epistasis using HSIC with one genotype input
Calculate epistasis using HSIC with two genotype inputs
Scan pairwise epistasis
Get correlation matrix
index set for idx-th chunk of size chunk for n elements
Write out epistasis result (normal matrix)
Write out epistasis result (symmetric matrix)
Convert Z-score to correponding p-value
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. Pütz, N. Karbalai, B. Müller-Myhsok, and K. Borgwardt. (2011). <doi:10.1093/bioinformatics/btr218>.)