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Software The
W-test website: http://www2.ccrb.cuhk.edu.hk/wtest/
·
Software available in R and C++ ·
This software conducts the W-test
for main effect and pairwise epistasis effect testing in genetic association
study (GWAS) case and control data set. ·
Reference: MH Wang, R Sun, J Guo, H
Weng, J Lee, I Hu, PC Sham and BCY Zee (2016). A fast and powerful W-test for pairwise
epistasis testing. Nucleic Acids Research. The
Zoom-Focus Algorithm (zfa) software ·
zfa package in R - updated 2018.06.29 o Reference manual: zfa.pdf o Windows binaries: zfa_3.0.zip o Package source: zfa_3.0.tar.gz o The zfa3.0 version adds a visualizing plot to show the distribution of association
effect size and direction, and enables the calculation for any gene size
using a method called fuzzy-zfa (not published yet). A function is added to
calculate genomic control factor for rare variants to control potential
population stratification ·
Description: o This software locates the optimal testing region to conduct rare
variant association test and performs the test. Currently incorporated rare
variant tests include: SKAT, SKAT-O, weighted burden test, and the W-test
collapsing method. The function calls the existing package ‘SKAT’. It is
suitable to be applied on whole exome or genome-sequencing data set composed
of variants with minor allele frequency < 1%. ·
Reference: MH Wang, H Weng, R Sun, J Lee, WKK Wu, KC Chong, BCY Zee (2017) A
Zoom-Focus Algorithm (ZFA) to locate the optimal testing region for rare
variant association tests. Bioinformatics. doi:
10.1093/bioinformatics/btx130 PDF Feedback to our software is
welcomed! Please drop a message to maggiew@cuhk.edu.hk.
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