CCRB – Statgene (Statistical Genetics)

  JC School of Public Health and Primary Care (JC SPHPC)  |  Faculty of Medicine |  The Chinese University of Hong Kong (CUHK)  |  Hong Kong SAR













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    The W-test website:


·        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:

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



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