JC School of Public Health and Primary Care
(JC SPHPC) | Faculty of Medicine | The Chinese University of Hong Kong
(CUHK) | Hong Kong SAR
JC School of Public Health and Primary Care (JC SPHPC) | Faculty of Medicine | The Chinese University of Hong Kong (CUHK) | Hong Kong SAR
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
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 firstname.lastname@example.org.