================================= INSTRUCTIONS =============================== This document contains the instructions for installing and using the Zmax package in R. Note: please install and use the package under the R (version 3.5.1) environment with 64-bit, otherwise R may report errors and the package cannot work. The Zmax package will use the R package "mvtnorm". Therefore, make sure that this package has been installed and loaded into R. 1. Install Connect the computer to the internet and choose a CRAN mirror. Then, run the following command in R >install.packages(pkgs="mvtnorm") to install the R package "mvtnorm". For Windows users, download the compiled R package file for Windows "Zmax_0.1.0.zip". Then, use the following command in R to install the package >install.packages(pkgs="Zmax_0.1.0.zip",repos=NULL) For Linux and Unix users, download the compiled R package file for Linux and Unix "Zmax_0.1.0.tar.gz". Then, use the following command in R to install the package >install.packages(pkgs=" Zmax_0.1.0.tar.gz ",repos=NULL) 2. Use Use >library(mvtnorm) >library(Zmax) to load these two packages into R. Use >?Zmax to read the instructions. 3. Example >data <- rbind(c(46,62,28,30,29),c(78,75,37,22,7)) >Zmax(data,method="rmbs") statistic p.value method [1,] "2.199" "0.0405841910975668" "rmbs" >Zmax(data,method="norm") statistic p.value method [1,] "2.199" "0.0361811161504994" "norm" 4. Arguments data A 2x5 contingency table in matrix form. The first row is for cases and the second one is for controls. The first three columns are the number of females carrying 0, 1 and 2 copies of the reference allele, respectively. The last two columns are the number of males carrying 0 and 1 copies of the reference allele, respectively. method The method for calculating the p-value, either "rmbs" (rhombus formula) or "norm" (bivariate normal integral). Note that the default method for this option is ˇ°rmbsˇ±. 5. Values statistic The value of the test statistic Zmax. p.value The p value of Zmax. method A character string indicating the method for calculating the p value of Zmax. 6. References Peng Wang, Si-Qi Xu, Bei-Qi Wang, Wing Kam Fung and Ji-Yuan Zhou. 2018 A Robust and Powerful Test for Case-Control Genetic Association Study on X Chromosome. (submitted) ----------------------------------------------------------------- If you have any questions, please email Dr. Ji-Yuan Zhou at zhoujiyuan5460@hotmail.com