In jiabowang/GAPIT3: GAPIT (Genomic Association and Prediction Integrated Tool)

knitr::opts_chunk$set(collapse = T, comment = "#>")
options(tibble.print_min = 4, tibble.print_max = 4)

knitr::opts_chunk$set(eval=FALSE)

A few tips and tricks for installing GAPIT. You can skip these steps and try to run this:

remotes::install_github("jiabowang/GAPIT", force=TRUE)
library(GAPIT)

If you do not have {remotes} installed, then install it first:

install.packages("remotes")

If you are able to load the GAPIT library, congratulations! If not, read and implment the following instructions.

Windows Users

Install RTools.

GAPIT needs to be compiled. Mac and Linux systems already have C compilers installed on their systems, but Windows systems often do not. You may need to install RTools to access a C compiler (that is configured to work with R). RTools is a program, not a package, so follow the link and read the instructions for download and installation.

Everyone

Several accessory packages are used by GAPIT that must be downloaded from Bioconductor and GitHub.

Install Bioconductor Packages

1. Install Bioconductor:

install.packages("BiocManager")

1. Install snpStats & multtest from Bioconductor:

BiocManager::install("snpStats")
BiocManager::install("multtest")

Install GitHub packages

The package {LDheatmap} must be installed from GitHub since it is currently not on CRAN.

remotes::install_github("SFUStatgen/LDheatmap")

Install GAPIT

remotes::install_github("jpiaskowski/GAPIT",force=TRUE)
library(GAPIT)

jiabowang/GAPIT3 documentation built on March 6, 2025, 2:21 a.m.