In knausb/GAPIT3documentation: Documentation for GAPIT3

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
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library(GAPIT3documentation)
knitr::opts_chunk$set(fig.align = "center")

GAPIT3documentation

GAPIT3 is the Genome Association Predicted Integrated Tool, a tool to help discern genetic contributions to the phenotpyes we observe.

knitr::include_graphics("gapit3.png")

How to cite GAPIT3

The GAPIT project has been the result of several publications on methodology and tehir implementation as software. Please cite these in order to acknowledge their contribution and to encourage future contribution.

Method | Method paper | GAPIT Implementation -----------------------|----------------------|--------------------- CompressionMLM (CMLM) | @zhang2010mixed | @lipka2012gapit gBLUP | @zhang2007use | @lipka2012gapit Enriched CMLM | @li2014enrichment | @tang2016gapit SUPER | @wang2014super | @tang2016gapit MLMM | @segura2012efficient | @wang2020gapit FarmCPU | @liu2016iterative | @wang2020gapit cBLUP and sBLUP | @wang2018expanding | @wang2020gapit BLINK | @huang2019blink | @wang2020gapit

Installation

A first question for a new user is whetehr GAPIT3 is already installed? You can query your system for the presence of GAPIT3 with the following command.

find.package("GAPIT3")

If GAPIT3 is installed, this command should return the location of the package. If it returns an error then you probably need to install it as follows.

devtools::install_github("jiabowang/GAPIT3",force=TRUE)

You can install this documentation package as well.

devtools:install_github("knausb/GAPIT3documentation", build_vignettes = TRUE)

Decided you did not need this package after all? You can remove it as follows.

remove.packages(pkgs = "GAPIT3")
remove.packages(pkgs = "GAPIT3documentation")

Tutorials

A basic scenario

References

knausb/GAPIT3documentation documentation built on Sept. 24, 2022, 11:38 a.m.