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HAPPI.GWAS

A genome-wide association study (GWAS) tool written in R.

Installation

You can install the HAPPI.GWAS from Github with:

# Run this inside R environment
install.packages("devtools", dependencies = TRUE)
devtools::install_github("Angelovici-Lab/HAPPI.GWAS")

# Run this in your terminal
mkdir HAPPI_GWAS
cd HAPPI_GWAS
git clone https://github.com/Angelovici-Lab/HAPPI.GWAS.git
cd HAPPI.GWAS
Rscript setup.R

Usage

Rscript HAPPI_GWAS.R [-h] [-generateBLUP] [-generateBLUE] [-GAPIT] [-extractHaplotype] [-searchGenes] input

positional arguments:
  input              Input YAML File

optional arguments:
  -h, --help         show this help message and exit
  -generateBLUP      Generate BLUP data from raw data
  -generateBLUE      Generate BLUE data from raw data
  -GAPIT             Run GAPIT
  -extractHaplotype  Extract haplotype (Require: -GAPIT)
  -searchGenes       Search genes (Require: -GAPIT)

Example

This is a basic example which shows you how to use HAPPI.GWAS:

cd HAPPI_GWAS/HAPPI.GWAS
Rscript HAPPI_GWAS.R -GAPIT -extractHaplotype -searchGenes Demo_GLM.yaml
Rscript HAPPI_GWAS.R -GAPIT -extractHaplotype -searchGenes Demo_FarmCPU.yaml