HAPPI_GWAS

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

Usage

1. Clone the repository: git clone https://github.com/angelovicilab/HAPPI_GWAS.git
2. cd HAPPI_GWAS
3. Rscript setup.R
4. Rscript HAPPI_GWAS.R <yaml file> [COMMANDS]
   • COMMANDS:
     • -help (yaml file is not required)
     • -generateBLUP
     • -generateBLUE
     • -GAPIT
     • -extractHaplotype (optional, dependent on GAPIT parameter)
     • -searchGenes (optional, dependent on GAPIT parameter)

Upgrade Packages

update.packages(ask=FALSE, checkBuilt = TRUE)

Install Packages

• install.packages("dplyr", dependencies = TRUE)
• install.packages("tidyr", dependencies = TRUE)
• install.packages("ggplot2", dependencies = TRUE)
• install.packages("tibble", dependencies = TRUE)
• install.packages("stringr", dependencies = TRUE)
• install.packages("gplots", dependencies = TRUE)
• install.packages("ape", dependencies = TRUE)
• install.packages("BiocManager", dependencies = TRUE)
• install.packages("car", dependencies = TRUE)
• install.packages("data.table", dependencies = TRUE)
• install.packages("DataCombine", dependencies = TRUE)
• install.packages("EMMREML", dependencies = TRUE)
• install.packages("foreach", dependencies = TRUE)
• install.packages("doParallel", dependencies = TRUE)
• install.packages("lme4", dependencies = TRUE)
• install.packages("scatterplot3d", dependencies = TRUE)
• install.packages("genetics", dependencies = TRUE)
• install.packages("LDheatmap", dependencies = TRUE)
• install.packages("gridExtra", dependencies = TRUE)
• install.packages("yaml", dependencies = TRUE)
• install.packages("bigmemory", dependencies = TRUE)
• install.packages("biganalytics", dependencies = TRUE)
• BiocManager::install("Biobase", update = TRUE, ask = FALSE)
• BiocManager::install("BiocGenerics", update = TRUE, ask = FALSE)
• BiocManager::install("snpStats", update = TRUE, ask = FALSE)
• BiocManager::install("multtest", update = TRUE, ask = FALSE)
• BiocManager::install("zlibbioc", update = TRUE, ask = FALSE)

Updates

May 15, 2020:
We have made changes to the tool and hosted it on https://github.com/Angelovici-Lab/HAPPI.GWAS. Please checkout the latest tool.