README.md

Rscripts for genomics analysis

1) gemma_output_results.R

Overview

This R script extract results from gemma outputs, generates QQ plots and Manhattan plots, extracts significant (SNPs), and computes relevant statistics from log files.

Usage

Rscript gemma_output_results.R <P_wald_threshold>

Requirements

Make sure you have R installed on your system. Additionally, the script requires the following R packages, which will be installed automatically if not found:

• qqman
• extrafont

2) MDS.plots.from_plink.R

Usage

Rscript MDS.plots.from_plink.R plink_output.mds

Pefrom MDS plots from plink.mds file output after preforming IBD analysis please read from https://zzz.bwh.harvard.edu/plink/strat.shtml