This is a research repo for our project entitled "Empirical Comparisons of Different Statistical Modelsto Identify and Validate Kernel RowNumber-Associated Variants using NestedAssociation Mapping and Related Populations in Maize".
In this study, we compared different statistical models for doing GWAS and cross-validated the KRN-associated variants identified in the initial GWAS using three unrelated populations. The KRN-associated variants identified in this study have the potential to enhance our understanding of the developmental steps involved in ear development.
This project contains ~400 commits. A largedata directory was intentionally ignored by adding to gitignore because of the large size of the files within the folder. To guide the visitors having a better idea about the repo, here we briefly introduce the functions or sepecific purposes of the directory system. The layout of directories is based on the idea from ProjectTemplate.
- cache: Here we store intermediate data sets that are generated during a preprocessing step.
- data: Here we store our raw data of small size. Data of large size, i.e. > 100M, store in a
largedatafolder that has been ignored usinggitignore. - doc: Documentation codes (i.e. Rmd files) for generating the figures.
- graphs: Graphs produced during the study.
- lib: Some functions for our work.
- profilling: Analysis scripts for the project. It contains some sub-directories.
- table: Table produced during the study.
Rmd code to generate some of the Figures in the paper.
This repo is free and open source for research usage, licensed under GPLv2.