Investigation of SNP Allele Ratios in Selective Sweep Regions: Bermuda vs Domestics

This repo serves as a demonstration of a simple t-test to examine the distribution of SNP allelic ratio differences between Bermuda and Domestic chickens.

Folders

reports: Word documents that communicate analyses, logic, and assumptions.
colors: 2 RGB files with craft color schemes--superior to R or RColorBrewer for heatmap visualization (author: Jun Li)
docs: relevant documents to aid scripted analyses (usually excel files)
functions: functions loaded into scripts for functionally programming
lit: relevant literature to analyses
ppt: PowerPoints supporting analyses
scripts: scripts, almost always in R or R Markdown. To examine scripts and get a sense of the analysis, clone the repo and open the rendered HTML files locally
style: .css files to aid in script rendering from R Markdown to HTML

Nomenclature

File are often named with 3 parts separated by underscores:
- date as an identifier
- explanation
- author/editor

How to follow the analyses

Clone the repo and examine the rendered HTML files by date for a step-by-step analysis of processing these data.

A good example script to examine:
20220214_vcf-annotation_steep/scripts/20220214_vcf-annotation-bermuda_steep.html

Withheld

Data and additional scripts withheld for brevity

Contact