Data Analysis
The participants are required to download the data files and the excel add-in (Genalex file) from the server\escetu\courses\modules\TP génétique\PGDA.
GenAlEx
GenAlEx - Genetic Analysis in Excel \cite{Peakall_2012} is an Excel add-in that can be freely downloaded from \cite{website}. GenAlEx can be installed into the Excel ribbon or can be used directly into the Excel spreadsheet and provides very easy-to-use functions to handle the genetic data and simple analyses of forensic and population genetics interest. It is also useful to export the genotype data in a variety of other types of input files, that can be directly imported into other softwares (including R).
R Packages
The participants are advised to install following R packages;
- poppr \cite{Kamvar_2014}
- adegenet \cite{Jombart_2008}
- ggplot2 \cite{wickham2016}
- dplyr \cite{dplyr}
- FORSTAT (A shiny app available at \cite{Ristow_2017}
Description of data
The server folder contains three datasets containing DNA profiles collected from the individuals belonging to different populations of three different countries. Here is the description of each dataset;
US Dataset
This dataset contains genotypes of 1036 individuals at 29 autosomal STR loci from four populations living in the United States of America and is available at \cite{Hill2013}. This data includes STR profiles from African American (n = 342), Caucasian (n = 361), Hispanic (n = 236) and Asian (n = 97) population.
China Dataset
This dataset contains genotypes from 1814 individuals at 15 autosomal STR loci \cite{Zhan_2018} from Manchu (n = 296), Mongol (n = 507), Kyrgyz (n = 550) and Uzbek (n = 461) populations.
Pakistan Dataset
This dataset contains genotypes from 520 individuals from Punjabi (n = 130), Saraiki (n = 130), Sindhi (n = 130) and Pakhtun (n = 130) populations of Pakistan \cite{Anwar_2018}.
Input file preparation
We will start the data analyses by importing the dataset in GenAlEx , and then some statistical tests will be performed. In order to import the DNA profiles in GenAlEx, the participants are advised to follow the instructions given in Fig \ref{802017}.