Package Overview

pooledpeaks is designed for analyzing genetic data obtained from Fragment Analysis output files (.fsa) of pooled biological samples. It provides functions for a comprehensive analysis pipeline from processing .fsa files, to cleaning the peak data, and conducting population genetic analyses. Some features are listed below and a usage example of the entire pipeline is included as a vignette.

Features

• Peak Scoring: Process .fsa files and score peaks contained therein.
• Data Manipulation: Clean and prepare peak data for downstream analyses.
• Population Genetics Analysis:
  • Calculate Gene Identity Matrix and Genetic Distance Matrix
  • Calculate diversity indices
  • Calculate differentiation indices
  • Perform cluster analysis
• Visualization: Visualize the peak scoring and genetic analysis results.

The pooledpeaks package was developed by the Blanton Lab as part of Kathleen Kuesters’ dissertation.

Installation Instructions

You can install the package directly from GitHub using the following instructions:

Open R and copy the following code into your console

Install devtools and pooledpeaks from GitHub

• install.packages(“devtools”)

• devtools::install_github(“kmkuesters/pooledpeaks”)

Install pooledpeaks directly from CRAN

• install.packages(“pooledpeaks”)

References:

• Covarrubias-Pazaran et al. (2016) doi:10.1186/s12863-016-0365-6
• Long et al. (2022) doi:10.1038/s41598-022-04776-0
• Jost (2008) doi:10.1111/j.1365-294x.2008.03887.x
• Nei (1973) doi:10.1073/pnas.70.12.3321
• Foulley et al. (2006) doi:10.1016/j.livprodsci.2005.10.021
• Chao et al. (2008) doi:10.1111/j.1541-0420.2008.01010.x