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. Please check out the Contributing Guidelines for information on how to add to this package.

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")

Features

For a detailed example of how to apply the functions contained in this package please see the Introduction to Using the pooledpeaks Workflow. Example data can be found on GitHub under the inst/extdata folder including .fsa files and a formatted "Multiplex_frequencies.txt" file for the Genetic Analysis portion.

• Peak Scoring: Process .fsa files and score peaks contained therein.

check_fsa_v_batch()
fsa_metadata()
fsa_batch_imp()
associate_dyes()
score_markers_rev3()

• Data Manipulation: Clean and prepare peak data for downstream analyses.

clean_scores()
lf_to_tdf()
data_manipulation()
Rep_check()
PCDM()
LoadData()

• Population Genetics Analysis:

  • Calculate Gene Identity Matrix and Genetic Distance Matrix

  • Calculate diversity indices

  • Calculate differentiation indices

  • Perform cluster analysis

TypedLoci()
GeneIdentityMatrix()
GeneticDistanceMatrix()
GST()
JostD()
cluster()

• Visualization: Visualize the peak scoring and genetic analysis results.

MDSplot()

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

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