Genetic Analysis of Pooled Samples
Calculate Allelic Richness
Associate Dye Names in Batch Import Output
Perform Bootstrap Analysis
Check .fsa Version and Batch Information
Clean Scores Data
K-means Clustering
Cluster From Samples
Data Manipulation for Marker Data
Distance Correlation
Calculate Empirical Standard Error
Batch Import of .fsa files
Retrieve Metadata
Gene Identity Matrix
Genetic Distance Matrix
Nei's GST
Pairwise Jost D between replicates
Calculate Jost's D
Transform LF to TDF
Load Genetic Data
Multi Dimensional Scaling (MDS) Plot
Post-consolidation Data Manipulation
pooledpeaks: Genetic Analysis of Pooled Samples
Pre GST Calculation
Calculate Pre-Jost's D
Replicate Check for Duplicate Samples
Random Walk Covariance Distance Matrix
Sample Of Loci
Score Markers Wrapper
Calculate Two-Level GST
Typed Loci
Analyzing genetic data obtained from pooled samples. This package can read in Fragment Analysis output files, process the data, and score peaks, as well as facilitate various analyses, including cluster analysis, calculation of genetic distances and diversity indices, as well as bootstrap resampling for statistical inference. Specifically tailored to handle genetic data efficiently, researchers can explore population structure, genetic differentiation, and genetic relatedness among samples. We updated some functions from Covarrubias-Pazaran et al. (2016) <doi:10.1186/s12863-016-0365-6> to allow for the use of new file formats and referenced the following to write our genetic analysis functions: 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>.
Useful links