labroo2/deStructure: An S3 Class to work with structure files

This R package, deStructure, holds functions that facilitate working with the program STRUCTURE (Pritchard et al., 2003). The functions mainparams and extraparams write the input files (excluding the genotype data) needed to run STRUCTURE, while structure_scriptwriter outputs bash scripts which run STRUCTURE through a given value of K clusters and n replications. The scripts are compatible with UNIX-based high performance computing clusters. After STRUCTURE is run, the function deStruct parses the output file into R and can import each file into an object of the S3 class deStruct. If clusters are ordered consistently within the deStruct objects, average_runs can average across a list of deStruct objects which are replicated runs of STRUCTURE for a given value of K. Please note that in this implementation, the user must manually reorder clusters within the deStruct objects if needed, so that the clusters intended be averaged across runs are aligned in the same positions across files. Finally, structure_plot plots the Q values (ancestry) from each cluster for each individual in barplots. Please also note that the deStruct class only supports output files from STRUCTURE used with the parameters specified in the README file at this time. In the future, we hope to add support for more STRUCTURE output filetypes as well as automatic ordering of clusters within deStruct objects.

install.packages("remotes")
remotes::install_github("labroo2/deStructure")