Supporting data for Robledo-Ruiz et al. (2023)

Supporting data for manuscript:
Robledo-Ruiz D. A., Austin L., Amos J. N., Castrejón-Figueroa J., Magrath M. J.  L., Sunnucks P. & Pavlova A. (submitted)  Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex-assignment.

Data usage:
The three directories have the datasets and scripts for the eastern yellow robin (EYR), yellow-tufted honeyeater (YTH) and Leadbeater's possum (LBP), respectively.

*_Results.Rmd
R script to process outputs from 'standard regime' and 'removing sex-linked loci' regime.

filtering_regime_using_filter.sex.linked
Folder with the script and input data required for 'Removing sex-linked loci' filtering regime.

filtering_regime_notusing_filter.sex.linked
Folder with the script and input data required for 'Standard' filtering regime.

filter.sex.linked_requirements
Folder with the script and input data required to replicate the analyses that investigated the minimum requirements for functions filter.sex.linked and infer.sex

filter.sex.linked_validation
Folder with the script and input data required to replicate the analyses that validated the results of function filter.sex.linked