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Avalos-PanEtAl2020_GWAS

Repository containing raw code for kinship estimate and also individual-, and colony-level GWAS conducted in the Avalos & Pan et al., 2020 study

File information

01_kinship.R

  • The purpose of this script is to estimate the kinship and genetic relationship matrices.

02_GWAS_individual.R

  • The purpose of this script is to conduct a genome wide association analysis of individual phenotype.

03_GWAS_colony.R

  • The purpose of this script is to conduct a genome wide association analysis using per-colony phenotype and minor allele.

all210_idx.RDS

  • This is a file containing per-sample meta data for individuals used in this study.

snpset.RDS

  • This is a file containing IDs of markers concordant between two independent variant-calling pipelines (see source publication for details).

Note

In the code file: "worker_mvcall.phasedimputed.snp.gds" is referenced, this is a dataset file deposted in Dryad, see:

Avalos, Arián (2020), Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies, Dryad, Dataset, https://doi.org/10.5061/dryad.q573n5tg8