Code and analyses associated with "Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance" (Durbin et al., 2020)
- Initial data cleaning performed in
notebooks/angus_join.Rmd. A rendered walk-through of initial data cleaning can found athtml/angus_join.html. - Some formatting of genotype files for various programs in
notebooks/geno_format.Rmd - Some genotyped sample metadata formatting in
notebooks/f250_ids.Rmd
- Contemporary grouping
- Age analyses performed in
source_functions/age.snakefile - Calving season analyses performed in
source_functions/calving_season.snakefile - Grazing vs. not grazing toxic fescue analyses performed in
source_functions/fescue.snakefile
- Age analyses performed in
- Variance component & breeding value estimation using final contemporary group definition performed in
source_functions/general_varcomp.snakefile - Iterative variance component estimation for calculation of bias performed in
source_functions/bias.snakefile - Weaning weight
- All analyses involving the genetic relationship between hair shedding and weaning weight performed in
source_functions/ww_genetic_corr.snakefile - Analyses involving the phenotypic relationship between hair shedding and weaning weight, including simple linear models, performed in
notebooks/ww_pheno_corr.Rmd
- All analyses involving the genetic relationship between hair shedding and weaning weight performed in
- GWAS using SNP1101 performed in
source_functions/snp1101_gwas.snakefile
For each analysis Snakefile, the corresponding config file can be found in source_functions/config and the corresponding BLUPF90 parameter file with starting variances in source_functions/par. Each analysis also has a corresponding RMarkdown of results at notebooks/ with rendered results at html/. For most analyses, raw variance component and genetic correlation estimates can be found in data/derived_data/.