Data for "A benchmark for the next generation of genotype–phenotype mapping"

This dataset contains files related to benchmarking different linear methods for genotype-phenotype mapping. This release accompanies the pub, “A benchmark for the next generation of genotype–phenotype mapping.” The following files are different formats of the yeast genotype data created by Nguyen Ba et al. (2022): | File | Description | | --- | --- | | `genotypes_binarized.feather` | Yeast genotype matrix in feather format | | `genotypes_binarized.transposed.tsv` | Yeast genotype matrix in TSV format | | `genotypes.vcf` | Yeast genotype matrix in VCF format | | `genotypes_binarized_subset_5000_snpsubset_1000_centered.feather` | Subsetted centered yeast genotype matrix for running pipeline locally | | `genotypes_binarized_subset_5000_snpsubset_1000_uncentered.feather` | Subsetted uncentered yeast genotype matrix for running pipeline locally | | `genotypes_binarized_subset_5000_snpsubset_1000_ids.feather` | Subsetted list of yeast strain IDs | | `yeast_subset_5000_snpsubset_1000_allele_frequencies.Rda` | Allele frequencies for subsetted yeast genotypes for running pipeline locally | | `SNP_list_pos_corrected.txt` | List of yeast SNP IDs | | `plink_bfile_prefix.fam` | Yeast genotype matrix in plink format (.fam file) | | `plink_bfile_prefix.bed` | Yeast genotype matrix in plink format (.bed file) | | `plink_bfile_prefix.bim` | Yeast genotype matrix in plink format (.bim file) | The following files contain aggregated results from our work. "1510" refers to the seed used to simulate phenotypes for the yeast data and "1105" refers to the seed for the human phenotype generation. The human data orignates from UK Biobank but note that these files contain only downstream summary statistics. Not all yeast files have an equivalent human file so as to protect sensitive data. | File | Description | | --- | --- | | `combined_all_betas_human_1105.feather` | Estimated SNP effects for all methods and traits in human | | `combined_all_betas_yeast_1510.feather` | Estimated SNP effects for all methods and traits in yeast | | `human_littlelonger_with_fullinfo_1105.feather` | Simulated true and estimated effect sizes for all methods and traits in human (in long format) | | `yeast_littlelonger_with_fullinfo_1510.feather` | Simulated true and estimated effect sizes for all methods and traits in yeast (in long format) | | `human_true_avg_distance_1105.feather` | Average distances between simulated true and top estimates for all methods and traits in human | | `yeast_true_avg_distance_1510.feather` | Average distances between simulated true and top estimates for all methods and traits in yeast | | `yeast_cumulative_1510.feather` | Cumulative true and false positives for ROC plot in yeast | | `yeast_roc_1510.feather` | Summarized true and false positives for ROC plot in yeast | | `yeast_roc_approx_250_1510.feather` | Summarized true and false positives for approximate ROC plot in yeast | | `yeast_snp_pairs_1510.feather` | Distances between SNP pairs in yeast | | `all_methods_effects_correlations_yeast_simulated_data_1510_ukbb_simulated_traits_1105.feather` | Variant effect r^2 for all methods and traits for human and yeast in feather format | | `all_methods_max_prediction_correlations_yeast_simulated_data_1510_ukbb_simulated_traits_1105.feather` | Maximum phenotype prediction r^2 for all methods and traits for human and yeast in feather format | | `all_methods_parameters_yeast_simulated_data_1510_ukbb_simulated_traits_1105.feather` | Training parameters for relevant methods and traits for human and yeast in feather format | | `all_methods_prediction_correlations_yeast_simulated_data_1510_ukbb_simulated_traits_1105.feather` | Phenotype prediction r^2 for all methods and traits for human and yeast in feather format | | `yeast_simulated_data_seed_1510_additive_effects_wide.feather` | Simulated true and estimated effect sizes for all traits in yeast (in wide format) | | `yeast_simulated_data_seed_1510_phenotypes.feather` | Simulated phenotypes in yeast | | `yeast_simulated_data_seed_1510_geneticvalues.feather` | Simulated genetic values in yeast (precursor to phenotype) | | `yeast_ld.vcor` | plink2 r2 between pairs of SNPs for yeast |