False Discovery Rate Calculations For Genome-Wide Association Study Of Reproductive Fitness In Drosophila Melanogaster (Sussex Lhm Sample)

R code and results of applying false discovery (FDR) rate calculations to establish statistical signficance in a genome-wide association study of reproductive fitness in Drosophila melanogaster. Phenotype values were generated on hemiclone female and male lines from an outbred, laboratory adapted population. Thus, GWAS were previously performed seperately on the phenotype values for each sex, and also using a bivariate GWAS implemented in the R package multiPhen. FDR calculations were performed using the R package 'fdrtool' on all SNPs, and on LD-independent SNPs, the latter of which was used to determine p-value thresholds for genome-wide significance when all SNPs were considered.本数据集包含将错误发现率（False Discovery Rate，FDR）计算应用于黑腹果蝇（Drosophila melanogaster）繁殖适合度全基因组关联研究（Genome-Wide Association Study，GWAS）以确立统计学显著性的R代码与分析结果。研究所用表型值取自远交且适应实验室环境的种群的半克隆（hemiclone）雌性与雄性品系。此前，研究团队已分别针对两性的表型值开展全基因组关联分析，同时借助R包multiPhen实现双变量全基因组关联分析。 本研究借助R包fdrtool对所有单核苷酸多态性（Single Nucleotide Polymorphism，SNP）开展FDR计算，并针对连锁不平衡（Linkage Disequilibrium，LD）独立的SNP子集进行了相同计算；后者被用于确定当纳入全部SNP时，全基因组显著性所需的P值阈值。