False discovery rate calculations for genome-wide association study of reproductive fitness in Drosophila melanogaster (Sussex LHM sample)

<p>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.</p> <p>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.</p> <p>This version differs from the original in that: i) Some gene positions/names have been reassigned for accuaracy in the input data. ii) A file containing the p-value thresholds corresponding to an FDR of 0.1 has been added. The 95% credible intervals for each SNP association have been added to the results data files.