lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection.

Abstract

Genome-wide association study (GWAS) of a biomarker is complicated when the assay procedure of the biomarker is restricted by a Limit of Detection (LOD). Those observations falling outside the LOD cannot be simply discarded, but should be included into the analysis by applying an appropriate statistical method. However, the problem of LOD in GWAS analysis of such biomarkers is usually overlooked. 'lodGWAS' is a flexible, easy-to-use R package that provides a simple and elegant way for GWAS analysis of such biomarkers while simultaneously accommodating the problem of LOD by applying a parametric survival analysis method. http://cran.r-project.org/web/packages/lodGWAS CONTACTS: a.vaez@umcg.nl or i.m.nolte@umcg.nl Supplementary data are available at Bioinformatics online.