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

Ahmad Vaez | Zendy; Peter J. van der Most | Zendy; Bram P. Prins | Zendy; Harold Snieder | Zendy; Edwin R. van den Heuvel | Zendy; Behrooz Z. Alizadeh | Zendy; Ilja M. Nolte | Zendy

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

Author(s) -

Ahmad Vaez,

Peter J. van der Most,

Bram P. Prins,

Harold Snieder,

Edwin R. van den Heuvel,

Behrooz Z. Alizadeh,

Ilja M. Nolte

Publication year - 2016

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btw021

Subject(s) - r package , genome wide association study , computer science , limit (mathematics) , software , parametric statistics , computational biology , bioinformatics , data mining , biology , statistics , mathematics , genetics , genotype , programming language , single nucleotide polymorphism , mathematical analysis , gene

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.

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