Statistical analysis of a biomarker is often complicated because the detection range of the assay of the biomarker is restricted. The limits of detection (LOD) are the floor and/or ceiling values of the biomarker that can be accurately measured by a particular assay type. Any value of the biomarker beyond the range of LOD, either smaller than the lower LOD or larger than the upper LOD, cannot be determined accurately. Those observations, so-called non-detects (NDs), cannot simply be excluded from the analysis, because NDs are not 'missing at random'. They can be considered as censored data, and can therefore be best analyzed by using statistical methods for survival analysis.
lodGWAS is a flexible package for running genome-wide association analysis of a biomarker that accounts for the problem of limit of detection of the assay. It treats non-detected values as censored, and performs a parametric survival analysis on the phenotype of interest.
The analysis itself is carried out by the function
A second function,
lod_QC, can be used to check
if the coding of LOD values in the phenotype file is correct.
|License:||GPL (>= 3)|
Ahmad Vaez, Ilja M. Nolte, Peter J. van der Most
Maintainer: Ilja M. Nolte <firstname.lastname@example.org>
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