CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals.

ABSTRACT:

Background

In population association studies, standard methods of statistical inference assume that study subjects are independent samples. In genetic association studies, it is therefore of interest to diagnose undocumented close relationships in nominally unrelated study samples.

Results

We describe the R package CrypticIBDcheck to identify pairs of closely-related subjects based on genetic marker data from single-nucleotide polymorphisms (SNPs). The package is able to accommodate SNPs in linkage disequibrium (LD), without the need to thin the markers so that they are approximately independent in the population. Sample pairs are identified by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from

SUBMITTER: Nembot-Simo A 

PROVIDER: S-EPMC3764977 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature