CrypticIBDcheck can be used 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 as related by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from one of several common close relationships. The methods are particularly relevant to candidate-gene association studies, in which dependent SNPs cluster in a relatively small number of genes spread throughout the genome.
The main function in CrypticIBDcheck is IBDcheck,
which uses SNP information to estimate
IBD coefficients for pairs of study subjects and optionally for
simulated pairs of subjects and returns an object of class IBD.
The plot method for the IBD class, plot.IBD,
displays the IBD coefficients for
pairs of study subjects, along with prediction ellipses for known
relationship pairs.
The package comes with two vignettes: CrypticIBDcheck gives
an overview of the package and describes the methodology used, and
IBDcheck-hapmap illustrates how to use the package
to explore cryptic relatedness using genome-wide data from HapMap.
rJPSGCS