Sib-pair Command: ibs


ClassAnalysis and data manipulation command
Nameibs
Arguments ibs [kin | moment | <binary trait> | <quantitative trait> >|>=|<|<=|==|^= <threshold>]

Prints the estimated mean identity-by-state sharing at all active markers for all pairs in the dataset as a list of pairs. If a binary trait is specified, sharing is only calculated for pairs where both are affected. Ungenotyped individuals are skipped completely, but genotyped individuals sharing no markers with any other individual will be evaluated (so the mean IBS will be printed as missing). If a binary trait is specified, only affected individuals are utilized.

If the kin modifier is present, MLEs for the kinship coefficients are printed. These are estimated using the EM algorithm of Choi et al 2009. The moment modifier gives the shrinkage estimate of the kinship matrix of Endelman and Jannink [2012]. Those authors claim the method gives better genomic EBVs using sparse SNP sets when phenotypes are available.

Example:

>> include linclex.in
>> ibs 
>> ibs lincl

References

Choi Y, Wijsman EM, Weir BS (2009): Case-Control Association Testing in the Presence of Unknown Relationships. Genetic Epidemiology 33: 668­678.

Endelman JB, Jannink J-L (2012): Shrinkage Estimation of the Realized Relationship Matrix. G3 2: 1405-1413.


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