GENESIS (version 2.2.2)

pcrelateMakeGRM: Creates a Genetic Relationship Matrix (GRM) of Pairwise Kinship Coefficient Estimates from PC-Relate Output

Description

pcrelateMakeGRM is used to create a genetic relationship matrix (GRM) of pairwise kinship coefficient estimates from the output of pcrelate.

Usage

pcrelateMakeGRM(pcrelObj, scan.include = NULL, scaleKin = 2)

Arguments

pcrelObj

The object containing the output from pcrelate. This could be a list of class pcrelate or an object of class gds.class read into R using the function openfn.gds from the gdsfmt package.

scan.include

A vector of IDs for samples to be included in the GRM. The default is NULL, which includes all samples in pcrelObj.

scaleKin

Specifies a numeric constant to scale each estimated kinship coefficient by in the GRM. The default value is 2.

Details

This function provides a quick and easy way to construct a genetic relationship matrix (GRM) from the output of pcrelate.

References

Conomos M.P., Reiner A.P., Weir B.S., & Thornton T.A. (2016). Model-free Estimation of Recent Genetic Relatedness. American Journal of Human Genetics, 98(1), 127-148.

See Also

pcrelate for the function that performs PC-Relate. pcrelateReadKinship for the function that creates a table of pairwise kinship coefficient and IBD sharing probabilities from the same PC-Relate output file. pcrelateReadInbreed for the function that creates a table of inbreeding coefficient estimates from the same PC-Relate output file.