GENESIS (version 2.2.2)

pcrelateReadInbreed: Create a Table of Inbreeding Coefficient Estimates from PC-Relate Output

Description

pcrelateReadInbreed is used to create a table of inbreeding coefficient estimates from the output of pcrelate.

Usage

pcrelateReadInbreed(pcrelObj, scan.include = NULL, f.thresh = NULL)

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 table. The default is NULL, which includes all samples in pcrelObj.

f.thresh

Specifies a minimum value of the estimated inbreeding coefficient to include in the table; i.e. only individuals with an estimated inbreeding coefficient greater than f.thresh will be included in the table. The default is NULL, which includes all individuals.

Details

This function provides an easy way to make a table of estimated inbreeding coefficients.

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. pcrelateMakeGRM for the function that creates a genetic relationship matrix (GRM) of pairwise kinship coefficient estimates from the same PC-Relate output file.