GENESIS (version 2.2.2)

pcrelateReadKinship: Create a Table of Pairwise Kinship Coefficient and IBD Sharing Probability Estimates from PC-Relate Output

Description

pcrelateReadKinship is used to create a table of pairwise kinship coefficient and IBD sharing probability (k0, k1, k2) estimates from the output of pcrelate.

Usage

pcrelateReadKinship(pcrelObj, scan.include = NULL, ibd.probs = TRUE,  kin.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.

ibd.probs

Logical indicator of whether or not the output in pcrelObj has estimates of IBD sharing probabilities.

kin.thresh

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

Details

This function provides an easy way to make a table of pairwise relatedness estimates.

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. pcrelateReadInbreed for the function that creates a table of inbreeding coefficient estimates 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.