pcrelateToMatrix: Creates a Genetic Relationship Matrix (GRM) of Pairwise...

In smgogarten/GENESIS: GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness

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

Description

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

Usage

## S4 method for signature 'pcrelate'
pcrelateToMatrix(pcrelobj, sample.include = NULL, thresh = NULL, scaleKin = 2, 
                 verbose = TRUE)

Arguments

pcrelobj	The object containing the output from pcrelate. This should be a list of class pcrelate containing two data.frames; kinSelf with inbreeding coefficient estimates and kinBtwn with pairwise kinship coefficient estimates.
sample.include	A vector of IDs for samples to be included in the GRM. The default is NULL, which includes all samples in pcrelobj.
thresh	Kinship threshold for clustering samples to make the output matrix sparse block-diagonal. This thresholding is done after scaling kinship values by scaleKin. When NULL, no clustering is done. See 'Details'.
scaleKin	Specifies a numeric constant to scale each estimated kinship coefficient by in the GRM. The default value is 2.
verbose	Logical indicator of whether updates from the function should be printed to the console; the default is TRUE.

Details

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

thresh sets a threhsold for clustering samples such that any pair with an estimated kinship value greater than thresh is in the same cluster. All pairwise estimates within a cluster are kept, even if they are below thresh. All pairwise estimates between clusters are set to 0, creating a sparse, block-diagonal matrix. When thresh is NULL, no clustering is done and all samples are returned in one block. This feature may be useful for creating a sparse GRM when running association tests with very large sample sizes. Note that thresholding is done after scaling kinship values by scaleKin.

Value

An object of class 'Matrix' with pairwise kinship coefficients.

Author(s)

Matthew P. Conomos

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.

smgogarten/GENESIS documentation built on Nov. 10, 2024, 8:49 p.m.