pcrelateMakeGRM {GENESIS} | R Documentation

## 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`.

### 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. `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.

[Package GENESIS version 2.10.1 Index]