pcrelateReadKinship {GENESIS} | R Documentation

## 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`. This function is deprecated; `pcrelate` now returns this table as `kinBtwn`.

### 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.

### 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. `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.

[Package GENESIS version 2.12.4 Index]