pcrelateReadKinship {GENESIS} | R Documentation |
pcrelateReadKinship
is used to create a table of pairwise kinship coefficient and IBD sharing probability (k0, k1, k2) estimates from the output of pcrelate
.
pcrelateReadKinship(pcrelObj, scan.include = NULL, ibd.probs = TRUE, kin.thresh = NULL)
pcrelObj |
The object containing the output from |
scan.include |
A vector of IDs for samples to be included in the table. The default is NULL, which includes all samples in |
ibd.probs |
Logical indicator of whether or not the output in |
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 |
This function provides an easy way to make a table of pairwise relatedness estimates.
Matthew P. Conomos
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.
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.