pairscan_kin {cape} | R Documentation |
Run the pairscan with a kinship correction
Description
This function is called by pairscan
when a kinship correction is requested. It adjusts
each variable according to the kinship matrix using
kin_adjust
and then fits linear
pairwise models to the adjusted data.
Usage
pairscan_kin(
data_obj,
geno_obj,
scan_what,
marker_pairs,
kin_obj,
verbose = FALSE,
run_parallel = FALSE,
n_cores = 2
)
Arguments
data_obj |
a |
geno_obj |
a genotype object |
scan_what |
A character string uniquely identifying whether eigentraits or raw traits should be scanned. Options are "eigentraits", "raw_traits" |
marker_pairs |
A two-column matrix containing the marker pairs to be tested. |
kin_obj |
a kinship object |
verbose |
A logical value indicating whether to print progress to the screen |
run_parallel |
A logical value indicating whether parallel processing should be used |
n_cores |
The number of cores to be used if run_parallel is TRUE |
Value
This function returns a list with three elements.
The elements contain the marker pair effect sizes, the marker
pair standard errors, and the covariance matrix for each test.
The output is then further processed by pairscan
.