one_pairscan_parallel {cape} | R Documentation |
This is an internal function to run a single pairscan
It is used both to do the actual pairscan
(pairscan_kin
and pairscan_noKin
),
as well as to do the permutations of the pairscan
pairscan_null
).
Description
This is an internal function to run a single pairscan
It is used both to do the actual pairscan
(pairscan_kin
and pairscan_noKin
),
as well as to do the permutations of the pairscan
pairscan_null
).
Usage
one_pairscan_parallel(
data_obj,
phenotype_vector,
genotype_matrix,
int = NULL,
covar_vector = NULL,
paired_markers,
n_perm = 0,
run_parallel = FALSE,
verbose = FALSE,
n_cores = 4
)
Arguments
data_obj |
a |
phenotype_vector |
A vector of trait values |
genotype_matrix |
A matrix of genotypes for markers to be tested |
int |
the interaction term added to the linear model
when the kinship correction is being used. This term is
calculated in |
covar_vector |
a vector or matrix of covariates to be used. |
paired_markers |
a two-column matrix indicating which
marker pairs should be tested. The pairs are assigned in
|
n_perm |
the number of permutations to be performed. |
run_parallel |
a logical value indicating whether to use parallel computing |
verbose |
a logical value indicating whether progress should be printed to the screen. |
n_cores |
the number of CPUs to use if run_parallel is TRUE. |
Value
This function returns a list with two slots: pairscan_results and pairscan_perm Each of these elements is also a list containing effect sizes, standard errors, and covariance matrices for the pairwise tests.