View source: R/one_pairscan_parallel.R
one_pairscan_parallel  R Documentation 
pairscan_kin
and pairscan_noKin
),
as well as to do the permutations of the pairscan
pairscan_null
).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
).
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 )
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 twocolumn 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. 
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.
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