one_pairscan_parallel: This is an internal function to run a single pairscan It is...

In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

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 Cape object
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 pairscan_kin.
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 pairscan by get_pairs_for_pairscan. They are checked for pairwise correlations before being sent to the pairscan.
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.

cape documentation built on May 20, 2022, 1:06 a.m.