pairscan_noKin: Perform pairscan without a kinship correction

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

Perform pairscan without a kinship correction

Description

This internal function is called by pairscan when no kinship correction is requested. It can be compared to pairscan_kin. It fits pairwise linear models to estimate the effects of marker pairs on each trait.

Usage

pairscan_noKin(
  data_obj,
  pheno_mat,
  geno_mat,
  covar_table,
  marker_pairs,
  n_perm,
  verbose = FALSE,
  run_parallel = FALSE,
  n_cores = NULL
)

Arguments

data_obj	a Cape object
pheno_mat	The matrix of trait values with individuals in rows and traits in columns.
geno_mat	The matrix of genotypes to be tested
covar_table	The matrix of covariates with individuals in rows.
marker_pairs	A two-column matrix containing the marker pairs to be tested.
n_perm	The number of permutations to be run
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 calls one_pairscan_parallel and returns results for each trait as an element in a list.

cape documentation built on May 29, 2024, 5:11 a.m.