cape (version 3.1.0)

pairscan_noKin: 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.