one_singlescanDO: Performs marker regression

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

Performs marker regression

Description

This is an internal function called by pairscan_null when generating the null distribution for significance testing. To perform permutations, we permute trait values, and then re-do the singlescan, marker selection, and the pair scan on the permuted data. This function performs the singlescan on the permuted data.

Usage

one_singlescanDO(
  phenotype_vector,
  genotype_mat,
  model_family,
  ref_allele = "A",
  covar_table = NULL,
  run_parallel = FALSE,
  n_cores = 4
)

Arguments

phenotype_vector	A vector of phenotype values, one entry for each individual.
genotype_mat	A matrix of genotype values with individuals in rows and markers in columns. Matrix entries contain the probability of the reference allele at each position for each individual.
model_family	Indicates the model family of the phenotypes. This can be either "gaussian" or "binomial".
ref_allele	the reference allele from the Cape data_obj
covar_table	A matrix of covariates with one row per individual.
run_parallel	A logical value indicating whether multiple processors should be used
n_cores	The number of processors to use if run_parallel is TRUE.

Value

This function returns the t_statistics for all linear models testing the effects of each marker on the phenotype.

TheJacksonLaboratory/cape documentation built on Feb. 12, 2024, 4:34 p.m.