one_singlescanDO {cape} | R Documentation |
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.