get_stats_multiallele: Perform linear regression on multi-allele markers.

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

Perform linear regression on multi-allele markers.

Description

This function performs the multi-allele version of linear regression. It is used in singlescan and one_singlescanDO. It performs marker-by-marker linear regressions for each trait and adjusts for covariates. It collects parameters from the linear models and returns for downstream use.

Usage

get_stats_multiallele(phenotype, genotype, covar_table, ph_family, ref_col)

Arguments

phenotype	A phenotype vector
genotype	genotypes of the marker being tested. If this is a vector, it will be converted into a one-column matrix. If it is a matrix, each column represents an allele, and each row represents an individual.
covar_table	The covariate matrix, with each covariate in a column, and each individual in a row.
ph_family	a character string for a description of the error distribution. Can be either "gaussian" or "binomial"
ref_col	The column belonging to the reference allele. The reference allele is removed from the genotype matrix so that the matrix is linearly independent. There are only n-1 degrees of freedom in the genotype matrix, where n is the number of alleles.

Value

a list with "stats", "pval", "score" stats is a matrix holding the t statistics and slopes (beta coefficients) from the linear model. pval holds the p value for the marker overall and score holds the test statistic for the marker overall.

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