get_marker_covar: Get genotype or covariate values

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

Get genotype or covariate values

Description

In some cape results plotting functions either marker genotypes or covariates can be used for plotting effects on traits. However markers and covariates are stored in different places so it can be annoying to retrieve their values.

Usage

get_marker_covar(data_obj, geno_obj, marker_covar_names)

Arguments

data_obj	A Cape object
geno_obj	A genotype object
marker_covar_names	A vector of strings which can contain marker names with alleles appended or covariate names.

Details

This function looks both in the genotype matrix and in covariate tables to find those values.

Value

This function returns a matrix with individuals in rows and markers/covariates in columns.

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