get_geno_with_covar: Return the genotype matrix with covariates added.

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

Return the genotype matrix with covariates added.

Description

For pairwise testing, cape appends the covariates to the genotype matrix. This function performs that task.

Usage

get_geno_with_covar(
  data_obj,
  geno_obj = NULL,
  g_covar = TRUE,
  p_covar = TRUE,
  for_pairscan = TRUE
)

Arguments

data_obj	The cape object. See Cape.
geno_obj	A genotype object.
g_covar	A logical value indicating whether to append genotype-derived covariates to the final matrix. Defaults to TRUE.
p_covar	A logical value indicating whether to append phenotype-derived covariates to the final matrix. Defaults to TRUE.
for_pairscan	If TRUE, the function returns the genotype matrix already designated for the pairscan. Otherwise it returns the full genotype matrix as specified by data_obj$geno_names.

Value

Returns a genotype matrix with covariates appended.

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