get_geno_with_covar: Return the genotype matrix with covariates added.

Description Usage Arguments Value

View source: R/get_geno_with_covar.R

Description

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

Usage

1
2
3
4
5
6
7
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.


cape documentation built on Feb. 10, 2021, 5:06 p.m.