select_pheno: This function selects the phenotypes in a Cape object

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

This function selects the phenotypes in a Cape object

Description

Updates the pheno object to include only 'pheno_which' columns. Optionally scale and/or normalize traits.

Usage

select_pheno(
  data_obj,
  pheno_which,
  min_entries = 5,
  scale_pheno = FALSE,
  rank_norm_pheno = FALSE
)

Arguments

data_obj	a Cape object
pheno_which	vector of names from the parameters YAML file. This vector should include both traits and covariates. The covariates are assigned after trait selection.
min_entries	minimum number of data entries the phenotype needs to have for it to be included. If any trait has fewer than min_entries, It will be removed with a warning.
scale_pheno	if TRUE then phenotypes are mean-centered and standardized
rank_norm_pheno	if TRUE then phenotypes are rank Z normalized

Value

updated Cape object

Examples

## Not run: 
data_obj <- select_pheno(data_obj, pheno_which = c("BW_24", "INS_24", "log_GLU_24"))

## End(Not run)

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