extract.categories: Read category tracker and extract categorical levels
In NCI-CGR/construct.model.matrix: Construct Model Matrix for `plco-analysis`

Description Usage Arguments See Also

View source: R/categorical.handling.R

This function takes the preprocessor *.categories file, loads its contents, and then uses its annotations to merge/filter categorical levels until a single binary comparison is left. This binary comparison is what is actually run through SAIGE for categorical traits.

1	extract.categories(df, phenotype.name, category.filename)

`df`	data.frame, working data frame with phenotype variable present for all relevant subjects, plus possibly some extra rows or columns
`phenotype.name`	character vector, column name of the phenotype variable in `df`
`category.filename`	character vector, name of preprocessor *.categories tracker file with rows of category levels and either "reference" or "comparison", delimited by tabs