Load Case Annotations from CSV — load_case

Loads annotation features from a pre-annotated case variants CSV file.

load_case_annotations(csv_path, features = .default_PI_features())

Arguments

csv_path: Path to the annotated CSV file. Must contain a VarInfo column and the requested feature columns.
features: Character vector of annotation column names to extract. Default: 11 FAVOR features from .default_PI_features().

Value

Numeric matrix with dimensions (N_variants x M_features). Row names are set to VarInfo values. May contain NA values.

Details

The CSV file should have been generated by annotate_favor() or similar FAVOR annotation tools. Expected columns include VarInfo (variant identifier in CHR-POS-REF-ALT format) and the annotation features.

NA Handling

This function preserves NA values in the output. Use impute_na_median() before passing to model_PI() if needed.

Examples

if (FALSE) { # \dontrun{
case_annot <- load_case_annotations("cases_annotated.csv")
dim(case_annot)  # N_cases x 11
} # }