Identifies likely contaminant organisms using multi-path logic.
Usage
flag_contaminants(
data,
method = "auto",
organism_col = "organism_normalized",
specimen_col = "specimen_type"
)
Arguments
- data
Data frame
- method
Character. "auto" (try all methods), "device_based",
"heuristic", "provided". Default "auto".
- organism_col
Character. Normalized organism column.
- specimen_col
Character. Specimen type column.
Value
Data frame with is_contaminant, contaminant_confidence,
contaminant_method columns