Tag Low-Confidence Predictions and Add Status Column

Replaces low-confidence cell type predictions with a placeholder label (e.g., "unknown") and adds a confidence status column ("confident" or "uncertain").

Usage

filterLowConfidenceCells(
  prediction_df,
  threshold = 0.5,
  low_conf_label = "unknown",
  keep_confidence = TRUE
)

Arguments

prediction_df

A data frame from predictRankModel (return_confidence = TRUE).

threshold

Numeric. Confidence threshold below which predictions are flagged. Default is 0.5.

low_conf_label

Character. Replacement for low-confidence predictions. Default is "unknown".

keep_confidence

Logical. Whether to retain the original confidence column. Default is TRUE.

Value

A data frame with columns: cell_id, predicted_cell_type, status, nd optionally confidence.

Examples

# Simulated predictions with confidence
pred_df <- data.frame(
    cell_id = paste0("cell", 1:5),
    predicted_cell_type = c("B", "T", "B", "Myeloid", "T"),
    confidence = c(0.92, 0.47, 0.88, 0.33, 0.76)
)

# Apply threshold of 0.5 to flag low-confidence cells
result <- filterLowConfidenceCells(pred_df, threshold = 0.5)

# Show result
print(result)
#>   cell_id predicted_cell_type confidence    status
#> 1   cell1                   B       0.92 confident
#> 2   cell2             unknown       0.47 uncertain
#> 3   cell3                   B       0.88 confident
#> 4   cell4             unknown       0.33 uncertain
#> 5   cell5                   T       0.76 confident

# Remove confidence column and use custom label
# for low-confidence predictions
result2 <- filterLowConfidenceCells(pred_df,
    threshold = 0.6,
    low_conf_label = "low_conf",
    keep_confidence = FALSE
)