alphapepttools.metrics.calculate_qc_metrics

alphapepttools.metrics.calculate_qc_metrics(adata, *, layer=None)

Calculate all QC metrics and add them to adata.obs.

This function computes and adds the following metrics: - total_intensity: Sum of intensities per observation and per feature - num_features_detected: Number of detected features per observation and per feature - fraction_complete: Fraction of detected features per observation and per feature

Parameters:

• adata (AnnData) – AnnData object

• layer (str | None (default: None)) – Name of the layer to use. If None (default), the data matrix X is used.

Return type:

None

Returns:

None Modifies adata inplace by adding the following columns to adata.obs: - adata.obs["total_sample_intensity"]: Sum of intensities per observation - adata.obs["num_features_detected"]: Number of detected features per observation - adata.obs["fraction_detected_features"]: Fraction of detected features per observation - adata.var["total_feature_intensity"]: Sum of intensities per feature across all observations - adata.var["num_samples_detected"]: Number of samples in which the features was detected - adata.var["fraction_detected_samples"]: Fraction of detected observations per feature (across all observations)