scallops.spots.peak_thresholds_from_bases

scallops.spots.peak_thresholds_from_bases(bases_array, n_reads=500000, seed=239753, Q_cutoff=60, remove_zero_entropy_barcodes=True)

Calculate recall, precision, f1, and accuracy for different cutoff value of peaks.

Parameters:

  • bases_array (DataArray) – DataArray containing the bases data.

  • n_reads (int | None) – Number of reads to consider.

  • seed (int) – Seed for random number generator.

  • Q_cutoff (float) – Threshold for binarization of reads.

  • remove_zero_entropy_barcodes (bool) – Whether to remove zero entropy barcodes.

Returns:

Result data frame.

Return type:

DataFrame