Identify optimal reads per cell range for power analysis grid

This function determines the minimum and maximum reads per cell values for power analysis grid generation based on experimental platform capabilities and S-M curve saturation analysis.

Usage

identify_library_size_range(experimental_platform, library_parameters)

Arguments

experimental_platform

Character. Experimental platform identifier (e.g., "10x Chromium v3", "Other").

library_parameters

List. rSAC_fn_wrapper format from library_estimation containing method_used, UMI_per_cell_at_saturation, reads_norm, n_cells, and method-specific parameters for saturation curve analysis.

Value

List with elements:

min_reads_per_cell

Minimum reads per cell based on platform

max_reads_per_cell

Maximum reads per cell for ~80% UMI saturation

Details

This function is a wrapper around the optimized C++ implementation identify_library_size_range_cpp which provides significant performance improvements for power analysis computations.

The function operates in two phases:

Minimum determination: Platform-specific minimum sequencing depth based on typical experimental capabilities and quality thresholds.

Maximum determination: Uses binary search on the S-M curve to find the reads per cell that achieves approximately 80% UMI saturation. If 80% saturation is not achievable within practical limits (10x UMI_per_cell), returns the practical upper bound.

See also

fit_read_UMI_curve_cpp for S-M curve evaluation get_pilot_data_from_package for obtaining library parameters identify_library_size_range_cpp for C++ implementation