Compute the average total UMI per cell and UMI variation parameters.

Compute the average total UMI per cell and UMI variation parameters.

Usage

library_estimation(QC_data, downsample_ratio = 0.7, D2_rough = 0.3)

Arguments

QC_data

Data frame. UMI-level molecule information from obtain_qc_read_umi_table containing columns num_reads, UMI_id, cell_id, and response_id.

downsample_ratio

Numeric or numeric vector. Proportion(s) for downsampling the dataset to create additional observation points. Must be between 0 and 1. Can be a vector for multiple downsampling levels, but one level is often sufficient. Default: 0.7.

D2_rough

Numeric. Rough prior estimate for the variation parameter (D2) in the S-M curve model. Represents PCR amplification bias. Typically 0.3 for perturb-seq, higher (e.g., 0.8) for TAP-seq. Default: 0.3.

Value

A list with elements:

UMI_per_cell

Total UMI per cell parameter

variation

Variation parameter characterizing PCR bias