Compute approximate edge saturation

Computes an approximate edge saturation for each component in the edgelist using SQL queries on a DuckDB connection. Edge saturation measures how many unique edges have been observed relative to the total number of reads.

Usage

approximate_edge_saturation(db, components = NULL, table_name = NULL)

Arguments

db

A PixelDB object with an active DuckDB connection.

components

Optional character vector of component names to filter the edgelist. If NULL (default), all components are included.

table_name

Optional name for the computed remote table. If provided, the result is materialized as a table in the DuckDB connection.

Value

A lazy tbl (DuckDB query) with columns:

component

The component (cell) identifier.

edges

The number of unique edges.

read_count

The total read count for the component.

edge_saturation

The edge saturation value (0 to 1).

Details

Edge saturation is calculated as: $$S_{edge} = 1 - \frac{E}{R}$$ where \(E\) is the number of unique edges and \(R\) is the total read count.

Higher saturation values indicate that additional sequencing reads are unlikely to reveal new edges, suggesting the sample has been sequenced to near-saturation.

See also

approximate_node_saturation for node-based saturation. approximate_saturation_curve for computing saturation at multiple downsampling fractions.