Calculate Sequencing Saturation

This function calculates the sequencing saturation of a sample or a graph component, which can be applied to unique reads, nodes, or edges.

Usage

sequencing_saturation(graph_elements, graph_reads)

Arguments

graph_elements

The number of graph elements (e.g., nodes, edges).

graph_reads

The number of reads or supporting elements.

Value

The sequencing saturation of the graph expressed as a percentage.

Details

The sequencing saturation is calculated using the formula: $$S = 100 \times \left(1 - \frac{E}{R}\right)$$ where:

• \(S\) is the saturation (as a percentage),

• \(E\) is the number of unique reads or graph elements (e.g., nodes, edges), and

• \(R\) is the number of reads or supporting elements in the graph.

This function can be used for calculating the saturation of:

• Reads: Number of deduplicated reads vs. reads

• Nodes: Number of nodes vs. reads

• Edges: Number of edges vs. reads

• Other graph elements: Adjust the input accordingly

Examples

# For a graph with 300 unique reads, 100 nodes, and 200 edges,
# sequenced at 400 total reads

# Read sequencing saturation
sequencing_saturation(300, 400)
#> [1] 25

# Node sequencing saturation
sequencing_saturation(100, 400)
#> [1] 75

# Edge sequencing saturation
sequencing_saturation(200, 400)
#> [1] 50