Calculate the Overlap Coefficient for Highly Variable Genes

Calculates the overlap coefficient between the sets of highly variable genes from a reference dataset and a query dataset.

calculateHVGOverlap(reference_genes, query_genes)

Arguments

reference_genes

A character vector of highly variable genes from the reference dataset.

query_genes

A character vector of highly variable genes from the query dataset.

Value

Overlap coefficient, a value between 0 and 1, where 0 indicates no overlap and 1 indicates complete overlap of highly variable genes between datasets.

Details

The overlap coefficient measures the similarity between two gene sets, indicating how well-aligned reference and query datasets are in terms of their highly variable genes. This metric is useful in single-cell genomics to understand the correspondence between different datasets.

The coefficient is calculated using the formula:

$$Coefficient(X, Y) = \frac{|X \cap Y|}{min(|X|, |Y|)}$$

where X and Y are the sets of highly variable genes from the reference and query datasets, respectively, \(|X \cap Y|\) is the number of genes common to both \(X\) and \(Y\), and \(min(|X|, |Y|)\) is the size of the smaller set among \(X\) and \(Y\).

References

Luecken et al. Benchmarking atlas-level data integration in single-cell genomics. Nature Methods, 19:41-50, 2022.

Author

Anthony Christidis, anthony-alexander_christidis@hms.harvard.edu

Examples

# Load data
data("reference_data")
data("query_data")

# Selecting highly variable genes
ref_var <- scran::getTopHVGs(reference_data, n = 500)
query_var <- scran::getTopHVGs(query_data, n = 500)
overlap_coefficient <- calculateHVGOverlap(reference_genes = ref_var, 
                                           query_genes = query_var)
overlap_coefficient
#> [1] 0.93