This function selects the most highly variable genes from a normalized gene expression matrix or a `SummarizedExperiment` object.
Usage
highly_variable_genes(gexp, n_hvg = 2000)
Arguments
- gexp
A normalized gene expression matrix (genes in rows, samples in columns), or a `SummarizedExperiment` object containing normalized counts in the `"norm"` assay.
- n_hvg
An integer specifying the number of highly variable genes to select. Default is `2000`.
Value
A character vector containing the names of the top `n_hvg` highly variable genes.
Details
The function computes the robust coefficient of variation (CV) for each gene and selects the top `n_hvg` genes with the highest CV values.
If the input is a `SummarizedExperiment` object, the `"norm"` assay is automatically extracted for processing.