Calculate module activity scores in Rust
rs_module_scoring.RdCalculates module activity scores following Seurat's AddModuleScore.
For each module (gene set), computes the average expression of genes in the
set minus the average expression of randomly selected control genes from the
same expression bins. Genes are binned based on their average expression
across cells to ensure controls are expression-matched.
Usage
rs_module_scoring(
f_path_cells,
f_path_genes,
gs_list,
cells_to_keep,
nbin,
ctrl,
seed,
streaming,
verbose
)Arguments
- f_path_cells
String. Path to the cell-based binary file.
- f_path_genes
String. Path to the gene-based binary file.
- gs_list
List. List of integer vectors, where each vector contains gene indices (0-based) for a module/gene set.
- cells_to_keep
Integer. Vector of indices of the cells to keep.
- nbin
Integer. Number of bins for gene stratification.
- ctrl
Integer. Number of control genes to sample per gene in each module.
- seed
Integer. Random seed for reproducible control gene sampling.
- streaming
Logical. If TRUE, processes cells and genes are read in in chunks to reduce memory usage.
- verbose
Logical. Controls verbosity of the function.