Rust version of the ssGSEA algorithm — rs_ssgsea • bixverse

Rust-based implementation of the popular single sample GSEA algorithm. Has further performance optimisations compared to the original implementation.

Usage

rs_ssgsea(exp, gs_list, alpha, normalise, timings)

Arguments

exp: Numerical matrix. The expression matrix with rows = genes, and columns = samples
gs_list: List. A list containing the indices of the pathway genes (needs to be null indexed). See rs_prepare_gsva_gs().
alpha: Float. The alpha parameter to adjust the weights.
normalise: Boolean. Shall the scores be normalised.
timings: Boolean. Prints timings from the algorithm.

Value

Returns a matrix of gene set ES scores x samples.