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Bixverse implementation of ssGSEA

calc_ssgsea.Rd

Implementation of the bixverse version of the single sample gene set enrichment analysis (ssGSEA)

Usage

calc_ssgsea(exp, pathways, ssgsea_params = params_ssgsea(), .verbose = FALSE)

Arguments

exp

Numerical matrix. Rows represents the features, columns the features/genes.

pathways

List. A named list with each element containing the genes for this pathway.

ssgsea_params

List. The GSVA parameters, see params_ssgsea() wrapper function. This function generates a list containing:

  • alpha - Float. The exponent defining the weight of the tail in the random walk performed by ssGSEA.

  • min_size - Integer. Minimum size for the gene sets.

  • max_size - Integer. Maximum size for the gene sets.

  • normalise - Boolean. Shall the scores be normalised.

.verbose

Boolean. Controls verbosity.

Value

A matrix of shape pathways (that passed the thresholds) x samples.