Calculate PROGENy pathway activity scores based on normalized gene expression data.
Usage
score_progeny(exp_data, species = "Homo sapiens")
Arguments
- exp_data
A `SummarizedExperiment` object containing normalized gene expression data in the `assays(exp_data)$norm` slot.
- species
A character string specifying the species, either `"Homo sapiens"` (default) or `"Mus musculus"`.
Value
A data frame containing PROGENy pathway activity scores for each sample.
Details
The function uses the normalized gene expression data from the specified assay of the `SummarizedExperiment` object to compute PROGENy scores.
PROGENy scores represent pathway activity and are computed based on predefined pathway models for the specified species.