Calculate VISION scores — vision

Calculates an VISION-type scores for pathways based on DeTomaso, et al. Compared to other score types, you can also calculate delta-type scores between positive and negative gene indices, think epithelial vs mesenchymal gene signature, etc.

Usage

vision_sc(object, gs_list, streaming = FALSE, .verbose = TRUE)

Arguments

object: SingleCells class.
gs_list: Named nested list. The elements have the gene identifiers of the respective gene sets and have the option to have a "pos" and "neg" gene sets. The names need to be part of the variables of the SingleCells class.
streaming: Boolean. Shall the cell data be streamed in. Useful for larger data sets.
.verbose: Boolean. Controls the verbosity of the function.

Value

Matrix of cells x signatures with the VISION pathway scores as values.

References

DeTomaso, et al., Nat. Commun., 2019