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Calculate VISION pathway scores in Rust (for meta cells)

rs_mc_vision.Rd

[Experimental] The function will take in a list of gene sets that contains lists of "pos" and "neg" gene indices (0-indexed). You don't have to provide the "neg", but it can be useful to classify the delta of two stats (EMT, Th1; Th2) etc. This version works on MetaCell counts which are stored in memory directly.

Usage

rs_mc_vision(sparse_data, gs_list, verbose)

Arguments

sparse_data

A named list that needs to have data, indptr, indices, nrow, ncol and cs_type. Shape is (metacells, genes) and the data need to be the normalised counts.

gs_list

Nested list. Each sublist contains the (0-indexed!) positive and negative gene indices of that specific gene set.

verbose

Integer. 0L - quiet; 1L - normal verbosity; 2L - detailed verbosity.

Value

A matrix of meta cells x vision scores per gene set.

References

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