Calculate ScType scores and assign cell types for one level

Calculate ScType scores and assign cell types for one level

Usage

hitype_score_level(z, gs_level, norm = "sqrt", use_sensitivity = TRUE)

Arguments

z

Z-scaled expression matrix (rownames - gene names, colnames - cell names)

gs_level

One level of gene sets prepared by gs_prepare

norm

Normalization method for scoring. "sqrt" (default) divides by sqrt(n); "weight" divides by sum(abs(weights)).

use_sensitivity

Whether to multiply expression z-scores by marker sensitivity scores. Set to FALSE when using learned weights to avoid double-penalizing shared markers. Default is TRUE.

Value

A matrix of cell type scores for each cell (rownames - cell types, colnames - cell names)