Build a DWLS signature matrix — dwls_signature • spatialDWLS

Mean expression per cell type over the signature features: the reference dwls() expects.

Usage

dwls_signature(expr, sign_gene, cell_type)

Arguments

expr: single-cell expression, features (rows) by cells (columns). Pass the scale the spots will be solved on, i.e. normalised and not logged (dwls() reverse-logs the spot expression before solving).
sign_gene: character. signature features, e.g. cell type markers. Features missing from expr are dropped.
cell_type: cell type of each column of expr.

Value

a numeric matrix, signature features (rows) by cell type (columns, in order of first appearance in cell_type).

Examples

set.seed(1)
x <- matrix(rpois(200, 3), 20, 10,
            dimnames = list(paste0("g", 1:20), paste0("c", 1:10)))
dwls_signature(x, sign_gene = paste0("g", 1:5),
               cell_type = rep(c("A", "B"), each = 5))
#>      A   B
#> g1 4.2 4.0
#> g2 2.6 2.8
#> g3 3.2 3.0
#> g4 2.6 3.6
#> g5 3.0 4.2