f_score_ctgenes_U: Calculate cell type score

In scROSHI: Robust Supervised Hierarchical Identification of Single Cells

Calculate cell type score

Description

Calculate cell type score

Usage

f_score_ctgenes_U(
  sce,
  gset,
  count_data = "normcounts",
  gene_symbol = "SYMBOL",
  min_genes = 5,
  verbose = 0
)

Arguments

sce	A SingleCellExperiment object containing the expression profiles of the single cell analysis.
gset	Marker gene list for all cell types.
count_data	Assay name in the SingleCellExperiment object containing the count data.
gene_symbol	Variable name in the row data of the SingleCellExperiment object containing the gene names.
min_genes	Minimum number of genes.
verbose	Level of verbosity. Zero means silent, one makes a verbose output.

Value

Matrix containing the cell type scores. The rows represent the cell types, whereas the columns represent the samples.

Examples

data("test_sce_data")
gset <- list(cell_type1 = c("CD79A", "TCL1A", "VPREB3"),
cell_type2 = c("FCER1A", "CLEC10A", "ENHO"))
f_score_ctgenes_U(test_sce_data[,1:3], gset, count_data = "normcounts",
gene_symbol = "SYMBOL", min_genes = 3, verbose = 0)

scROSHI documentation built on Jan. 10, 2023, 5:11 p.m.