f_score_ctgenes_U {scROSHI} | R Documentation |
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)
[Package scROSHI version 1.0.0.0 Index]