f_annot_ctgenes: Choose best matching cell type

In scROSHI: Robust Supervised Hierarchical Identification of Single Cells

Choose best matching cell type

Description

Choose best matching cell type

Usage

f_annot_ctgenes(m.cts, unknown, uncertain)

Arguments

m.cts	Matrix containing the cell type scores. The rows represent the cell types, whereas the columns represent the samples.
unknown	If none of the probabilities is above this threshold, the cell type label is assigned to the class unknown.
uncertain	If the ratio between the largest and the second largest probability is below this threshold, the cell type label is assigned to the class uncertain for the major cell types.

Value

Data frame containing the best matching cell type for each sample.

Examples

m.cts <- matrix(c(0.2, 0.001, 0.002, 0.1), nrow=2)
colnames(m.cts) <- c("sample1", "sample2")
rownames(m.cts) <- c("cell_type1", "cell_type2")
f_annot_ctgenes(m.cts, 0.05, 0.1)

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