get_cell_type_info: Computes cell type profiles in a scRNA-seq dataset

In dmcable/RCTD: SpatialeXpressionR: Cell type identification and cell type-specific differential expression in spatial transcriptomics

Computes cell type profiles in a scRNA-seq dataset

Description

Computes averaged normalized expression (summing to 1) for all cells within a cell type

Usage

get_cell_type_info(raw.data, cell_types, nUMI, cell_type_names = NULL)

Arguments

raw.data	a Digital Gene Expression matrix, with gene names as rownames and single cells as columns (barcodes for colnames)
cell_types	a named list of cell type assignment for each cell in raw.data
nUMI	a named list of total UMI count for each cell in raw.data

Value

Returns cell_type_info, a list of three elements: (1) cell_type_means (a data_frame (genes by cell types) for mean normalized expression) (2) cell_type_names (a list of cell type names) and (3) the number of cell types

dmcable/RCTD documentation built on Feb. 24, 2024, 11:03 p.m.