get_muscat_exprs_frac: get_muscat_exprs_frac

In saeyslab/multinichenetr: MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

get_muscat_exprs_frac

Description

get_muscat_exprs_frac Calculate sample- and group-average of fraction of cells in a cell type expressing a gene.

Usage

get_muscat_exprs_frac(sce, sample_id, celltype_id, group_id)

Arguments

sce	SingleCellExperiment object of the scRNAseq data of interest. Contains both sender and receiver cell types.
sample_id	Name of the meta data column that indicates from which sample/patient a cell comes from
celltype_id	Name of the column in the meta data of sce that indicates the cell type of a cell.
group_id	Name of the meta data column that indicates from which group/condition a cell comes from

Value

List with two dataframes: one with fraction of cells in a cell type expressing a gene, averaged per sample; and one averaged per group.

Examples

## Not run: 
library(dplyr)
sample_id = "tumor"
group_id = "pEMT"
celltype_id = "celltype"
muscat_exprs_frac = get_muscat_exprs_frac(sce = sce, sample_id = sample_id, celltype_id =  celltype_id, group_id = group_id)

## End(Not run)

saeyslab/multinichenetr documentation built on Jan. 15, 2025, 7:55 p.m.