get_muscat_exprs_avg: get_muscat_exprs_avg

In saeyslab/muscatWrapper: Wrapper functions around muscat for differential expression analysis of multi-sample multi-condition scRNAseq datasets

get_muscat_exprs_avg

Description

get_muscat_exprs_avg Calculate sample- and group-average of gene expression per cell type.

Usage

get_muscat_exprs_avg(sce, sample_id, celltype_id, group_id)

Arguments

sce	SingleCellExperiment object of the scRNAseq data of interest.
sample_id	Name of the meta data column that indicates from which sample/patient a cell comes from (in sce)
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 (in sce)

Value

Data frame with average gene expression per sample and per group.

Examples

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

## End(Not run)

saeyslab/muscatWrapper documentation built on March 11, 2023, 6:14 p.m.