get_avg_pb_exprs: get_avg_pb_exprs

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

get_avg_pb_exprs

Description

get_avg_pb_exprs Calculate the average and normalized pseudobulk expression of each gene per sample and per group.

Usage

get_avg_pb_exprs(sce, sample_id, celltype_id, group_id, batches = NA, min_cells = 10)

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
batches	NA if no batches should be corrected for. If there should be corrected for batches during DE analysis and pseudobulk expression calculation, this argument should be the name(s) of the columns in the meta data that indicate the batch(s). Should be categorical. Pseudobulk expression values will be corrected for the first element of this vector.
min_cells	Indicates the minimal number of cells that a sample should have to be considered in the DE analysis. Default: 10. See 'muscat::pbDS'.

Value

List containing data frames with average and normalized pseudobulk of expression per sample and per group.

Examples

## Not run: 
library(dplyr)
sample_id = "tumor"
group_id = "pEMT"
celltype_id = "celltype"
celltype_info = get_avg_pb_exprs(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.