get_avg_pb_exprs

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

if (FALSE) { # \dontrun{
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)
} # }