get_expressed_genes: Determine expressed genes of a cell type from an input object

In saeyslab/nichenetr: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

Determine expressed genes of a cell type from an input object

Description

Return the genes that are expressed in given cell cluster(s) based on the fraction of cells in the cluster(s) that should express the cell.

Usage

get_expressed_genes(celltype_oi, object, ...)

## Default S3 method:
get_expressed_genes(celltype_oi, object, celltype_annot, pct = 0.1)

## S3 method for class 'Seurat'
get_expressed_genes(celltype_oi, seurat_obj, pct = 0.1, assay_oi = NULL, ...)

Arguments

celltype_oi	Character vector of cell type(s) to be considered. If input is a Seurat object, these must correspond to the cell identities from Idents.
object	Input matrix with rows as genes and columns as cells
...	additional parameters passed to GetAssayData (in case the slot/layer needs to be specified)
celltype_annot	Vector of cell type annotations
pct	We consider genes expressed if they are expressed in at least a specific fraction of cells of the given cluster(s). This number indicates this fraction. Default: 0.10. Choice of this parameter is important and depends largely on the used sequencing platform. We recommend to require a lower fraction (like the default 0.10) for 10X data than for e.g. Smart-seq2 data.
seurat_obj	Single-cell expression or spatial dataset as Seurat object
assay_oi	If wanted: specify yourself which assay to look for. If not NULL, the DefaultAssay of the Seurat object is used.

Value

A vector containing gene symbols of the expressed genes

Examples

## Not run: 
# For sparse matrix
get_expressed_genes("CD8 T", GetAssayData(seuratObj), seuratObj$celltype, pct = 0.10)

## End(Not run)

## Not run: 
# For Seurat object
get_expressed_genes(celltype_oi = "CD8 T", seurat_obj = seuratObj, pct = 0.10)

## End(Not run)

saeyslab/nichenetr documentation built on March 26, 2024, 9:22 a.m.