nichenetr (version 0.1.0)

get_expressed_genes: Determine expressed genes of a cell type from a Seurat object single-cell RNA seq dataset or Seurat spatial transcriptomics dataset

Description

get_expressed_genes Return the genes that are expressed in a given cell cluster based on the fraction of cells in that cluster that should express the cell.

Usage

get_expressed_genes(ident, seurat_obj, pct = 0.10, assay_oi = NULL)

Arguments

ident

Name of cluster identity/identities of cells

seurat_obj

Single-cell expression dataset as Seurat v3 object https://satijalab.org/seurat/. Should contain a column "aggregate" in the metadata. This column indicates the condition/sample where cells came from.

pct

We consider genes expressed if they are expressed in at least a specific fraction of cells of a cluster. 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.

assay_oi

If wanted: specify yourself which assay to look for. Default this value is NULL and as a consequence the 'most advanced' assay will be used to define expressed genes.

Value

A character vector with the gene symbols of the expressed genes

Examples

# NOT RUN {
get_expressed_genes(ident = "CD8 T", seurat_obj = seuratObj, pct = 0.10)
# }
# NOT RUN {
# }