Determine expressed genes of a cell type.
get_expressed_genes.RdNicheNetR function to determine expressed genes of a cell type from a Seurat object single-cell RNA seq dataset or Seurat spatial transcriptomics dataset.
Function is modified from nichenetr v1.1.1 (GPL3.0): Browaeys, R., Saelens, W. & Saeys, Y. (2019). Nat Methods.
Modified to deal with non-sparse matrices, and avoids the (non-trivial) installation of NicheNet.
Arguments
- ident
Name of cluster identity/identities of cells
- seurat_obj
Single-cell expression dataset as Seurat object https://satijalab.org/seurat/.
- 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.