get_gene_symbol: Internal - get gene symbol from Panglao.db assigned...

In scMappR: Single Cell Mapper

Internal – get gene symbol from Panglao.db assigned gene-names (symbol-ensembl).

Description

Internal – removes Ensembl signature appended to signature matrix from Panglao and figure out species by pre-fix Ensembl of the Ensembl ID that is appended to gene names.

Usage

get_gene_symbol(wilcoxon_rank_mat_t)

Arguments

wilcoxon_rank_mat_t

Matrix where row names are "GeneSymbol-Ensembl" (human or mouse).

Details

Internal: This function removes the ENGMUS/ENGS tag from Panglao created gene names (symbol-ENGS). From the ENSG/ENSMUS, this function determines if the species is mouse/human and returns the gene symbols.

Value

List with the following elements:

rowname	Genes in the signature matrix excluding the ensemble name.
species	"mouse" or "human" depending on appended ensembl symbols.

Examples

 # load signature
data(POA_example) 
POA_OR_signature <- POA_example$POA_OR_signature
symbols <- get_gene_symbol(POA_OR_signature)

scMappR documentation built on July 9, 2023, 6:26 p.m.