StandardizeGeneSymbols: Standardize gene symbols

In carmonalab/STACAS: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat

Standardize gene symbols

Description

Converts gene names of a Seurat single-cell object to a dictionary of standard symbols. This function is useful prior to integration of datasets from different studies, where gene names may be inconsistent.

Usage

StandardizeGeneSymbols(
  obj,
  assay = NULL,
  slots = c("counts", "data"),
  EnsemblGeneTable = NULL,
  EnsemblGeneFile = NULL
)

Arguments

obj	A Seurat object
assay	Assay where gene names should be translated
slots	Slots where gene names should be translated
EnsemblGeneTable	A data frame of gene name mappings. This should have the format of Ensembl BioMart tables with fields "Gene name", "Gene Synonym" and "Gene stable ID" (and optionally "NCBI gene (formerly Entrezgene) ID"). See also the default conversion table in STACAS with data(EnsemblGeneTable.Mm)
EnsemblGeneFile	If EnsemblGeneTable==NULL, read a gene mapping table from this file

Value

Returns a Seurat object with standard gene names. Genes not found in the standard list are removed. Synonyms are accepted when the conversion is not ambiguous.

Examples

data(EnsemblGeneTable.Mm)
obj <- StandardizeGeneSymbols(obj, EnsemblGeneTable=EnsemblGeneTable.Mm)

carmonalab/STACAS documentation built on Feb. 3, 2024, 7:42 a.m.