Updated_MGI_Symbols: Update MGI Gene Symbols

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Update MGI Gene Symbols

Description

Update mouse gene symbols using data from MGI This function will store cached data in package directory using (BiocFileCache). Use of this function requires internet connection on first use (or if setting update_symbol_data = TRUE). Subsequent use does not require connection and will pull from cached data.

Usage

Updated_MGI_Symbols(input_data, update_symbol_data = NULL, verbose = TRUE)

Arguments

input_data	Data source containing gene names. Accepted formats are: charcter vector Seurat Objects data.frame: genes as rownames dgCMatrix/dgTMatrix: genes as rownames tibble: genes in first column
update_symbol_data	logical, whether to update cached MGI data, default is NULL. If NULL BiocFileCache will check and prompt for update if cache is stale. If FALSE the BiocFileCache stale check will be skipped and current cache will be used. If TRUE the BiocFileCache stale check will be skipped and MGI data will be downloaded.
verbose	logical, whether to print results detailing numbers of symbols, found, updated, and not found; default is TRUE.

Value

data.frame containing columns: input_features, Approved_Symbol (already approved; output unchanged), Not_Found_Symbol (symbol not in MGI; output unchanged), Updated_Symbol (new symbol from MGI; output updated).

Examples

## Not run: 
new_names <- Updated_MGI_Symbols(input_data = Seurat_Object)

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.