Update MGI Gene Symbols

Source: R/Utilities.R

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.

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

if (FALSE) {
new_names <- Updated_MGI_Symbols(input_data = Seurat_Object)
}