Updated_HGNC_Symbols {scCustomize} | R Documentation |
Update HGNC Gene Symbols
Description
Update human gene symbols using data from HGNC. 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_HGNC_Symbols(
input_data,
update_symbol_data = NULL,
case_check_as_warn = FALSE,
verbose = TRUE
)
Arguments
input_data |
Data source containing gene names. Accepted formats are:
|
update_symbol_data |
logical, whether to update cached HGNC data, default is NULL.
If |
case_check_as_warn |
logical, whether case checking of features should cause abort or only warn, default is FALSE (abort). Set to TRUE if atypical names (i.e. old LOC naming) are present in input_data. |
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 HGNC; output unchanged), Updated_Symbol (new symbol from HGNC; output updated).
Examples
## Not run:
new_names <- Updated_HGNC_Symbols(input_data = Seurat_Object)
## End(Not run)