Update HGNC Gene Symbols

Source: R/Utilities.R

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.

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:

  • 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 HGNC 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 HGNC data will be downloaded.

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

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