Standardize a vector of gene symbols to STRING preferred names for Homo sapiens.
This is intended as a one-time workflow helper so downstream network retrieval
functions can use a consistent symbol vocabulary across STRING, GeneMANIA,
and kinase-substrate resources.
Usage
StandardizeGeneSymbols(
genes,
species = 9606,
string.version = "12.0",
keep.unmapped = TRUE
)
Arguments
- genes
Character vector of gene symbols.
- species
NCBI taxonomy ID. Default is 9606 (Homo sapiens).
- string.version
STRING version. Default is "12.0".
- keep.unmapped
Logical. If TRUE, unmapped input symbols are retained as-is
in the standard_symbol column. Default is TRUE.
Value
A data frame with columns:
- input_symbol
Original supplied symbol
- STRING_id
Mapped STRING protein identifier, if available
- standard_symbol
STRING preferred_name when mapped; otherwise input symbol if keep.unmapped = TRUE
- mapped
Logical indicating whether a STRING mapping was found
Examples
# sym.map <- StandardizeGeneSymbols(c("EPRS", "QARS", "DDR1", "DDR2"))
# unique(sym.map$standard_symbol)
