UpdateSymbolList {Seurat}

Get updated synonyms for gene symbols

Description

Find current gene symbols based on old or alias symbols using the gene names database from the HUGO Gene Nomenclature Committee (HGNC)

Usage

GeneSymbolThesarus(
  symbols,
  timeout = 10,
  several.ok = FALSE,
  search.types = c("alias_symbol", "prev_symbol"),
  verbose = TRUE,
  ...
)

UpdateSymbolList(
  symbols,
  timeout = 10,
  several.ok = FALSE,
  verbose = TRUE,
  ...
)

Arguments

symbols

A vector of gene symbols

timeout

Time to wait before canceling query in seconds

several.ok

Allow several current gene symbols for each provided symbol

search.types

Type of query to perform:

“alias_symbol”

Find alternate symbols for the genes described by symbols

“prev_symbol”

Find new new symbols for the genes described by symbols

This parameter accepts multiple options and short-hand options (eg. “prev” for “prev_symbol”)

verbose

Show a progress bar depicting search progress

...

Extra parameters passed to GET

Details

For each symbol passed, we query the HGNC gene names database for current symbols that have the provided symbol as either an alias (alias_symbol) or old (prev_symbol) symbol. All other queries are not supported.

Value

GeneSymbolThesarus:, if several.ok, a named list where each entry is the current symbol found for each symbol provided and the names are the provided symbols. Otherwise, a named vector with the same information.

UpdateSymbolList: symbols with updated symbols from HGNC's gene names database

Note

This function requires internet access

Source

https://www.genenames.org/ https://www.genenames.org/help/rest/

See Also

GET

Examples

## Not run: 
GeneSybmolThesarus(symbols = c("FAM64A"))

## End(Not run)

## Not run: 
UpdateSymbolList(symbols = cc.genes$s.genes)

## End(Not run)