UpdateSymbolList: Get updated synonyms for gene symbols

In ibseq/scs-analysis: Tools for Single Cell Genomics

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,
  verbose = TRUE,
  ...
)

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

Arguments

symbols	A vector of gene symbols
timeout	Time to wait before cancelling query in seconds
several.ok	Allow several current gene sybmols for each provided 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

For 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.

For 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)

ibseq/scs-analysis documentation built on Feb. 27, 2021, 12:35 a.m.