Seurat: UpdateSymbolList – R documentation

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UpdateSymbolList

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,
  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/

Examples

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

## End(Not run)

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

## End(Not run)

Seurat

Tools for Single Cell Genomics

v4.0.1

GPL-3 | file LICENSE

Authors

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17