wb_clean_gene_names: Clean up old gene names

In AlexWeinreb/wbData: Download And Use WormBase Data

Clean up old gene names

Description

Takes a list of (potentially old) Wormbase gene IDs, and replaces the Dead ones with current IDs. This corresponds to the [Gene Name Sanitizer](https://wormbase.org/tools/mine/gene_sanitizer.cgi) available on Wormbase.

Note this function only works with gene IDs (of the form WBGene00000001), not symbols or other sequence names, while the online tool can potentially correct old gene names. The file downloaded by the (unexported) function 'wb_get_gene_name_history()' contains additional information, ask if you need this functionality to be added to the package.

Usage

wb_clean_gene_names(
  gene_id,
  warn_missing = TRUE,
  dir_cache = NULL,
  refresh = 20
)

Arguments

gene_id	Vector of gene IDs to clean.
warn_missing	Warn if some gene IDs are not found.
dir_cache	Directory where the downloaded files are cached.
refresh	Number of days after which the downloaded list needs to be refreshed.

Value

An updated list of gene IDs.

Examples

## Not run: 
gids <- wb_load_gene_ids(294)
genes_of_interest <- c("WBGene00012733", "WBGene00000424", "WBGene00007566", "WBGene00045409")
i2s(genes_of_interest, gids, warn_missing = TRUE)
cleaned_genes <- wb_clean_gene_names(genes_of_interest)
i2s(cleaned_genes, gids, warn_missing = TRUE)

## End(Not run)

AlexWeinreb/wbData documentation built on April 3, 2025, 1:24 p.m.