Convert gene names between different formats

Usage

gene_name_conversion(
  genes,
  infmt,
  outfmt,
  dup = "first",
  species = "human",
  notfound = "na",
  suppress_messages = TRUE
)

Arguments

genes

A character/integer vector of gene names/ids

infmt

A character vector of input gene name formats See the available scopes at https://docs.mygene.info/en/latest/doc/data.html#available-fields You can use ensg as a shortcut for ensembl.gene

outfmt

A character vector of output gene name formats

dup

How to deal with duplicate gene names found.

"first": keep the first one (default), sorted by score descendingly
"last": keep the last one, sorted by score descendingly
"all": keep all of them, each will be a separate row
"<X>": combine them into a single string, separated by X

species

A character vector of species names

notfound

How to deal with gene names that are not found

"error": stop with an error message
"use-query": use the query gene name as the converted gene name
"skip": skip the gene names that are not found
"ignore": Same as "skip"
"na"/"NA": use NA as the converted gene name (default)

suppress_messages

Whether to suppress the warning messages

Value

A tibble with the query gene names and the converted gene names When a gene name is not found, the converted name will be NA When duplicate gene names are found, the one with the highest score will be kept