geneToSymbol: Get gene symbols from Ensembl gene ids

In JokingHero/ORFik: Open Reading Frames in Genomics

Get gene symbols from Ensembl gene ids

Description

If your organism is not in this list of supported organisms, manually assign the input arguments. There are 2 main fetch modes:
By gene ids (Single accession per gene)
By tx ids (Multiple accessions per gene)
Run the mode you need depending on your required attributes.

Will check for already existing table of all genes, and use that instead of re-downloading every time (If you input valid experiment or txdb and have run makeTxdbFromGenome with symbols = TRUE, you have a file called gene_symbol_tx_table.fst) will load instantly. If df = NULL, it can still search cache to load a bit slower.

Usage

geneToSymbol(
  df,
  organism_name = organism(df),
  gene_ids = filterTranscripts(df, by = "gene", 0, 0, 0),
  org.dataset = paste0(tolower(substr(organism_name, 1, 1)), gsub(".* ", replacement =
    "", organism_name), "_gene_ensembl"),
  ensembl = biomaRt::useEnsembl("ensembl", dataset = org.dataset),
  attribute = "external_gene_name",
  include_tx_ids = FALSE,
  uniprot_id = FALSE,
  force = FALSE,
  verbose = TRUE
)

Arguments

df	an ORFik experiment or TxDb object with defined organism slot. If set will look for file at path of txdb / experiment reference path named: 'gene_symbol_tx_table.fst' relative to the txdb/genome directory. Can be set to NULL if gene_ids and organism is defined manually.
organism_name	default, organism(df). Scientific name of organism, like ("Homo sapiens"), remember capital letter for first name only!
gene_ids	default, filterTranscripts(df, by = "gene", 0, 0, 0). Ensembl gene IDs to search for (default all transcripts coding and noncoding) To only get coding do: filterTranscripts(df, by = "gene", 0, 1, 0)
org.dataset	default, paste0(tolower(substr(organism_name, 1, 1)), gsub(".* ", replacement = "", organism_name), "_gene_ensembl") the ensembl dataset to use. For Homo sapiens, this converts to default as: hsapiens_gene_ensembl
ensembl	default, useEnsembl("ensembl",dataset=org.dataset) .The mart connection.
attribute	default, "external_gene_name", the biomaRt column / columns default(primary gene symbol names). These are always from specific database, like hgnc symbol for human, and mgi symbol for mouse and rat, sgd for yeast etc.
include_tx_ids	logical, default FALSE, also match tx ids, which then returns as the 3rd column. Only allowed when 'df' is defined. If
uniprot_id	logical, default FALSE. Include uniprotsptrembl and/or uniprotswissprot. If include_tx_ids you will get per isoform if available, else you get canonical uniprot id per gene. If both uniprotsptrembl and uniprotswissprot exists, it will make a merged uniprot id column with rule: if id exists in uniprotswissprot, keep. If not, use uniprotsptrembl column id.
force	logical FALSE, if TRUE will not look for existing file made through makeTxdbFromGenome corresponding to this txdb / ORFik experiment stored with name "gene_symbol_tx_table.fst".
verbose	logical TRUE, if FALSE, do not output messages.

Value

data.table with 2, 3 or 4 columns: gene_id, gene_symbol, tx_id and uniprot_id named after attribute, sorted in order of gene_ids input. (example: returns 3 columns if include_tx_ids is TRUE), and more if additional columns are specified in 'attribute' argument.

Examples

## Without ORFik experiment input
gene_id_ATF4 <- "ENSG00000128272"
#geneToSymbol(NULL, organism_name = "Homo sapiens", gene_ids = gene_id_ATF4)
# With uniprot canonical isoform id:
#geneToSymbol(NULL, organism_name = "Homo sapiens", gene_ids = gene_id_ATF4, uniprot_id = TRUE)

## All genes from Organism using ORFik experiment
# df <- read.experiment("some_experiment)
# geneToSymbol(df)

## Non vertebrate species (the ones not in ensembl, but in ensemblGenomes mart)
#txdb_ylipolytica <- loadTxdb("txdb_path")
#dt2 <- geneToSymbol(txdb_ylipolytica, include_tx_ids = TRUE,
#   ensembl = useEnsemblGenomes(biomart = "fungi_mart", dataset = "ylipolytica_eg_gene"))

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.