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Convert Gene IDs to Ensembl

Source: R/convert_id.R
convert_id.Rd

Queries the database to map user-provided gene identifiers to Ensembl/Entrez IDs. To ensure best matching and conversion, please verify that all gene identifiers have no whitespace and are at least 2 characters long. Results are often more conservative of initial genes if data is provided, as duplicate removal is done by variance of each gene (highest variance is kept).

Usage

convert_id(genes, data = NULL, species_id, id_type = "ens")

Arguments

genes

A vector or character string of gene identifiers to convert.

data

Optional data frame or matrix. If provided, the function attempts to match genes to the row names or a column in data and merges the conversion results with the original data.

species_id

Numeric. The ID of the species for the database connection.

id_type

Character. The type of ID to convert to:

  • "ens" = Ensembl gene IDs (Default)

  • "entrez" = Entrez gene IDs

    • WARNING: Not all species or genes have Entrez gene IDs available

    • May take longer than Ensembl IDs

    • Will likely have duplicate Entrez IDs

Value

A data frame.

  • If data is NULL: Returns a mapping table with original IDs and IDs of selected type.

  • If data is provided: Returns data merged with the IDs of selected type. Returns NULL if species_id is missing or no matches are found.

  • Any whitespace found in original IDs will be removed.

Examples

if (FALSE) { # interactive() && curl::has_internet()
# CAUTION: The human database is very large, running these examples require
# the download of the human database.

# View our experimental gene IDs
head(rownames(hypoxia_reads))

# Convert IDs to Ensembl format for further analysis
ens_conv <- convert_id(genes = rownames(hypoxia_reads),
                       species_id = 96)

# Yields a conversion table for our genes
head(ens_conv)

# Can also convert to Entrez IDs, if needed
entrez_conv <- convert_id(genes = rownames(hypoxia_reads),
                          species_id = 96,
                          id_type = "entrez")

# Yields a conversion table for our genes
head(entrez_conv)

# We want to automatically convert our IDs within our data
ens_hypoxia <- convert_id(genes = rownames(hypoxia_reads),
                          species_id = 96,
                          data = hypoxia_reads)

# Original data
head(hypoxia_reads)

# Converted data
head(ens_hypoxia)
}