Map Ensembl Gene IDs to Genomic Positions using biomaRt

This function uses biomaRt to retrieve genomic positions (chr, bp_start, bp_end, and strand) from the Ensembl database based on Ensembl gene IDs.

Usage

map_ensg_to_chrbp_using_biomaRt(
  ensembl_ids,
  ensembl_col = NULL,
  genome = c("hg19", "hg38"),
  verbose = FALSE
)

Arguments

ensembl_ids

A character vector of Ensembl gene IDs, or a data frame containing this information.

ensembl_col

If ensembl_ids is a data frame, specify the column name containing the Ensembl gene IDs.

genome

The genome version to use: "hg19" or "hg38".

verbose

Logical indicating whether to print the unmapped information.

Value

A data frame containing genomic position information, including ensembl_gene_id, chr, bp_start, bp_end, strand.

Examples

if (FALSE) { # \dontrun{
# Query using Ensembl gene IDs
ensembl_ids <- c("ENSG00000141510", "ENSG00000012048", "ENSG00000146648")
map_ensg_to_chrbp_using_biomaRt(ensembl_ids = ensembl_ids, genome = "hg19")

# Use a data frame as input
gene_df <- data.frame(ensembl_id = ensembl_ids, value = c(1.2, 3.4, 5.6))
map_ensg_to_chrbp_using_biomaRt(ensembl_ids = gene_df, ensembl_col = "ensembl_id", genome = "hg19")
} # }