Map Gene Symbols to Ensembl IDs

This function provides robust gene symbol to Ensembl ID mapping through:

1. Local org.Hs.eg.db annotations (default)

2. Ensembl BioMart web service (requires internet)

Usage

map_gene_to_ensembl(
  genes,
  gene_col = NULL,
  method = c("org.Hs.eg.db", "biomart"),
  genome = c("hg19", "hg38"),
  type = c("first", "combine"),
  sep = "/",
  batch_size = 100
)

Arguments

genes

Input containing gene symbols. Can be:

• Character vector of gene symbols

• Data frame containing gene symbol column

gene_col

Column name containing gene symbols when genes is data frame

method

Mapping methodology:

• "org.Hs.eg.db": Local Bioconductor annotations (default)

• "biomart": Ensembl BioMart service

genome

Genome assembly version (BioMart only):

• "hg19": GRCh37 (default)

• "hg38": GRCh38

type

Multi-mapping handling:

• "first": Return first valid ID (default)

• "combine": Concatenate multiple IDs

sep

Separator for combined IDs (default: "/")

batch_size

BioMart query batch size (default: 100)

Value

Data frame with original data + ensembl_id column

Examples

if (FALSE) { # \dontrun{
# Local annotation method
genes <- c("TP53", "BRCA1", "VEGFA")
result_local <- map_gene_to_ensembl(genes)

# BioMart with custom parameters
gene_df <- data.frame(
  my_symbol = c("TP53", "BRCA1", "NONEXISTENT"),
  values = rnorm(3)
)
result_biomart <- map_gene_to_ensembl(
  gene_df,
  gene_col = "my_symbol",
  method = "biomart",
  genome = "hg19",
  batch_size = 50
)
} # }