Map Gene Symbols to Genomic Positions — leo_map

TODO: Merge all gene annotation function into one simple command. This function maps gene symbols to their genomic positions (chromosome, start, end, strand) using the specified method and genome assembly.

Usage

leo_map_GtoCP(
  genes,
  gene_col = NULL,
  method = c("bioconductor", "gtf"),
  genome = c("hg19", "hg38"),
  ...
)

Arguments

genes: A character vector of gene symbols or a data frame containing gene symbols.
gene_col: The column name of gene symbols if genes is a data frame.
method: The method to use: "bioconductor" or "gtf".
genome: The genome assembly to use: "hg19" or "hg38".
...: Additional arguments to pass to the GTF method.

Value

A data frame with columns: gene_symbol, chr, bp_start, bp_end, strand.

Details

The function supports two methods:

"bioconductor": uses Bioconductor packages. See map_gene_to_chrbp_using_TxDb().
"gtf": uses a GTF file. See map_gene_to_chrbp_using_gtf().

Examples

if (FALSE) { # \dontrun{
# Using Bioconductor method with a character vector of gene symbols
leo_map_GtoCP(genes = c("TP53", "BRCA1", "EGFR"), method = "bioconductor", genome = "hg19")

# Using Bioconductor method with a data frame
leo_map_GtoCP(genes = data.frame(gene_name = c("TP53", "BRCA1", "EGFR"),
                                 value = c(1.2, 3.4, 5.6)),
              gene_col = "gene_name", method = "bioconductor", genome = "hg19")

# Using GTF method with a character vector of gene symbols
leo_map_GtoCP(genes = c("TP53", "BRCA1", "EGFR"), method = "gtf", genome = "hg38")

# Using GTF method with a data frame
leo_map_GtoCP(genes = data.frame(gene_name = c("TP53", "BRCA1", "EGFR"),
                                 value = c(1.2, 3.4, 5.6)),
              gene_col = "gene_name", method = "gtf", genome = "hg38",
              download_dir = "~/Project/ref/gtf")
} # }