Map Genes to Their TSS Positions — map_gene_to_tss_using

This function maps gene symbols to their transcription start sites (TSS) positions using hg19 or hg38 genome assembly.

Usage

map_gene_to_tss_using_gtf(
  genes,
  gene_col = NULL,
  genome = c("hg19", "hg38"),
  gtf_file = NULL,
  download_dir = "~/Project/ref/gtf",
  ...
)

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.
genome: The genome assembly to use: "hg19" or "hg38".
gtf_file: The path to a GTF file. If NULL, the function will download the appropriate GTF file.
download_dir: The path where you want to store the downloaded gtf file.
...: Pass to map_gene_to_chrbp_using_gtf. See map_gene_to_chrbp_using_gtf()

Value

A data frame with gene symbols and their TSS positions

Examples

if (FALSE) { # \dontrun{
genes <- c("TP53", "BRCA1", "EGFR")
map_gene_to_tss_using_gtf(genes = genes, genome = "hg38")

genes_df <- data.frame(GeneName = genes, OtherInfo = c(1,2,3))
map_gene_to_tss_using_gtf(genes = genes_df, gene_col = "GeneName", genome = "hg19")
} # }