h_get_granges_by_id: Conversion of 'BioMart' Coordinates into 'GRanges'

In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Conversion of BioMart Coordinates into GRanges

Description

This function extracts the chromosome number, the start position and the end position of transcripts in given data.frame with coordinates as returned by biomaRt::getBM() and converts them to a GRanges object.

Usage

h_get_granges_by_id(coords, id)

Arguments

coords	(data.frame) as returned by biomaRt::getBM(), containing the columns ensembl_gene_id, chromosome_name, exon_chrom_start, exon_chrom_end.
id	(string) single Ensembl gene ID to convert the coordinates for.

Value

GRange objects for the respective single gene ID.

Examples

if (interactive()) {
  mart <- biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  attrs <- c(
    "ensembl_gene_id",
    "ensembl_exon_id",
    "chromosome_name",
    "exon_chrom_start",
    "exon_chrom_end"
  )
  coords <- biomaRt::getBM(
    filters = "entrezgene_id",
    attributes = attrs,
    values = c("11185", "10677"),
    mart = mart
  )
  h_get_granges_by_id(coords, "ENSG00000135407")
}

insightsengineering/hermes documentation built on March 11, 2024, 11:04 p.m.