Get Ensembl biomaRt object — get

Get GC content, gene Ids, gene symbols, gene biotypes, gene lengths and other metadata from Ensembl BioMart. Object returned contains gene Ids as rownames.

get_biomart(
  count_df,
  synid,
  version,
  host,
  filters,
  organism,
  custom = FALSE,
  gtfID = NULL,
  gtfVersion = NULL,
  fastaID = NULL,
  fastaVersion = NULL,
  cores = NULL,
  isexon = FALSE
)

Arguments

count_df: A counts data frame with sample identifiers as column names and gene Ids are rownames.
synid: A character vector with a Synapse Id.
version: Optional. A numeric vector with the Synapse file version number.
host: An optional character vector specifying the release version. This specification is highly recommended for a reproducible workflow. (see "biomaRt::listEnsemblArchives()")
filters: A character vector listing biomaRt query filters. (For a list of filters see "biomaRt::listFilters()")
organism: A character vector of the organism name. This argument takes partial strings. For example,"hsa" will match "hsapiens_gene_ensembl".
custom: Defaults to FALSE If TRUE, the GC and Gene Length, and gene name are calculated from user specified FASTA and GTF File.
gtfID: Defaults to NULL. A character vector with a Synapse ID corresponding to a gtf formatted gene annotation file.
gtfVersion: Optional. A numeric vector with the gene GTF Synapse file version number.
fastaID: Defaults to NULL. A character vector with a Synapse ID corresponding to a FASTA formatted genome annotation file.
fastaVersion: Optional. A numeric vector with the genome FASTA Synapse file version number.
cores: An integer of cores to specify in the parallel backend (eg. 4).
isexon: Defaults to FALSE. If TRUE, the GC and Gene Length parameters will only consider exotic regions and omit intronic regions.