tr2g_ensembl: Get transcript and gene info from Ensembl

In lambdamoses/BUStoolsR: kallisto | bustools R utilities

Get transcript and gene info from Ensembl

Description

This function queries Ensembl biomart to convert transcript IDs to gene IDs.

Usage

tr2g_ensembl(
  species,
  type = c("vertebrate", "metazoa", "plant", "fungus", "protist"),
  out_path = ".",
  write_tr2g = TRUE,
  other_attrs = NULL,
  use_gene_name = TRUE,
  use_transcript_version = TRUE,
  use_gene_version = TRUE,
  transcript_biotype_col = "transcript_biotype",
  gene_biotype_col = "gene_biotype",
  transcript_biotype_use = "all",
  gene_biotype_use = "all",
  chrs_only = TRUE,
  ensembl_version = NULL,
  overwrite = FALSE,
  verbose = TRUE,
  ...
)

Arguments

species	Character vector of length 1, Latin name of the species of interest.
type	Character, must be one of "vertebrate", "metazoa", "plant", "fungus" and "protist". Passing "vertebrate" will use the default www.ensembl.org host. Gene annotation of some common invertebrate model organisms, such as Drosophila melanogaster, are available on www.ensembl.org so for these invertebrate model organisms, "vertebrate" can be used for this argument. Passing values other than "vertebrate" will use other Ensembl hosts. For animals absent from www.ensembl.org, try "metazoa".
out_path	Directory to save the outputs written to disk. If this directory does not exist, then it will be created. Defaults to the current working directory.
write_tr2g	Logical, whether to write tr2g to disk. If TRUE, then a file tr2g.tsv will be written into out_path.
other_attrs	Character vector. Other attributes to get from Ensembl, such as gene symbol and position on the genome. Use listAttributes to see which attributes are available.
use_gene_name	Logical, whether to get gene names.
use_transcript_version	Logical, whether to include version number in the Ensembl transcript ID. To decide whether to include transcript version number, check whether version numbers are included in the transcripts.txt in the kallisto output directory. If that file includes version numbers, then trannscript version numbers must be included here as well. If that file does not include version numbers, then transcript version numbers must not be included here.
use_gene_version	Logical, whether to include version number in the Ensembl gene ID. Unlike transcript version number, it's up to you whether to include gene version number.
transcript_biotype_col	Character vector of length 1. Tag in attribute field corresponding to transcript biotype.
gene_biotype_col	Character vector of length 1. Tag in attribute field corresponding to gene biotype.
transcript_biotype_use	Character, can be "all" or a vector of transcript biotypes to be used. Transcript biotypes aren't entirely the same as gene biotypes. For instance, in Ensembl annotation, retained_intron is a transcript biotype, but not a gene biotype. If "cellranger", then a warning will be given. See data("ensembl_tx_biotypes") for all available transcript biotypes from Ensembl.
gene_biotype_use	Character, can be "all", "cellranger", or a vector of gene biotypes to be used. If "cellranger", then the biotypes used by Cell Ranger's reference are used. See data("cellranger_biotypes") for gene biotypes the Cell Ranger reference uses. See data("ensembl_gene_biotypes") for all available gene biotypes from Ensembl. Note that gene biotypes and transcript biotypes are not always the same.
chrs_only	Logical, whether to include chromosomes only, for GTF and GFF files can contain annotations for scaffolds, which are not incorporated into chromosomes. This will also exclude haplotypes. Defaults to TRUE. Only applicable to species found in genomeStyles().
ensembl_version	Integer version number of Ensembl (e.g. 94 for the October 2018 release). This argument defaults to NULL, which will use the current release of Ensembl. Use listEnsemblArchives to see the version number corresponding to the Ensembl release of a particular date. The version specified here must match the version of Ensembl where the transcriptome used to build the kallisto index was downloaded. This only works for vertebrates and the most common invertebrate model organisms like Drosophila melanogaster and C. elegans (i.e. www.ensembl.org and its mirrors), not the other Ensembl sites for plants, protists, fungi, and metazoa.
overwrite	Logical, whether to overwrite if files with names of outputs written to disk already exist.
verbose	Whether to display progress.
...	Othe arguments to be passed to useMart, such as mirror. Note that setting mirrors other than the default, e.g. uswest, does not work for archived versions.

Value

A data frame with at least 2 columns: gene for gene ID, transcript for transcript ID, and optionally gene_name for gene names. If other_attrs has been specified, then those will also be columns in the data frame returned.

See Also

dl_transcriptome

Other functions to retrieve transcript and gene info: sort_tr2g(), tr2g_EnsDb(), tr2g_TxDb(), tr2g_fasta(), tr2g_gff3(), tr2g_gtf(), transcript2gene()

Examples

tr2g <- tr2g_ensembl(species = "Danio rerio", 
other_attrs = "description", write_tr2g = FALSE)
# This will use plants.ensembl.org as host instead of www.ensembl.org
tr2g <- tr2g_ensembl(species = "Arabidopsis thaliana", type = "plant",
  write_tr2g = FALSE)

lambdamoses/BUStoolsR documentation built on Aug. 1, 2024, 6:30 a.m.