dl_transcriptome: Download transcriptome from Ensembl

Description Usage Arguments Value Examples

View source: R/get_tx.R

Description

This function downloads the cDNA fasta file from specific version of Ensembl. It can also filter the fasta file by gene and transcript biotype and remove scaffolds and haplotypes.

Usage

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dl_transcriptome(
  species,
  out_path = ".",
  type = c("vertebrate", "metazoa", "plant", "fungus", "protist"),
  transcript_biotype_use = "all",
  gene_biotype_use = "all",
  chrs_only = TRUE,
  ensembl_version = NULL,
  verbose = TRUE,
  ...
)

Arguments

species

Character vector of length 1, Latin name of the species of interest.

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.

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".

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.

verbose

Whether to display progress.

...

Other arguments passed to tr2g_fasta.

Value

Invisibly returns the path to the fasta file. The following files are written to disk, in the out_path directory:

species.genome.cdna.all.fa.gz

The cDNA fasta file from Ensembl, from the specified version.

cdna_filtered.fa

The filtered cDNA fasta file, only keeping the desired biotypes and without scaffolds and haplotypes (if chrs_only = TRUE). This file will not be written if all gene and transcript biotypes are used and scaffolds and haplotypes are not removed.

tr2g.tsv

The transcript to gene file, without headers so can be directly used for bustools.

Examples

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dl_transcriptome("Drosophila melanogaster", gene_biotype_use = "cellranger",
                 chrs_only = FALSE)
# Clean up
file.remove("Drosophila_melanogaster.BDGP6.32.cdna.all.fa.gz")

lambdamoses/BUStoolsR documentation built on June 9, 2021, 6:15 p.m.