species2dataset: Convert Latin species name to dataset name

View source: R/utils.R

species2datasetR Documentation

Convert Latin species name to dataset name

Description

This function converts Latin species name to a dataset name in biomart to query gene and transcript ID.

Usage

species2dataset(
  species,
  type = c("vertebrate", "metazoa", "plant", "fungus", "protist")
)

Arguments

species

A character vector of Latin names of species present in this scRNA-seq dataset. This is used to retrieve Ensembl information from biomart.

type

A character vector indicating the type of each species. Each element must be one of "vertebrate", "metazoa", "plant", "fungus", and "protist". If length is 1, then this type will be used for all species specified here. Can be missing if fasta_file is specified.

Value

The appropriate dataset name for biomart.

Examples

species2dataset(species = "Homo sapiens")

lambdamoses/BUStoolsR documentation built on Aug. 28, 2022, 1:35 p.m.