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Get sequences for genomic loci as a DNAStringSet object

Source: R/get_sequences.R
get_sequences.Rd

Get sequences for genomic loci as a DNAStringSet object

Usage

get_sequences(
  species,
  type = c("CDS", "transcript", "protein"),
  transcripts = c("all", "longest")
)

Arguments

species

Character vector of PLAZA species IDs.

type

Character indicating what type of locus to extract. One of 'CDS', 'transcript', or 'protein'.

transcripts

Character indicating what genes for which sequences will be extracted. One of 'all' (for each gene, all transcripts and associated features), or 'longest' (for each gene, only longest transcripts and associated features).

Value

A DNAStringSet object for a single species, or a list of DNAStringSet objects for multiple species.

Examples

species <- "cre"
seq <- get_sequences(species, type = "protein", transcripts = "longest")