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Extract gene annotation as a GRanges object

Source: R/get_ranges.R
get_annotation.Rd

Extract gene annotation as a GRanges object

Usage

get_annotation(
  species,
  transcripts = c("all", "longest"),
  features = c("all", "exons")
)

Arguments

species

Character vector of PLAZA species IDs.

transcripts

Character indicating what genes for which ranges 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).

features

Character indicating what features to extract. One of 'all' (all features, including exons, mRNAs, CDS, UTRs, etc), or 'exons' (only exon features).

Value

A GRanges object for a single species, or a GRangesList object for multiple species.

Examples

ranges <- get_annotation(
    species = c("aly", "ath"), 
    transcripts = "longest", features = "all"
)