mapToCDS

Maps variants from genomic coordinates to CDS (coding sequence) positions.

mapToCDS(
  object,
  gff,
  exonPadding = 12,
  output = NULL,
  gene_id = NULL,
  transcript_id = NULL,
  biotype = NULL,
  verbose = TRUE
)

Arguments

object

Input gdb.

gff

Can be 1) a path to a valid gff- or gtf-file or 2) a GenomicRanges::GRanges object. Generated, for example, by importing an ensembl gtf file.

exonPadding

Remap variants within exonPadding base pairs from the exon border to the border. Defaults to 12.

output

Optional output (.gz). If NULL remapped coordinates will be returned to session.

gene_id

Optional vector of gene ids to keep in the gff/gtf file.

transcript_id

Optional vector of transcript ids to keep in the gff/gtf file.

biotype

Optional vector of biotypes to keep in the gff/gtf file.

verbose

Should the function be verbose? Defaults to TRUE.