utr.annotation (version 1.0.4)

getSeqTable: Get UTR sequences of a list of transcripts

Description

getSeqTable will query 5' UTR or 3' UTR sequences of a list of transcripts from Ensembl database

Usage

getSeqTable(
  transcriptIds,
  seqType,
  species,
  ensemblVersion,
  dataDir,
  downstream = NULL,
  upstream = NULL
)

Arguments

transcriptIds

a list of Ensembl transcript ids

seqType

Either '5utr' or '3utr'. 5utr' for 5' UTR sequence, '3utr' for 3' UTR sequences

species

human or mouse

dataDir

directory to store DB information

Value

sequences table containing columns: ensembl_transcript_id and seq