gather_utrs_txdb: Get UTR sequences using information provided by TxDb and...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Get UTR sequences using information provided by TxDb and fiveUTRsByTranscript

Description

For species like Mus musculus, load_orgdb_annotations(Mus.musculus) should return a list including the requisite GRanges for the 5'/3' UTRs.

Usage

gather_utrs_txdb(
  bsgenome,
  fivep_utr = NULL,
  threep_utr = NULL,
  start_column = "start",
  end_column = "end",
  strand_column = "strand",
  chr_column = "seqnames",
  name_column = "group_name",
  ...
)

Arguments

bsgenome	A BSGenome instance containing the encoded genome.
fivep_utr	Locations of the 5' UTRs.
threep_utr	Locations of the 3' UTRs.
start_column	What column in the annotation data contains the starts?
end_column	Column in the data with the end locations.
strand_column	What column in the annotation data contains the sequence strands?
chr_column	Column in the df with the chromosome names.
name_column	Finally, where are the gene names?
...	Parameters passed to child functions.

Value

UTRs!

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.