write_cds_entries: Extract CDS sequences from a genome and set of annotations.

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

Extract CDS sequences from a genome and set of annotations.

Description

Given a BSGenome and some annotations, write out the CDS entries.

Usage

write_cds_entries(
  genome,
  annot,
  ids = NULL,
  output = "all_cds.fasta",
  strand_column = "strand",
  chr_column = "chromosome",
  start_column = "start",
  end_column = "end",
  name_column = "rownames",
  name_prefix = "lpanamensis_mcol"
)

Arguments

genome	BSGenome containing the raw sequence.
annot	Annotation dataframe.
ids	Set of annotations to write, write them all if null.
output	Fasta file to write.
strand_column	Column name with the strand information.
chr_column	Column name with the chromosomes.
start_column	Column with the start positions.
end_column	Column with the end positions.
name_column	Names of the CDS
name_prefix	Prefix to add to the entries.

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