cubar (version 1.1.0)

check_cds: Quality control of CDS

Description

check_cds performs quality control of CDS sequences by filtering some peculiar sequences and optionally remove start or stop codons.

Usage

check_cds(
  seqs,
  codon_table = get_codon_table(),
  min_len = 6,
  check_len = TRUE,
  check_start = TRUE,
  check_stop = TRUE,
  check_istop = TRUE,
  rm_start = TRUE,
  rm_stop = TRUE,
  start_codons = c("ATG")
)

Value

DNAStringSet of filtered (and trimmed) CDS sequences

Arguments

seqs

input CDS sequences

codon_table

codon table matching the genetic code of seqs

min_len

minimum CDS length in nt

check_len

check whether CDS length is divisible by 3

check_start

check whether CDSs have start codons

check_stop

check whether CDSs have stop codons

check_istop

check internal stop codons

rm_start

whether to remove start codons

rm_stop

whether to remove stop codons

start_codons

vector of start codons

Examples

# CDS sequence QC for a sample of yeast genes
s <- head(yeast_cds, 10)
print(s)
check_cds(s)