refdb_clean_seq_crop_primers {refdb}

Crop genetic sequences with a set of primers

Description

Crop genetic sequences with a set of primers

Usage

refdb_clean_seq_crop_primers(
  x,
  primer_forward,
  primer_reverse,
  max_error_in = 0.1,
  max_error_out = 0.1,
  include_primers = TRUE
)

Arguments

x

a reference database with a defined sequence field.

primer_forward

primer forward.

primer_reverse

primer reverse.

max_error_in, max_error_out

maximum error for a match (frequency based on primer length).

include_primers

a logical indicating whether the detected primers are included in the cropped sequences.

Value

A reference database.

Examples

lib <- read.csv(system.file("extdata", "baetidae_bold.csv", package = "refdb"))
lib <- refdb_set_fields_BOLD(lib)
refdb_clean_seq_crop_primers(lib, "AGT", "TTTA")