doamp_auto: Automatically download sequences and extract potential...

In ong8181/rDoAMP: Extracting amplicons from target sequences using a user-specified primer set

Automatically download sequences and extract potential amplicons

Description

doamp_auto Automatically download sequences and extract potential amplicons

Usage

doamp_auto(
  search_query,
  F_primer,
  R_primer,
  n_retmax = 20,
  n_retidmax = n_retmax * 10,
  n_mismatch = 0,
  random_sampling = TRUE,
  random_sampling_seed = 1234,
  output_dir = "rDoAMP_Out",
  save_parameter = TRUE,
  save_stat = TRUE,
  overwrite_output_dir = FALSE
)

Arguments

search_query	Character. Search query for Entrez
F_primer	Character. Forward primer sequence. Degenerate base allowed.
R_primer	Character. Reverse primer sequence. Degenerate base allowed.
n_retmax	Numeric. The maximum number of sequences collected from Entrez
n_retidmax	Numeric. The maximum number of IDs collected from Entrez. Default is 10. If random_sampling = TRUE, n_retidmax IDs will be collected and then n_retmax sequences will be downloaded.
n_mismatch	Numeric. The maximum number of primer-template mismatches allowed
random_sampling	Logical. If TURE, n_retidmax IDs collected, and then n_retmax sequences are randomly collected
random_sampling_seed	Numeric. Random number seed for random_sampling
output_dir	Character. Output directory name
save_parameter	Logical. If TRUE, parameters used in the analysis saved
save_stat	Logical. If TRUE, summary of the analysis saved
overwrite_output_dir	Logical. If TRUE, overwrite the contents of output directory.

ong8181/rDoAMP documentation built on Aug. 27, 2023, 10:15 a.m.