iterative_primer_search {rCRUX}

R Documentation

Call primer_search with several parameters and aggregate the results

Description

This function acts like primerTree::primer_search() and primerTree's parse_primer() hits all in one.

Usage

iterative_primer_search(
  forwar_primer_seq,
  reverse_primer_seq,
  organisms,
  db = "nt",
  ...
)

Arguments

reverse_primer_seq	the reverse primer to search (e.g. reverse_primer_seq <- "TTAGATACCCCACTATGC")
organisms	a character vector containing an id or name parseable by NCBI as an organism. If it is a vector with multiple entries, each entry will be queried separately. (e.g. organism = c("1476529", "7776"))
db	which NCBI database to search. The default is db = 'nt' (e.g. nr).
forward_primer_seq	the forward primer to search (e.g. forward_primer_seq <- "TAGAACAGGCTCCTCTAG")

Details

It calls modifiedPrimerTree_Functions() to perform tasks. Its parameters are very similar to primerTree::primer_search(), but it takes vectors for organism and for database and performs a primer search for each combination. It downgrades errors from primer_search and parse_primer_hits into warnings. This is useful when searching for a large number of different combinations, allowing the function to output successful results.

Value

a data.table summarizing the results of several primer_searches

---