R: Remove accessions that do not match length and mismatch...

filter_primer_hits {rCRUX}

R Documentation

Remove accessions that do not match length and mismatch criteria determined by parameters

Remove accessions that do not match length and mismatch criteria determined by parameters

filter_primer_hits(
  hits_table,
  forward_primer_seq,
  reverse_primer_seq,
  mismatch = 3,
  minimum_length = 5,
  maximum_length = 500
)

`hits_table`	a data.frame generated by parse_primer_hits or by `iterative_primer_search()`
`forward_primer_seq`	passed to primer_search, which turns it into a list of each primer it could be based on its degenerate primers, then passes each one in turn to NCBI (e.g. forward_primer_seq <- "TAGAACAGGCTCCTCTAG")
`reverse_primer_seq`	passed to primer_search, which turns it into a list of each primer it could be based on its degenerate primers, then passes each one in turn to NCBI (e.g. reverse_primer_seq <- "TTAGATACCCCACTATGC")
`mismatch`	the highest acceptable mismatch value. `parse_primer_hits()` returns a table with a mismatch column. `get_seeds_remote()` removes each row with a mismatch greater than the specified value. The default is mismatch = 3 - Note this is smaller than `get_seeds_local()`
`minimum_length`	parse_primer_hits returns a table with a product_length column. `get_seeds_remote()` removes each row that has a value less than minimum_length in the product_length column. The default is minimum_length = 5
`maximum_length`	parse_primer_hits returns a table with a product_length column. `get_seeds_remote()` removes each row that has a value greater than maximum_length in the product_length column The default is maximum_length = 500

a data.table with problematic rows removed

[Package rCRUX version 0.0.1.000 ]