Run primer design
design(seqOpts, primerOpts = NULL, returnStats = TRUE, ...)
| seqOpts | parameters for the given sequence, i.e. template sequence, its name, junction position |
|---|---|
| primerOpts | (optional) thermodynamical and other primer-specific parameters. Can be created using p3Settings. |
| returnStats | (default: TRUE) if the "EXPLAIN" fields with the run statistics should be returned. This option overwrites the one provided in the `primerOpts$PRIMER_EXPLAIN_FLAG`. |
| ... | path parameters for the `runPrimer3` call. |
a data.frame with the designed primers
By default, if `primer3Config` is not secified/NULL, it is inferred on the basis of the `primer3Path` as a subdirectory `primer3_config`
# make up a sequence seq1 <- paste(c("A", "T", "G", "C")[sample(4, 300, replace = TRUE)], collapse = "") seqOpts <- seqSettings(seqId = "seq1", seq = seq1) res <- design(seqOpts) res$primers#> PRIMER_PAIR_PENALTY PRIMER_LEFT_PENALTY PRIMER_RIGHT_PENALTY #> 0 0.039002 0.026532 0.012470 #> 1 0.041723 0.029253 0.012470 #> 2 0.085786 0.073316 0.012470 #> 3 0.101563 0.026532 0.075031 #> 4 0.104284 0.029253 0.075031 #> PRIMER_LEFT_SEQUENCE PRIMER_RIGHT_SEQUENCE PRIMER_LEFT PRIMER_RIGHT #> 0 AGGGAATGTTGCAAGTGGAC TTCTAGACCACTCGCCGACT 26,20 260,20 #> 1 GTTGCAAGTGGACCCCTTTA TTCTAGACCACTCGCCGACT 33,20 260,20 #> 2 ATCTGGACGAGGGAATGTTG TTCTAGACCACTCGCCGACT 17,20 260,20 #> 3 AGGGAATGTTGCAAGTGGAC GCCTATCCGGGTTCTAGACC 26,20 271,20 #> 4 GTTGCAAGTGGACCCCTTTA GCCTATCCGGGTTCTAGACC 33,20 271,20 #> PRIMER_LEFT_TM PRIMER_RIGHT_TM PRIMER_LEFT_GC_PERCENT PRIMER_RIGHT_GC_PERCENT #> 0 59.973 60.012 50.000 55.000 #> 1 59.971 60.012 50.000 55.000 #> 2 59.927 60.012 50.000 55.000 #> 3 59.973 59.925 50.000 60.000 #> 4 59.971 59.925 50.000 60.000 #> PRIMER_LEFT_SELF_ANY_TH PRIMER_RIGHT_SELF_ANY_TH PRIMER_LEFT_SELF_END_TH #> 0 0.00 0.00 0.00 #> 1 0.00 0.00 0.00 #> 2 0.00 0.00 0.00 #> 3 0.00 0.00 0.00 #> 4 0.00 0.00 0.00 #> PRIMER_RIGHT_SELF_END_TH PRIMER_LEFT_HAIRPIN_TH PRIMER_RIGHT_HAIRPIN_TH #> 0 0.00 0.00 0.00 #> 1 0.00 0.00 0.00 #> 2 0.00 0.00 0.00 #> 3 0.00 0.00 46.61 #> 4 0.00 0.00 46.61 #> PRIMER_LEFT_END_STABILITY PRIMER_RIGHT_END_STABILITY PRIMER_PAIR_COMPL_ANY_TH #> 0 7.9000 8.1000 1.72 #> 1 6.3000 8.1000 1.72 #> 2 7.0000 8.1000 0.00 #> 3 7.9000 7.6000 0.00 #> 4 6.3000 7.6000 0.00 #> PRIMER_PAIR_COMPL_END_TH PRIMER_PAIR_PRODUCT_SIZE #> 0 0.00 235 #> 1 11.96 228 #> 2 0.00 244 #> 3 0.00 246 #> 4 0.00 239