pickPrimers {TAPseq} | R Documentation |
Pick based primers from designed primers for every target based on Primer3 penalty score or
off-target priming estimated with blastPrimers
.
pickPrimers(object, n = 1, by = c("penalty", "off_targets")) ## S4 method for signature 'TsIO' pickPrimers(object, n = 1, by = c("penalty", "off_targets")) ## S4 method for signature 'TsIOList' pickPrimers(object, n = 1, by = c("penalty", "off_targets"))
object |
|
n |
The number of top primers to pick (default: 1, which returns the best primer). |
by |
Attribute by which primers should be picked. Can be either |
If by
is set to off_targets
top primers are picked based on the lowest number of
exonic, intronic and intergenic off-targets (in that priority).
A TsIO
or TsIOList
object containing the picked primers.
TsIO
: Pick best primers in a TsIO
object
TsIOList
: Pick best primers per target in a TsIOList
object
# chr11 primers examples data("chr11_primers") # pick the best primer per gene based on the fewest exonic, intronic and intergenic off-targets # (in that order) best_primers <- pickPrimers(chr11_primers, by = "off_targets") tapseq_primers(best_primers) # pick the best two primers per gene based on the lowest penalty score computed by Primer3 best_primers <- pickPrimers(chr11_primers, n = 2, by = "penalty") tapseq_primers(best_primers)