checkPrimers {TAPseq} | R Documentation |
Check a TAP-seq primer set, i.e. outer or inner primers for a target gene panel, for potential
complementarity issues when multiplexing. Uses Primer3's check_primers
functionality.
checkPrimers( object, primer_opt_tm = 63, primer_min_tm = 59, primer_max_tm = 66, thermo_params_path = NA, primer3_core = getOption("TAPseq.primer3_core") ) ## S4 method for signature 'TsIO' checkPrimers( object, primer_opt_tm = 63, primer_min_tm = 59, primer_max_tm = 66, thermo_params_path = NA, primer3_core = getOption("TAPseq.primer3_core") ) ## S4 method for signature 'TsIOList' checkPrimers( object, primer_opt_tm = 63, primer_min_tm = 59, primer_max_tm = 66, thermo_params_path = NA, primer3_core = getOption("TAPseq.primer3_core") )
object |
|
primer_opt_tm, primer_min_tm, primer_max_tm |
Optimal, minumum and maximum primer melting temperature. Should be the same values that were used when designing the primers. |
thermo_params_path |
Optional path (character) to the |
primer3_core |
Path (character) to the |
A data.frame
with check_primers
results.
TsIO
: Check primers from TsIO
objects.
TsIOList
: Check primers from TsIOList
objects.
http://primer3.org/manual.html for Primer3 manual.
library(ggplot2) # chr11 primers example data data("chr11_primers") # pick best primers based on predicted off-targets for subset of all primers best_primers <- pickPrimers(chr11_primers, n = 1, by = "off_targets") # check for complementarity ## Not run: comp <- checkPrimers(best_primers) # plot complementarity scores for every pair. the lines indicate complementarity scores of 47, # the default value applied by Primer3 to identify high complementarity primer pairs ggplot(comp, aes(x = primer_pair_compl_any_th, y = primer_pair_compl_end_th)) + geom_hline(aes(yintercept = 47), colour = "darkgray", linetype = "dashed") + geom_vline(aes(xintercept = 47), colour = "darkgray", linetype = "dashed") + geom_point(alpha = 0.25) + theme_bw() ## End(Not run)