checkPrimers: Check primers for complementarity

In argschwind/TAPseq: Targeted scRNA-seq primer design for TAP-seq

Check primers for complementarity

Description

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.

Usage

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")
)

Arguments

object	A TsIO or TsIOList object containing designed primers.
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_config directory. Only required when using Primer3 < 2.5.0.
primer3_core	Path (character) to the primer3_core executable. Usually this is inferred when loading/attaching the package.

Value

A data.frame with check_primers results.

Methods (by class)

• checkPrimers(TsIO): Check primers from TsIO objects.

• checkPrimers(TsIOList): Check primers from TsIOList objects.

See Also

http://primer3.org/manual.html for Primer3 manual.

Examples

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)

argschwind/TAPseq documentation built on Feb. 9, 2024, 8:20 p.m.