pickPrimers: Pick best TAP-seq primers

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

Pick best TAP-seq primers

Description

Pick based primers from designed primers for every target based on Primer3 penalty score or off-target priming estimated with blastPrimers.

Usage

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"))

Arguments

object	A TsIO or TsIOList object containing designed primers.
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 penalty or off_targets.

Details

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).

Value

A TsIO or TsIOList object containing the picked primers.

Methods (by class)

• pickPrimers(TsIO): Pick best primers in a TsIO object

• pickPrimers(TsIOList): Pick best primers per target in a TsIOList object

Examples

# 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)

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