dropDimer: find the primer identifiers with self dimers

In cam315/barcodePrimer: A package to randomly generate barcoded primer set combinations without primer dimers

Description

This function will parse the primer checking report and give out the self-dimer primer identifiers.

Usage

dropDimer(report, ndimer)

Arguments

report	the report file which was generated by the webtool from Thermo Fisher.
ndimer	argument to specify thredshold at which self-dimer primer will be filtered out. If you specify 2, all primer with 2 or more than 2 self dimers will be found out.

Details

this function will find out the primer identifiers with two or three self-dimer in the barcoded primers. This function accept ndimer given in numeric values like 2 and 3, or in character 'two' or 'three'.

Value

return a vector containing the self-dimer primer identifiers.

Author(s)

Sizhong Yang <[e-mail]>

Examples

data(report)
selfdimers = dropDimer(report, ndimer = 3)

## remove the selfdimers from the result

data(PrimerLabels)

wcomb = reparser(report)
tcomb = primerCombi(PrimerLabels)

vcombs = slim(tcomb, wcomb)
moreprimers = pickmore(combi = vcombs, n = 120)
dim(moreprimers)

## further remove the primers with selfdimers

toDrop = apply(moreprimers, 1, function(x) any(match(x, selfdimers, nomatch = 0) > 0))
outprimers = moreprimers[!toDrop,]
dim(outprimers)

cam315/barcodePrimer documentation built on Dec. 9, 2020, 7:01 p.m.