ampcountr: Functions to predict the amplification generated by a strand...

In sherrillmix/ampCountR: Predict Amplification Products of Multiple Strand Displacement Amplification

Description

Given a list of forward and reverse primer binding sites predict the amplification that will result from a strand displacement reaction

Details

The main functions are:

countAmplifications:

to predict the number of amplifications for a single region

predictAmplifications:

to predict the number of amplifications across a whole genome

enumerateAmplifications:

to generate the predicted fragments for small sets of primers

Author(s)

Scott Sherrill-Mix, [e-mail]

References

https://en.wikipedia.org/wiki/Multiple_displacement_amplification

Examples

forwards<-ampcountr:::generateRandomPrimers(100000,1000)
reverses<-ampcountr:::generateRandomPrimers(100000,1000)
amps<-predictAmplifications(forwards,reverses,maxLength=10000)
plot(1,1,type='n',xlim=c(1,100000),ylim=c(1,max(amps)),
     xlab='Position',ylab='Amplifications',log='y')
segments(amps$start,amps$amplification,amps$end,amps$amplification)
segments(amps$end[-nrow(amps)],amps$amplification[-nrow(amps)],
         amps$start[-1],amps$amplification[-1])
abline(v=forwards,col='#FF000044',lty=2)
abline(v=reverses,col='#0000FF44',lty=2)

frags<-enumerateAmplifications(c(10,20,30),c(15,25,35),maxLength=40)
plotFrags(frags)

sherrillmix/ampCountR documentation built on May 29, 2019, 9:24 p.m.