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

ampCountR

Some R functions to count the expected amplifications for genomic regions given a set of primer binding locations for a multiple displacement amplification reaction. To install directly from github, use the devtools library and run:

devtools::install_github('sherrillmix/ampcountr')

The package assumes that forward primer binding sites (primers matching the genomic plus strand) are represented by their leftmost (5'-most in the genomic plus strand) base position and reverse primer binding sites (primers matching the genomic minus strand) are represented by their rightmost (3'-most in the genomic plus strand) base position.

Functions

library(ampcountr)

countAmplifications

countAmplifications(x,y) to count the number of amplifications predicted for a region with x upstream and y downstream primers (within range and correctly oriented). For example:

countAmplifications(10,20)

enumerateAmplifications

enumerateAmplifications() to list the expected amplification products. For example:

forwards<-c(1,11,21)
reverses<-c(25,35,45)
enumerateAmplifications(forwards,reverses,maxLength=50)

A simple example of generating predicted fragments for 3 forward primers and 3 reverse primers is:

forwards<-c(10,20,30)
reverses<-c(35,45,55)
frags<-enumerateAmplifications(forwards,reverses,maxLength=50)
par(mar=c(2.9,2.8,.2,.2),mgp=c(1.9,.75,0),las=1)
plotFrags(frags)
abline(v=forwards,lty=2,col='#FF000033')
abline(v=reverses,lty=2,col='#0000FF33')

This function is bit slow since it uses recursion without dynamic programming but countAmplifications() should easily handle any large sets.

predictAmplifications

predictAmplifications() to list the expected amplification products over a genome given primer binding sites on the forward and reverse strand. For example:

forwards<-c(1,11,21)
reverses<-c(25,35,45)
predictAmplifications(forwards,reverses,maxLength=50)

Example

A longer example (also accessible from example(ampcountr):

forwards<-ampcountr:::generateRandomPrimers(100000,1000)
reverses<-ampcountr:::generateRandomPrimers(100000,1000)
amps<-predictAmplifications(forwards,reverses,maxLength=10000)
par(mar=c(3.5,3.5,.2,.2))
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)

This generates an example predicted fold enrichments of: See generatePlots.R for complete plotting details.

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