predictAmplificationsSingleStrand: Calculate expected multiple strand displacement for a series...

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

Description

Calculate the expected amplifications across a genome for a set of forward and reverse primer binding sites used in multiple strand displacement amplification

Usage

predictAmplificationsSingleStrand(forwards, reverses, maxLength = 30000,
  genomeSize = max(c(forwards + maxLength - 1, reverses)))

predictAmplifications(forwards, reverses, maxLength = 30000,
  genomeSize = max(c(forwards + maxLength - 1, reverses)))

Arguments

forwards	Leftmost positions of primer binding sites landing on the 5' strand (1-based 5'-most base in the genome plus strand)
reverses	Rightmost positions of primer binding sites landing on the 3' strand (1-based 3'-most base in the genome plus strand)
maxLength	Maximum length fragment generated by polymerase
genomeSize	Maximum position possible for amplification

Value

A data frame with columns:

start:

1-based start coordinate of region

end:

1-based end coordinate of region

forwards:

number of forward primers spanning the region (for predictAmplificationsSingleStrand)

reverses:

number of reverse primers spanning the region (for predictAmplificationsSingleStrand)

amplifications:

expected amplifcations for the region

Functions

• predictAmplifications: Calculate the expected amplifications across a genome for a set of forward and reverse primer binding sites for both strands

Examples

predictAmplificationsSingleStrand(c(1,10,20),c(15,25,35),maxLength=40,genomeSize=45)
predictAmplifications(c(1,10,20),c(15,25,35),maxLength=40,genomeSize=45)

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