countAmplifications: Calculate expected multiple strand displacement amplification...

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

Description

Uses the amplificationLookup table stored in the package data to predict amplification based on the number of forward and reverse primers spanning a region. To keep the lookup table small, I limited this to 1000 forward and reverse primers but it could be extended easily.

Usage

countAmplifications(nForwards, nReverses, isTerminal = TRUE,
  onlyFirstPrimer = FALSE)

Arguments

nForwards	Calculate the expected amplifcations for a region with nForwards primers 5' on the correct strand and within range
nReverses	Calculate the expected amplifcations for a region with nReverses primers 3' on the correct strand and within range
isTerminal	If TRUE then there are no upstream forward primers to release the 5'-most forward primer in this set. If FALSE then the 5'-most forward primer is assumed to be released by an unknown upstream primer.
onlyFirstPrimer	If TRUE then count only fragments whose initial fragment initiating from the 5'-most forward primer (mostly for internal usage to allow individual counting of sets of primers where only subsets overlap)

Value

The number of expected amplifications

Examples

countAmplifications(20,20)
countAmplifications(0,20)
countAmplifications(20,0)

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