enumerateAmplifications: Enumerate the multiple strand displacement fragments...

Description Usage Arguments Value References See Also Examples

Description

Take two vectors of forward and reverse primer binding locations generate a list of amplification products predicted to be generated by multiple strand displacement amplification.

Usage

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enumerateAmplifications(forwards, reverses, strand = "+", maxLength = 50000,
  minLength = 1, maxTotalLength = Inf, fragmentStart = 1,
  fragmentEnd = Inf, baseName = "", vocal = FALSE, previousLength = 0,
  fullGenome = TRUE)

Arguments

forwards

Sorted positions of the start of the primers landing sites on the forward strand of the target sequence (5'-most base in the genome plus strand)

reverses

Sorted positions of the end of the primers landing sites on the reverse strand of the target sequence (3'-most base in the genome plus strand)

strand

"+" or "-" for indicating what strand the target sequence originates from. Note if starting with double stranded fragments then the function should be run once with "+" and once with "-" and the results concatenated.

maxLength

The expected max length fragment the polymerase can generate in one run.

minLength

Discard fragments shorter than minLength (can help with run time if many short fragments are generated)

maxTotalLength

Discard fragments for which the sum of all the ancestors bases are longer than maxTotalLength. If the polymerase has some probability of falling off each base amplified then it becomes less and less likely to reach a deeply amplified product. Using maxTotalLength to end the recursion once a certain total length is reach can help with run time.

fragmentStart

The 5' end of the current fragment (for use in recursion more than manually)

fragmentEnd

The 3' end of the current fragment (for use in recursion more than manually)

baseName

Prefix for tracking fragment ancestors (for use in recursion more than manually)

vocal

TRUE or FALSE Output progress?

previousLength

How many bases need to be amplified to reach this fragment (for use in recursion more than manually)

fullGenome

If TRUE then do not add the number of bases necessary to reach the primers to the previousLength (for use in recursion more than manually)

Value

A data frame with columns start, end, strand, name, previousLength and length. Start and end and strand are the positions of 5' and 3' end on the appropriate strand of the target sequence. Name is a concatenation of the ancestors of that fragment. Previous length is the sum of the fragment lengths of the ancestors of this fragment. Length is the width of this fragment. Returns NULL if no amplifications.

References

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

See Also

countAmplifications

Examples

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enumerateAmplifications(c(10,20,30),c(40,50,60),maxLength=45)

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