matchProbePair {Biostrings} | R Documentation

## Find "theoretical amplicons" mapped to a probe pair

### Description

In the context of a computer-simulated PCR experiment, one wants to find the amplicons mapped to a given primer pair. The `matchProbePair` function can be used for this: given a forward and a reverse probe (i.e. the chromosome-specific sequences of the forward and reverse primers used for the experiment) and a target sequence (generally a chromosome sequence), the `matchProbePair` function will return all the "theoretical amplicons" mapped to this probe pair.

### Usage

      matchProbePair(Fprobe, Rprobe, subject, algorithm="auto", logfile=NULL, verbose=FALSE)

### Arguments

`Fprobe` | The forward probe.
`Rprobe` | The reverse probe.
`subject` | A `DNAString` object (or an `XStringViews` object with a `DNAString` subject) containing the target sequence.
`algorithm` | One of the following: `"auto"`, `"naive-exact"`, `"naive-inexact"`, `"boyer-moore"` or `"shift-or"`. See `matchPattern` for more information.
`logfile` | A file used for logging.
`verbose` | `TRUE` or `FALSE`.

### Details

The `matchProbePair` function does the following: (1) find all the "plus hits" i.e. the Fprobe and Rprobe matches on the "plus" strand, (2) find all the "minus hits" i.e. the Fprobe and Rprobe matches on the "minus" strand and (3) from the set of all (plus_hit, minus_hit) pairs, extract and return the subset of "reduced matches" i.e. the (plus_hit, minus_hit) pairs such that (a) plus_hit <= minus_hit and (b) there are no hits (plus or minus) between plus_hit and minus_hit. This set of "reduced matches" is the set of "theoretical amplicons".

### Value

An XStringViews object containing the set of "theoretical amplicons".

### Author(s)

H. Pages

### See Also

`matchPattern`, `matchLRPatterns`, `findPalindromes`, `reverseComplement`, `XStringViews`

### Examples

      library(BSgenome.Dmelanogaster.UCSC.dm3)
      subject <- Dmelanogaster$chr3R

      ## With 20-nucleotide forward and reverse probes:
      Fprobe <- "AGCTCCGAGTTCCTGCAATA"
      Rprobe <- "CGTTGTTCACAAATATGCGG"
      matchProbePair(Fprobe, Rprobe, subject) # 1 "theoretical amplicon"

      ## With shorter forward and reverse probes, the risk of having multiple
      ## "theoretical amplicons" increases:
      Fprobe <- "AGCTCCGAGTTCC"
      Rprobe <- "CGTTGTTCACAA"
      matchProbePair(Fprobe, Rprobe, subject) # 2 "theoretical amplicons"
      Fprobe <- "AGCTCCGAGTT"
      Rprobe <- "CGTTGTTCACA"
      matchProbePair(Fprobe, Rprobe, subject) # 9 "theoretical amplicons"

[Package Biostrings version 2.8.18 Index]