checkMatch: Check how oligos and assays match to their target sequences
In sofpn/rprimer: Design Degenerate Oligos from a Multiple DNA Sequence Alignment
checkMatch R Documentation
Check how oligos and assays match to their target sequences
Description
checkMatch() investigates how well oligos or assays match with their
intended target sequences
within a multiple DNA sequence alignment.
Usage
checkMatch(x, target)
## S4 method for signature 'RprimerOligo'
checkMatch(x, target)
## S4 method for signature 'RprimerAssay'
checkMatch(x, target)
Arguments
x
An RprimerOligo or RprimerAssay object.
target
A Biostrings::DNAMultipleAlignment alignment with
intended target sequences. Note that it must be
same alignment that was used for generating the oligos/assays in x.
Details
The output provides information on the proportion and names of target
sequences
that match perfectly as well as with one, two, three, or four or more
mismatches to the oligo within the intended oligo binding region
in the input alignment (on-target match).
It also gives the proportion and names of target sequences that
match with a maximum of two mismatches to at least one sequence variant of
the oligo outside the
intended oligo binding region (off-target match).
The function is a wrapper to Biostrings::vcountPDict()
(Pages et al., 2020).
Value
An RprimerMatchOligo or RprimerMatchAssay object, depending
on whether an RprimerOligo or RprimerAssay object was used
as input.
RprimerMatchOligo objects contain the following information:
- iupacSequence
The oligo sequence in IUPAC format.
- perfectMatch
Proportion of target sequences that matches perfectly
to the oligo within the intended binding region.
- idPerfectMatch
Names of all sequences that matches perfectly.
- oneMismatch
Proportion of target sequences with one mismatch to
the oligo
within the intended binding region.
- idOneMismatch
Names of all sequences that matches with one
mismatch.
- twoMismatches
Proportion of target sequences with two mismatches
to the oligo
within the intended binding region.
- idTwoMismatches
Names of all sequences that matches with two
mismatches.
- threeMismatches
Proportion of target sequences with
three mismatches to the oligo
within the intended binding region.
- idThreeMismatches
Names of all sequences that matches with three
mismatches.
- fourOrMoreMismatches
Proportion of target sequences with
four or more mismatches to the oligo
within the intended binding region.
- idFourOrMoreMismatches
Names of all sequences that matches with four
or more mismatches.
- offTargetMatch
Proportion of target sequences with maximum two
mismatches to at least one site outside the intended
oligo binding region in the input alignment.
- idOffTargetMatch
Names of all off-target matching sequences.
RprimerMatchAssay objects contain the following information:
- iupacSequenceFwd
The forward primer sequence in IUPAC format.
- perfectMatchFwd
Proportion of target sequences that matches
perfectly
with the forward primer withing the intended binding region.
- idPerfectMatchFwd
Names of all sequences that matches perfectly.
- oneMismatchFwd
Proportion of target sequences with one mismatch to
the forward primer
within the intended binding region.
- idOneMismatchFwd
Names of all sequences that matches with one
mismatch.
- twoMismatchesFwd
Proportion of target sequences with two mismatches
to the forward primer
within the intended binding region.
- idTwoMismatchesFwd
Names of all sequences that matches with two
mismatches.
- threeMismatchesFwd
Proportion of target sequences with
three mismatches to the forward primer
within the intended binding region.
- idThreeMismatchesFwd
Names of all sequences that matches with three
mismatches.
- fourOrMoreMismatchesFwd
Proportion of target sequences with
four or more mismatches to the forward primer
within the intended binding region.
- idFourOrMoreMismatchesFwd
Names of all sequences that matches with
four or more mismatches.
- offTargetMatchFwd
Proportion of target sequences with maximum two
mismatches to at least one site outside the intended
forward primer binding region in the input alignment.
- idOffTargetMatchFwd
Names of all off-target matching sequences.
- iupacSequenceRev
The reverse primer sequence in IUPAC format.
- perfectMatchRev
Proportion of target sequences that matches
perfectly
with the reverse primer withing the intended binding region.
- idPerfectMatchRev
Names of all sequences that matches perfectly.
- oneMismatchRev
Proportion of target sequences with one mismatch to
the reverse primer
within the intended binding region.
- idOneMismatchRev
Names of all sequences that matches with one
mismatch.
- twoMismatchesRev
Proportion of target sequences with two mismatches
to the reverse primer
within the intended binding region.
- idTwoMismatchesRev
Names of all sequences that matches with two
mismatches.
- threeMismatchesRev
Proportion of target sequences with
three mismatches to the reverse primer
within the intended binding region.
- idThreeMismatchesRev
Names of all sequences that matches with three
mismatches.
- fourOrMoreMismatchesRev
Proportion of target sequences with
four or more mismatches to the reverse primer
within the intended binding region.
- idFourOrMoreMismatchesRev
Names of all sequences that matches with
four or more mismatches.
- offTargetMatchRev
Proportion of target sequences with maximum two
mismatches to at least one site outside the intended
reverse primer binding region in the input alignment.
- idOffTargetMatchRev
Names of all off-target matching sequences.
If the input assay contains probes, the following information
is also added:
- iupacSequencePr
The probe sequence in IUPAC format.
- perfectMatchPr
Proportion of target sequences that matches perfectly
with the probe withing the intended binding region.
- idPerfectMatchPr
Names of all sequences that matches perfectly.
- oneMismatchPr
Proportion of target sequences with one mismatch to
the probe
within the intended binding region.
- idOneMismatchPr
Names of all sequences that matches with one
mismatch.
- twoMismatchesPr
Proportion of target sequences with two mismatches
to the probe
within the intended binding region.
- idTwoMismatchesPr
Names of all sequences that matches with two
mismatches.
- threeMismatchesPr
Proportion of target sequences with
three mismatches to the probe
within the intended binding region.
- idThreeMismatchesPr
Names of all sequences that matches with three
mismatches.
- fourOrMoreMismatchesPr
Proportion of target sequences with
four or more mismatches to the probe
within the intended binding region.
- idFourOrMoreMismatchesPr
Names of all sequences that matches with
four or more mismatches.
- offTargetMatchPr
Proportion of target sequences with maximum two
mismatches to at least one site outside the intended
probe binding region in the input alignment.
- idOffTargetMatchPr
Names of all off-target matching sequences.
Methods (by class)
-
checkMatch(RprimerOligo):
-
checkMatch(RprimerAssay):
Limitations
There are a few limitations with this function, which is important to be
aware of:
False negatives or positives may occur due to
poorly aligned sequences
The output does not tell which strand
(minus or plus) the oligo matches to.
This is important to consider when
assessing off-target matches to single-stranded
targets
Ambiguous bases and gaps in the
target sequences are identified as mismatches
The function checks strictly on- and off-target, and may therefore
miss off-target matches that partially overlap the intended target
References
Pages, H., Aboyoun, P., Gentleman R., and DebRoy S. (2020). Biostrings:
Efficient manipulation of biological strings. R package version
2.57.2.
Examples
#### RprimerOligo objects
data("exampleRprimerOligo")
data("exampleRprimerAlignment")
x <- exampleRprimerOligo[1:2, ]
target <- exampleRprimerAlignment
checkMatch(x, target)
#### RprimerAssay objects
data("exampleRprimerAssay")
data("exampleRprimerAlignment")
x <- exampleRprimerAssay[1:2, ]
target <- exampleRprimerAlignment
checkMatch(x, target)
sofpn/rprimer documentation built on Aug. 19, 2024, 4:19 p.m.
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| checkMatch | R Documentation |
Check how oligos and assays match to their target sequences
Description
checkMatch() investigates how well oligos or assays match with their
intended target sequences
within a multiple DNA sequence alignment.
Usage
checkMatch(x, target)
## S4 method for signature 'RprimerOligo'
checkMatch(x, target)
## S4 method for signature 'RprimerAssay'
checkMatch(x, target)
Arguments
x |
An |
target |
A |
Details
The output provides information on the proportion and names of target
sequences
that match perfectly as well as with one, two, three, or four or more
mismatches to the oligo within the intended oligo binding region
in the input alignment (on-target match).
It also gives the proportion and names of target sequences that
match with a maximum of two mismatches to at least one sequence variant of
the oligo outside the
intended oligo binding region (off-target match).
The function is a wrapper to Biostrings::vcountPDict()
(Pages et al., 2020).
Value
An RprimerMatchOligo or RprimerMatchAssay object, depending
on whether an RprimerOligo or RprimerAssay object was used
as input.
RprimerMatchOligo objects contain the following information:
- iupacSequence
The oligo sequence in IUPAC format.
- perfectMatch
Proportion of target sequences that matches perfectly to the oligo within the intended binding region.
- idPerfectMatch
Names of all sequences that matches perfectly.
- oneMismatch
Proportion of target sequences with one mismatch to the oligo within the intended binding region.
- idOneMismatch
Names of all sequences that matches with one mismatch.
- twoMismatches
Proportion of target sequences with two mismatches to the oligo within the intended binding region.
- idTwoMismatches
Names of all sequences that matches with two mismatches.
- threeMismatches
Proportion of target sequences with three mismatches to the oligo within the intended binding region.
- idThreeMismatches
Names of all sequences that matches with three mismatches.
- fourOrMoreMismatches
Proportion of target sequences with four or more mismatches to the oligo within the intended binding region.
- idFourOrMoreMismatches
Names of all sequences that matches with four or more mismatches.
- offTargetMatch
Proportion of target sequences with maximum two mismatches to at least one site outside the intended oligo binding region in the input alignment.
- idOffTargetMatch
Names of all off-target matching sequences.
RprimerMatchAssay objects contain the following information:
- iupacSequenceFwd
The forward primer sequence in IUPAC format.
- perfectMatchFwd
Proportion of target sequences that matches perfectly with the forward primer withing the intended binding region.
- idPerfectMatchFwd
Names of all sequences that matches perfectly.
- oneMismatchFwd
Proportion of target sequences with one mismatch to the forward primer within the intended binding region.
- idOneMismatchFwd
Names of all sequences that matches with one mismatch.
- twoMismatchesFwd
Proportion of target sequences with two mismatches to the forward primer within the intended binding region.
- idTwoMismatchesFwd
Names of all sequences that matches with two mismatches.
- threeMismatchesFwd
Proportion of target sequences with three mismatches to the forward primer within the intended binding region.
- idThreeMismatchesFwd
Names of all sequences that matches with three mismatches.
- fourOrMoreMismatchesFwd
Proportion of target sequences with four or more mismatches to the forward primer within the intended binding region.
- idFourOrMoreMismatchesFwd
Names of all sequences that matches with four or more mismatches.
- offTargetMatchFwd
Proportion of target sequences with maximum two mismatches to at least one site outside the intended forward primer binding region in the input alignment.
- idOffTargetMatchFwd
Names of all off-target matching sequences.
- iupacSequenceRev
The reverse primer sequence in IUPAC format.
- perfectMatchRev
Proportion of target sequences that matches perfectly with the reverse primer withing the intended binding region.
- idPerfectMatchRev
Names of all sequences that matches perfectly.
- oneMismatchRev
Proportion of target sequences with one mismatch to the reverse primer within the intended binding region.
- idOneMismatchRev
Names of all sequences that matches with one mismatch.
- twoMismatchesRev
Proportion of target sequences with two mismatches to the reverse primer within the intended binding region.
- idTwoMismatchesRev
Names of all sequences that matches with two mismatches.
- threeMismatchesRev
Proportion of target sequences with three mismatches to the reverse primer within the intended binding region.
- idThreeMismatchesRev
Names of all sequences that matches with three mismatches.
- fourOrMoreMismatchesRev
Proportion of target sequences with four or more mismatches to the reverse primer within the intended binding region.
- idFourOrMoreMismatchesRev
Names of all sequences that matches with four or more mismatches.
- offTargetMatchRev
Proportion of target sequences with maximum two mismatches to at least one site outside the intended reverse primer binding region in the input alignment.
- idOffTargetMatchRev
Names of all off-target matching sequences.
If the input assay contains probes, the following information is also added:
- iupacSequencePr
The probe sequence in IUPAC format.
- perfectMatchPr
Proportion of target sequences that matches perfectly with the probe withing the intended binding region.
- idPerfectMatchPr
Names of all sequences that matches perfectly.
- oneMismatchPr
Proportion of target sequences with one mismatch to the probe within the intended binding region.
- idOneMismatchPr
Names of all sequences that matches with one mismatch.
- twoMismatchesPr
Proportion of target sequences with two mismatches to the probe within the intended binding region.
- idTwoMismatchesPr
Names of all sequences that matches with two mismatches.
- threeMismatchesPr
Proportion of target sequences with three mismatches to the probe within the intended binding region.
- idThreeMismatchesPr
Names of all sequences that matches with three mismatches.
- fourOrMoreMismatchesPr
Proportion of target sequences with four or more mismatches to the probe within the intended binding region.
- idFourOrMoreMismatchesPr
Names of all sequences that matches with four or more mismatches.
- offTargetMatchPr
Proportion of target sequences with maximum two mismatches to at least one site outside the intended probe binding region in the input alignment.
- idOffTargetMatchPr
Names of all off-target matching sequences.
Methods (by class)
-
checkMatch(RprimerOligo): -
checkMatch(RprimerAssay):
Limitations
There are a few limitations with this function, which is important to be aware of:
False negatives or positives may occur due to poorly aligned sequences
The output does not tell which strand (minus or plus) the oligo matches to. This is important to consider when assessing off-target matches to single-stranded targets
Ambiguous bases and gaps in the target sequences are identified as mismatches
The function checks strictly on- and off-target, and may therefore miss off-target matches that partially overlap the intended target
References
Pages, H., Aboyoun, P., Gentleman R., and DebRoy S. (2020). Biostrings: Efficient manipulation of biological strings. R package version 2.57.2.
Examples
#### RprimerOligo objects
data("exampleRprimerOligo")
data("exampleRprimerAlignment")
x <- exampleRprimerOligo[1:2, ]
target <- exampleRprimerAlignment
checkMatch(x, target)
#### RprimerAssay objects
data("exampleRprimerAssay")
data("exampleRprimerAlignment")
x <- exampleRprimerAssay[1:2, ]
target <- exampleRprimerAlignment
checkMatch(x, target)
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