PairwiseAlignments class is a container for storing
a set of pairwise alignments. The PairwiseAlignmentsSingleSubject class is a container for storing
a set of pairwise alignments with a single subject.
The PairwiseAlignmentsSingleSubjectSummary class is a container for storing
the summary of a set of pairwise alignments.
## Constructors:
## When subject is missing, pattern must be of length 2
"PairwiseAlignments"(pattern, subject, type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = 1)
"PairwiseAlignments"(pattern, subject, type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = 1)
"PairwiseAlignments"(pattern, subject, type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = 1, baseClass = "BString")
"PairwiseAlignments"(pattern, subject, type = "global", substitutionMatrix = NULL, gapOpening = 0, gapExtension = 1, baseClass = "BString")XString,
or an XStringSet object of length 1 or 2.XString object."global", "local",
"overlap", "global-local", and "local-global" where
"global" = align whole strings with end gap penalties,
"local" = align string fragments,
"overlap" = align whole strings without end gap penalties,
"global-local" = align whole strings in pattern with
consecutive subsequence of subject,
"local-global" = align consecutive subsequence of pattern
with whole strings in subject.XString class to use in the alignment.x is a PairwiseAlignments object, except otherwise noted. pattern(x):
The AlignedXStringSet object for the pattern.
subject(x):
The AlignedXStringSet object for the subject.
summary(object, ...):
Generates a summary for the PairwiseAlignments.
x is a PairwiseAlignments object, except otherwise noted. alphabet(x):
Equivalent to alphabet(unaligned(subject(x))).
length(x):
The length of the aligned(pattern(x)) and
aligned(subject(x)).
There is a method for PairwiseAlignmentsSingleSubjectSummary as well.
type(x):
The type of the alignment ("global", "local",
"overlap", "global-local", or "local-global").
There is a method for PairwiseAlignmentsSingleSubjectSummary as well.
x is a PairwiseAlignmentsSingleSubject object, except
otherwise noted. aligned(x, degap = FALSE, gapCode="-", endgapCode="-"):
If degap = FALSE, "align" the alignments by returning an
XStringSet object containing the aligned patterns without
insertions. If degap = TRUE, returns
aligned(pattern(x), degap=TRUE).
The gapCode and endgapCode arguments denote the code in the
appropriate alphabet to use for the internal and end gaps.
as.character(x):
Converts aligned(x) to a character vector.
as.matrix(x):
Returns an "exploded" character matrix representation of aligned(x).
toString(x):
Equivalent to toString(as.character(x)).
x is a PairwiseAlignmentsSingleSubject object, except otherwise noted. consensusMatrix(x, as.prob=FALSE, baseOnly=FALSE, gapCode="-",
endgapCode="-")
See `consensusMatrix` for more information.
consensusString(x)
See `consensusString` for more information.
coverage(x, shift=0L, width=NULL, weight=1L)
See `coverage,PairwiseAlignmentsSingleSubject-method` for more
information.
Views(subject, start=NULL, end=NULL, width=NULL, names=NULL):
The XStringViews object that represents the pairwise alignments
along unaligned(subject(subject)). The start and end
arguments must be either NULL/NA or an integer vector
of length 1 that denotes the offset from start(subject(subject)).
x is a PairwiseAlignments object, except otherwise noted. nchar(x):
The nchar of the aligned(pattern(x)) and aligned(subject(x)).
There is a method for PairwiseAlignmentsSingleSubjectSummary as well.
insertion(x):
An CompressedIRangesList
object containing the
locations of the insertions from the perspective of the pattern.
deletion(x):
An CompressedIRangesList
object containing the
locations of the deletions from the perspective of the pattern.
indel(x):
An InDel object containing the locations of the insertions and
deletions from the perspective of the pattern.
nindel(x):
An InDel object containing the number of insertions and deletions.
score(x):
The score of the alignment.
There is a method for PairwiseAlignmentsSingleSubjectSummary
as well.
x[i]:
Returns a new PairwiseAlignments object made of the selected
elements.
rep(x, times):
Returns a new PairwiseAlignments object made of the repeated
elements.
For example, this is an alignment between LAND and LEAVES:
L-A
LEA
An alignment can be seen as a compact representation of one set of basic operations that transforms string1 into align1. There are 3 different kinds of basic operations: "insertions" (gaps in align1), "deletions" (gaps in align2), "replacements". The above alignment represents the following basic operations:
insert E at pos 2
insert V at pos 4
insert E at pos 5
replace by S at pos 6 (N is replaced by S)
delete at pos 7 (D is deleted)
Note that "insert X at pos i" means that all letters at a position >= i
are moved 1 place to the right before X is actually inserted.There are many possible alignments between two given strings string1 and string2 and a common problem is to find the one (or those ones) with the highest score, i.e. with the lower total cost in terms of basic operations.
pairwiseAlignment,
writePairwiseAlignments,
AlignedXStringSet-class,
XString-class,
XStringViews-class,
align-utils,
pid
PairwiseAlignments("-PA--W-HEAE", "HEAGAWGHE-E")
pattern <- AAStringSet(c("HLDNLKGTF", "HVDDMPNAL"))
subject <- AAString("SMDDTEKMSMKL")
nw1 <- pairwiseAlignment(pattern, subject, substitutionMatrix = "BLOSUM50",
gapOpening = 3, gapExtension = 1)
pattern(nw1)
subject(nw1)
aligned(nw1)
as.character(nw1)
as.matrix(nw1)
nchar(nw1)
score(nw1)
nw1
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