| PairwiseAlignedFixedSubject-class {Biostrings} | R Documentation |
The PairwiseAlignedFixedSubject class is a container for storing an alignment.
The PairwiseAlignedFixedSubjectSummary class is a container for storing the
summary of an alignment.
Before we define the notion of alignment, we introduce the notion of "filled-with-gaps subsequence". A "filled-with-gaps subsequence" of a string string1 is obtained by inserting 0 or any number of gaps in a subsequence of s1. For example L-A–ND and A–N-D are "filled-with-gaps subsequences" of LAND. An alignment between two strings string1 and string2 results in two strings (align1 and align2) that have the same length and are "filled-with-gaps subsequences" of string1 and string2.
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.
In the code snippets below,
x is a PairwiseAlignedFixedSubject object, except otherwise noted.
pattern(x):
The AlignedXStringSet object for the pattern.
subject(x):
The AlignedXStringSet object for the subject.
type(x):
The type of the alignment ("global", "local",
"overlap", "patternOverlap", or "subjectOverlap").
There is a method for PairwiseAlignedFixedSubjectSummary as well.
score(x):
The score of the alignment (integer).
There is a method for PairwiseAlignedFixedSubjectSummary as well.
nindel(x):
An InDel object containing the number of insertions and deletions.
length(x):
The length of the aligned(pattern(x)) and aligned(subject(x)).
There is a method for PairwiseAlignedFixedSubjectSummary as well.
nchar(x):
The nchar of the aligned(pattern(x)) and aligned(subject(x)).
There is a method for PairwiseAlignedFixedSubjectSummary as well.
alphabet(x):
Equivalent to alphabet(unaligned(subject(x))).
summary(object, ...):
Generates a summary for the PairwiseAlignedFixedSubject.
aligned(x):
Returns an XStringSet object containing the aligned patterns
without insertions. This operation ``aligns" the alignments.
as.character(x):
Converts aligned(x) to a character vector.
as.matrix(x):
Returns an "exploded" character matrix representation of aligned(x).
Views(subject, start=NA, end=NA, names=NULL):
The XStringViews object that represents the pairwise alignments
along unaligned(subject(subject)). The start and end
arguments must be either NA or an integer vector of length 1 that
denotes the offset from start(subject(subject)).
toString(x):
Equivalent to toString(as.character(x)).
x[i]:
Returns a new PairwiseAlignedFixedSubject object made of the selected elements.
rep(x, times):
Returns a new PairwiseAlignedFixedSubject object made of the repeated elements.
P. Aboyoun and H. Pages
pairwiseAlignment,
AlignedXStringSet-class,
XString-class,
XStringViews-class,
match-utils
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