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