MIndex-class {Biostrings} | R Documentation |
MIndex objects
Description
The MIndex class is the basic container for storing the matches of a set of patterns in a subject sequence.
Details
An MIndex object contains the matches (start/end locations) of a set of patterns found in an XString object called "the subject string" or "the subject sequence" or simply "the subject".
matchPDict
function returns an MIndex object.
Accessor methods
In the code snippets below, x
is an MIndex object.
-
length(x)
: The number of patterns that matches are stored for. -
names(x)
: The names of the patterns that matches are stored for. -
startIndex(x)
: A list containing the starting positions of the matches for each pattern. -
endIndex(x)
: A list containing the ending positions of the matches for each pattern. -
elementNROWS(x)
: An integer vector containing the number of matches for each pattern.
Subsetting methods
In the code snippets below, x
is an MIndex object.
-
x[[i]]
: Extract the matches for the i-th pattern as an IRanges object.
Coercion
In the code snippets below, x
is an MIndex object.
-
as(x, "CompressedIRangesList")
: Turnsx
into an CompressedIRangesList object. This coercion changesx
from one IntegerRangesList subtype to another with the underlying IntegerRanges values remaining unchanged.
Other utility methods and functions
In the code snippets below,
x
and mindex
are MIndex objects
and subject
is the XString object
containing the sequence in which the matches were found.
-
unlist(x, recursive=TRUE, use.names=TRUE)
: Return all the matches in a single IRanges object.recursive
anduse.names
are ignored. -
extractAllMatches(subject, mindex)
: Return all the matches in a single XStringViews object.
Author(s)
H. Pagès
See Also
matchPDict
,
PDict-class,
IRanges-class,
XStringViews-class
Examples
## See ?matchPDict and ?`matchPDict-inexact` for some examples.