| MIndex-class {Biostrings} | R Documentation |
The MIndex class is the basic container for storing the matches of a set of patterns in a subject sequence.
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.
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.
In the code snippets below, x is an MIndex object.
x[[i]]:
Extract the matches for the i-th pattern as an
IRanges object.
In the code snippets below, x is an MIndex object.
as(x, "CompressedIRangesList"):
Turns x into an
CompressedIRangesList object.
This coercion changes x from one
RangesList
subtype to another with the underlying
Ranges values remaining unchanged.
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 and use.names are ignored.
extractAllMatches(subject, mindex):
Return all the matches in a single XStringViews object.
H. Pagès
matchPDict,
PDict-class,
IRanges-class,
XStringViews-class
## See ?matchPDict and ?`matchPDict-inexact` for some examples.