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

THIS IS STILL WORK IN PROGRESS!

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".

The matchPDict function returns an MIndex object.

MORE TO COME SOON...

Accesor 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.
countIndex(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.

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 and use.names are ignored.
extractAllMatches(subject, mindex): Return all the matches in a single XStringViews object.

Author(s)

H. Pages

See Also

matchPDict, PDict-class, IRanges-class, XStringViews-class

Examples

  ## See ?matchPDict and ?`matchPDict-inexact` for some examples.

[Package Biostrings version 2.10.22 Index]