RangesMatchingList-class {IRanges}R Documentation

List of Matchings between Ranges

Description

The RangesMatchingList class stores a set of matchings, represented as RangesMatching objects, between the ranges in one RangesList object and the ranges in another.

Details

Roughly the same set of utilities are provided for RangesMatchingList as for RangesMatching:

The as.matrix method coerces a RangesMatchingList in a similar way to RangesMatching, except a column is prepended that indicates which space (or element in the query RangesList) to which the row corresponds.

The as.table method flattens or unlists the list, counts the number of matchings for each query range and outputs the counts as a table, which has the same shape as from a single RangesMathing.

To transpose a RangesMatchingList x, so that the subject and query in each space are interchanged, call t(x). This allows, for example, counting the number of subjects that matched using as.table.

To get the actual regions of intersection between the overlapping ranges, use the ranges accessor.

Coercion

In the code snippets below, x is a RangesMatchingList object.

as.matrix(x): calls as.matrix on each RangesMatching, combines them row-wise and offsets the indices so that they are aligned with the result of calling unlist on the query and subject.
as.table(x): counts the number of matchings for each query range in x and outputs the counts as a table, which is aligned with the result of calling unlist on the query.
t(x): Interchange the query and subject in each space of x, returns a transposed RangesMatchingList.

Accessors

queryHits(x): Gets the indices of overlapping ranges in the query, equivalent to as.matrix(x)[,1].
subjectHits(x): Gets the indices of overlapping ranges in the subject, equivalent to as.matrix(x)[,2].
space(x): gets the character vector naming the space in the query RangesList for each match, or NULL if the query did not have any names.
ranges(x, query, subject): returns a RangesList holding the intersection of the ranges in the RangesList objects query and subject, which should be the same subject and query used to generate x. Eventually, we might store the query and subject inside x, in which case the arguments would be redundant.

Note

This class is highly experimental. It has not been well tested and may disappear at any time.

Author(s)

Michael Lawrence

See Also

findOverlaps, which generates an instance of this class.


[Package IRanges version 1.6.16 Index]