RangesMatching-class {IRanges}R Documentation

Matchings between Ranges

Description

The RangesMatching class stores a set of matchings between the ranges in one Ranges object and the ranges in another. Currently, RangesMatching are used to represent the result of a call to findOverlaps, though other matching operations are imaginable.

Details

The as.matrix method coerces a RangesMatching to a two column matrix with one row for each matching, where the value in the first column is the index of a range in the first (query) Ranges and the index of the matched subject range is in the second column. The matchMatrix function returns the same thing, but use of as.matrix is preferred.

The as.table method counts the number of matchings for each query range and outputs the counts as a table.

To transpose a RangesMatching x, so that the subject and query 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 RangesMatching object.

as.matrix(x): Coerces x to a two column integer matrix, with each row representing a matching between a query index (first column) and subject index (second column).
as.table(x): counts the number of matchings for each query range in x and outputs the counts as a table.
t(x): Interchange the query and subject in x, returns a transposed RangesMatching.

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].
matchMatrix(x): A synonym for as.matrix, above.
ranges(x, query, subject): returns a Ranges holding the intersection of the ranges in the Ranges 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.
length(x): get the number of matches
nrow(x): get the number of queries in the matching
ncol(x): get the number of subjects in the matching
dim(x): get a two-element integer vector, essentially c(nrow(x), ncol(x)).

Author(s)

Michael Lawrence

See Also

findOverlaps, which generates an instance of this class.

Examples

  query <- IRanges(c(1, 4, 9), c(5, 7, 10))
  subject <- IRanges(c(2, 2, 10), c(2, 3, 12))
  tree <- IntervalTree(subject)
  matchings <- findOverlaps(query, tree)

  as.matrix(matchings)

  as.table(matchings) # hits per query
  as.table(t(matchings)) # hits per subject

[Package IRanges version 1.6.16 Index]