| RangesMatchingList-class {IRanges} | R Documentation |
The RangesMatchingList class stores a set of
matchings, represented as RangesMatching objects,
between the ranges in one RangesList object and the
ranges in another.
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.
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 long as the names on
each, if any, are in the same order).
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.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.
This class is highly experimental. It has not been well tested and may disappear at any time.
Michael Lawrence
overlap, which generates an instance of this class.