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.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
.
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.
This class is highly experimental. It has not been well tested and may disappear at any time.
Michael Lawrence
findOverlaps
, which generates an instance of this class.