RangesMatching-class {IRanges} | R Documentation |
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.
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.
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
.
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 matchesnrow(x)
: get the number of queries in the matchingncol(x)
: get the number of subjects in the matchingdim(x)
: get a two-element integer vector, essentially
c(nrow(x), ncol(x))
.
Michael Lawrence
findOverlaps
, which generates an instance of this class.
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