HitsList class stores a set of Hits objects.
It's typically used to represent the result of findOverlaps
on two RangesList objects.x is a HitsList
object. as.matrix(x): calls as.matrix on each
Hits, 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 hits for each
query element 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 HitsList.queryHits(x): Equivalent to
unname(as.matrix(x)[,1]).
subjectHits(x): Equivalent to
unname(as.matrix(x)[,2]).
space(x): gets the character vector naming the space
in the query RangesList for each hit, 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 in the call to
findOverlaps that generated x. Eventually, we might
store the query and subject inside x, in which case the
arguments would be redundant.
HitsList as for Hits:
The as.matrix method coerces a HitsList in a
similar way to Hits, 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 hits for each query range and outputs the counts as a
table, which has the same shape as from a single Hits
object.
To transpose a HitsList x, so that the subject
and query in each space are interchanged, call t(x). This
allows, for example, counting the number of hits for each subject
element using as.table.
When the HitsList object is the result of a call to
findOverlaps on two RangesList objects,
the actual regions of intersection between the overlapping
ranges can be obtained with the ranges accessor.
findOverlaps, which generates an instance of this class.