Hits class stores a set of hits between 2 vector-like objects,
one called the "query" and the other one the "subject". For example, the findOverlaps function, defined
and documented in the IRanges package, returns the hits between
the query and subject arguments in a Hits object.
x is a Hits
object. as.matrix(x): Coerces x to a two
column integer matrix, with each row representing a hit
between a query index (first column) and subject index (second
column).
as.table(x): counts the number of hits for each
query element in x and outputs the counts as a table.
t(x): Interchange the query and subject in x,
returns a transposed Hits.x[i]: Subset the Hits object.length(x): get the number of hitsqueryHits(x): Equivalent to as.data.frame(x)[[1]].subjectHits(x): Equivalent
to as.data.frame(x)[[2]].queryLength(x), nrow(x): get the number of
elements in the querysubjectLength(x), ncol(x): get the number of
elements in the subjectcountQueryHits(x): Counts the number of hits for
each query, returning an integer vector.
countSubjectHits(x): Counts the number of hits for
each subject, returning an integer vector.
remapHits(x, query.map=NULL, new.queryLength=NA,
subject.map=NULL, new.subjectLength=NA):
Remaps the hits in x thru a "query map" and/or a "subject map"
map. The query hits are remapped thru the "query map", which is specified
via the query.map and new.queryLength arguments. The
subject hits are remapped thru the "subject map", which is specified via
the subject.map and new.subjectLength arguments. The "query map" is conceptually a function (in the mathematical sense)
and is also known as the "mapping function". It must be defined on the
1..M interval and take values in the 1..N interval, where N is
queryLength(x) and M is the value specified by the user via the
new.queryLength argument. Note that this mapping function doesn't
need to be injective or surjective. Also it is not represented by an R
function but by an integer vector of length M with no NAs. More precisely
query.map can be NULL (identity map), or a vector of
queryLength(x) non-NA integers that are >= 1 and
<= queryLength(x)
with no NAs (a factor is treated as an integer vector, and, if missing,
new.queryLength is taken to be its number of levels). Note that
a factor will typically be used to represent a mapping function that is
not injective. The same apply to the "subject map". remapHits returns a Hits object where all the query and subject
hits (accessed with queryHits and subjectHits,
respectively) have been remapped thru the 2 specified maps. This
remapping is actually only the 1st step of the transformation, and is
followed by 2 additional steps: (2) the removal of duplicated hits,
and (3) the reordering of the hits (first by query hits, then by subject
hits). Note that if the 2 maps are injective then the remapping won't
introduce duplicated hits, so, in that case, step (2) is a no-op (but
is still performed). Also if the "query map" is strictly ascending and
the "subject map" ascending then the remapping will preserve the order
of the hits, so, in that case, step (3) is also a no-op (but is still
performed).
as.matrix method coerces a Hits object to a two column
matrix with one row for each hit, where the value in the first
column is the index of an element in the query and the value in the second
column is the index of an element in the subject. The as.table method counts the number of hits for each
query element and outputs the counts as a table.
To transpose a Hits x, so that the subject and query
are interchanged, call t(x). This allows, for example, counting
the number of hits for each subject element using as.table.
findOverlaps in the IRanges package,
which generates an instance of this class.
## See ?`Hits-examples` in the IRanges package for examples of basic
## manipulation of Hits objects.
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