S4Vectors (version 0.10.1)

HitsList-class: List of Hits objects

Description

The HitsList class stores a set of Hits objects. It's typically used to represent the result of findOverlaps on two RangesList objects.

Details

Roughly the same set of utilities are provided for HitsList as for Hits: The as.matrix method coerces a HitsList object 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 object 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.

See Also

• findOverlapsin theIRangespackage, which returns a HitsList object when the query and subject areRangesListobjects.