HitsList-class: List of Hits objects

In Bioconductor/S4Vectors: Foundation of vector-like and list-like containers in Bioconductor

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 IntegerRangesList 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 IntegerRangesList) 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.

Accessors

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 IntegerRangesList for each hit, or NULL if the query did not have any names.

Coercion

In the code snippets below, 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 object.

Note

This class is highly experimental. It has not been well tested and may disappear at any time.

Author(s)

Michael Lawrence

See Also

• findOverlaps in the IRanges package, which returns a HitsList object when the query and subject are IntegerRangesList objects.

Examples

hits <- Hits(rep(1:20, each=5), 100:1, 20, 100)
hlist <- splitAsList(hits, 1:5)
hlist
hlist[[1]]
hlist[[2]]

## Some sanity checks:

hits1 <- Hits(c(4, 4, 15, 15), c(1, 2, 3, 4), 20, 4)
hits2 <- Hits(c(4, 4, 15, 15), c(1, 2, 3, 4), 20, 4, sort.by.query=TRUE)

fA <- c(1, 1, 2, 2)
hlist1A <- split(hits1, fA)
hlist2A <- split(hits2, fA)
stopifnot(identical(as(hlist1A, "SortedByQueryHitsList"), hlist2A))
stopifnot(identical(hlist1A, as(hlist2A, "HitsList")))

fB <- c(1, 2, 1, 2)
hlist1B <- split(hits1, fB)
hlist2B <- split(hits2, fB)
stopifnot(identical(as(hlist1B, "SortedByQueryHitsList"), hlist2B))
stopifnot(identical(hlist1B, as(hlist2B, "HitsList")))

Bioconductor/S4Vectors documentation built on Nov. 17, 2024, 6:55 p.m.