Hits-class: Hits objects

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

Description

The Hits class is a container for representing a set of hits between a set of left nodes and a set of right nodes. Note that only the hits are stored in the object. No information about the left or right nodes is stored, except their number.

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.

Usage

## Constructor functions

Hits(from=integer(0), to=integer(0), nLnode=0L, nRnode=0L, ...,
     sort.by.query=FALSE)

SelfHits(from=integer(0), to=integer(0), nnode=0L, ...,
     sort.by.query=FALSE)

Arguments

from, to	2 integer vectors of the same length. The values in from must be >= 1 and <= nLnode. The values in to must be >= 1 and <= nRnode.
nLnode, nRnode	Number of left and right nodes.
...	Metadata columns to set on the Hits object. All the metadata columns must be vector-like objects of the same length as from and to.
sort.by.query	Should the hits in the returned object be sorted by query? If yes, then a SortedByQueryHits object is returned (SortedByQueryHits is a subclass of Hits).
nnode	Number of nodes.

Accessors

In the code snippets below, x is a Hits object.

length(x): get the number of hits

from(x): Equivalent to as.data.frame(x)[[1]].

to(x): Equivalent to as.data.frame(x)[[2]].

nLnode(x), nrow(x): get the number of left nodes

nRnode(x), ncol(x): get the number of right nodes

countLnodeHits(x): Counts the number of hits for each left node, returning an integer vector.

countRnodeHits(x): Counts the number of hits for each right node, returning an integer vector.

The following accessors are just aliases for the above accessors:

queryHits(x): alias for from(x).

subjectHits(x): alias for to(x).

queryLength(x): alias for nLnode(x).

subjectLength(x): alias for nRnode(x).

countQueryHits(x): alias for countLnodeHits(x).

countSubjectHits(x): alias for countRnodeHits(x).

Coercion

In the code snippets below, x is a Hits object.

as.matrix(x): Coerces x to a two column integer matrix, with each row representing a hit between a left node (first column) and a right node (second column).

as.table(x): Counts the number of hits for each left node in x and outputs the counts as a table.

as(x, "DataFrame"): Creates a DataFrame by combining the result of as.matrix(x) with mcols(x).

as.data.frame(x): Attempts to coerce the result of as(x, "DataFrame") to a data.frame.

Subsetting

In the code snippets below, x is a Hits object.

x[i]: Return a new Hits object made of the elements selected by i.

x[i, j]: Like the above, but allow the user to conveniently subset the metadata columns thru j.

x[i] <- value: Replacement version of x[i].

See ?`[` in this package (the S4Vectors package) for more information about subsetting Vector derivatives and for an important note about the x[i, j] form.

Concatenation

c(x, ..., ignore.mcols=FALSE): Concatenate Hits object x and the Hits objects in ... together. See ?c in this package (the S4Vectors package) for more information about concatenating Vector derivatives.

Other transformations

In the code snippets below, x is a Hits object.

t(x): Transpose x by interchanging the left and right nodes. This allows, for example, counting the number of hits for each right node using as.table.

remapHits(x, Lnodes.remapping=NULL, new.nLnode=NA, Rnodes.remapping=NULL, new.nRnode=NA): Only supports SortedByQueryHits objects at the moment.

Remaps the left and/or right nodes in x. The left nodes are remapped thru the map specified via the Lnodes.remapping and new.nLnode arguments. The right nodes are remapped thru the map specified via the Rnodes.remapping and new.nRnode arguments.

Lnodes.remapping must represent a function defined on the 1..M interval that takes values in the 1..N interval, where N is nLnode(x) and M is the value specified by the user via the new.nLnode 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 Lnodes.remapping can be NULL (identity map), or a vector of nLnode(x) non-NA integers that are >= 1 and <= new.nLnode, or a factor of length nLnode(x) with no NAs (a factor is treated as an integer vector, and, if missing, new.nLnode 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 applies to the Rnodes.remapping.

remapHits returns a Hits object where from(x) and to(x) 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).

breakTies(x, method=c("first", "last"), rank): Restrict the hits so that every left node maps to at most one right node. If method is “first”, for each left node, select the edge with the first (lowest rank) right node, if any. If method is “last”, select the edge with the last (highest rank) right node. If rank is not missing, it should be a formula specifying an alternative ranking according to its terms (see rank).

SelfHits

A SelfHits object is a Hits object where the left and right nodes are identical. For a SelfHits object x, nLnode(x) is equal to nRnode(x). The object can be seen as an oriented graph where nLnode is the nb of nodes and the hits are the (oriented) edges. SelfHits objects support the same set of accessors as Hits objects plus the nnode() accessor that is equivalent to nLnode() and nRnode().

We also provide two little utilities to operate on a SelfHits object x:

isSelfHit(x): A self hit is an edge from a node to itself. isSelfHit(x) returns a logical vector parallel to x indicating which elements in x are self hits.

isRedundantHit(x): When there is more than 1 edge between 2 given nodes (regardless of orientation), the extra edges are considered to be redundant hits. isRedundantHit(x) returns a logical vector parallel to x indicating which elements in x are redundant hits.

Author(s)

Michael Lawrence and Hervé Pagès

See Also

• Hits-comparison for comparing and ordering hits.

• The findOverlaps function in the IRanges package which returns SortedByQueryHits object.

• Hits-examples in the IRanges package, for some examples of Hits object basic manipulation.

• setops-methods in the IRanges package, for set operations on Hits objects.

Examples

from <- c(5, 2, 3, 3, 3, 2)
to <- c(11, 15, 5, 4, 5, 11)
id <- letters[1:6]

Hits(from, to, 7, 15, id)
Hits(from, to, 7, 15, id, sort.by.query=TRUE)

## ---------------------------------------------------------------------
## selectHits()
## ---------------------------------------------------------------------

x <- c("a", "b", "a", "c", "d")
table <- c("a", "e", "d", "a", "a", "d")
hits <- findMatches(x, table)  # sorts the hits by query
hits

selectHits(hits, select="all")  # no-op

selectHits(hits, select="first")
selectHits(hits, select="first", nodup=TRUE)

selectHits(hits, select="last")
selectHits(hits, select="last", nodup=TRUE)

selectHits(hits, select="arbitrary")
selectHits(hits, select="count")

## ---------------------------------------------------------------------
## remapHits()
## ---------------------------------------------------------------------

Lnodes.remapping <- factor(c(a="A", b="B", c="C", d="D")[x],
                           levels=LETTERS[1:4])
remapHits(hits, Lnodes.remapping=Lnodes.remapping)

## See ?`Hits-examples` in the IRanges package for more examples of basic
## manipulation of Hits objects.

## ---------------------------------------------------------------------
## SelfHits objects
## ---------------------------------------------------------------------

hits2 <- SelfHits(c(2, 3, 3, 3, 3, 3, 4, 4, 4), c(4, 3, 2:4, 2, 2:3, 2), 4)
## Hits 2 and 4 are self hits (from 3rd node to itself):
which(isSelfHit(hits2))
## Hits 4, 6, 7, 8, and 9, are redundant hits:
which(isRedundantHit(hits2))

hits3 <- findMatches(x)
hits3[!isSelfHit(hits3)]
hits3[!(isSelfHit(hits3) | isRedundantHit(hits3))]

S4Vectors documentation built on Dec. 11, 2020, 2:02 a.m.