pair: Pair up two vectors

In lawremi/HelloRanges: Introduce *Ranges to bedtools users

Pair up two vectors

Description

Creates a Pairs from two vectors, optionally via a left outer join.

Usage

pair(x, y, ...)
## S4 method for signature 'Vector,Vector'
pair(x, y, by = findMatches(x, y), all.x = FALSE,
                   NA.VALUE = y[NA])

Arguments

x	The “first” vector.
y	The “second” vector.
by	The Hits-class object that matches up the elements into pairs.
all.x	If TRUE, keep every member of x, even if it has no hits. The “second” component is filled with the NA.VALUE.
NA.VALUE	The value to fill holes in y when all.x is TRUE.
...	Arguments for methods.

Details

This might move to S4Vectors at some point. It is distinct from simple Pairs construction, because it performs transformations like a left outer join. More options might be added in the future.

For GRanges and other ranged objects, pair adds “.” to the seqlevels, because that is the seqname of the missing GRanges.

Value

A Pairs object

Author(s)

Michael Lawrence

See Also

Pairs-class, created by this function. bedtools_intersect, whose loj argument motivated the creation of this function.

lawremi/HelloRanges documentation built on Oct. 29, 2023, 4:08 p.m.