Hits-comparison: Comparing and ordering hits

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

Comparing and ordering hits

Description

==, !=, <=, >=, <, >, match(), %in%, order(), sort(), and rank() can be used on Hits objects to compare and order hits.

Note that only the "pcompare", "match", and "order" methods are actually defined for Hits objects. This is all what is needed to make all the other comparing and ordering operations (i.e. ==, !=, <=, >=, <, >, %in%, sort(), and rank()) work on these objects (see ?`Vector-comparison` for more information about this).

Usage

## S4 method for signature 'Hits,Hits'
pcompare(x, y)

## S4 method for signature 'Hits,Hits'
match(x, table, nomatch=NA_integer_, incomparables=NULL,
      method=c("auto", "quick", "hash"))

## S4 method for signature 'Hits'
order(..., na.last=TRUE, decreasing=FALSE, method=c("auto", "shell", "radix"))

Arguments

x, y, table	Compatible Hits objects, that is, Hits objects with the same subject and query lengths.
nomatch	The value to be returned in the case when no match is found. It is coerced to an integer.
incomparables	Not supported.
method	For match: Use a Quicksort-based (method="quick") or a hash-based (method="hash") algorithm. The latter tends to give better performance, except maybe for some pathological input that we've not encountered so far. When method="auto" is specified, the most efficient algorithm will be used, that is, the hash-based algorithm if length(x) <= 2^29, otherwise the Quicksort-based algorithm. For order: The method argument is ignored.
...	One or more Hits objects. The additional Hits objects are used to break ties.
na.last	Ignored.
decreasing	TRUE or FALSE.

Details

Only hits that belong to Hits objects with same subject and query lengths can be compared.

Hits are ordered by query hit first, and then by subject hit. On a Hits object, order, sort, and rank are consistent with this order.

pcompare(x, y):

Performs element-wise (aka "parallel") comparison of 2 Hits objects x and y, that is, returns an integer vector where the i-th element is less than, equal to, or greater than zero if x[i] is considered to be respectively less than, equal to, or greater than y[i]. See ?`Vector-comparison` for how x or y is recycled when the 2 objects don't have the same length.

match(x, table, nomatch=NA_integer_, method=c("auto", "quick", "hash")):

Returns an integer vector of the length of x, containing the index of the first matching hit in table (or nomatch if there is no matching hit) for each hit in x.

order(...):

Returns a permutation which rearranges its first argument (a Hits object) into ascending order, breaking ties by further arguments (also Hits objects).

Author(s)

Hervé Pagès

See Also

• Hits objects.

• Vector-comparison for general information about comparing, ordering, and tabulating vector-like objects.

Examples

## ---------------------------------------------------------------------
## A. ELEMENT-WISE (AKA "PARALLEL") COMPARISON OF 2 Hits OBJECTS
## ---------------------------------------------------------------------
hits <- Hits(c(2, 4, 4, 4, 5, 5), c(3, 1, 3, 2, 3, 2), 6, 3)
hits

pcompare(hits, hits[3])
pcompare(hits[3], hits)

hits == hits[3]
hits != hits[3]
hits >= hits[3]
hits < hits[3]

## ---------------------------------------------------------------------
## B. match(), %in%
## ---------------------------------------------------------------------
table <- hits[-c(1, 3)]
match(hits, table)

hits %in% table

## ---------------------------------------------------------------------
## C. order(), sort(), rank()
## ---------------------------------------------------------------------
order(hits)
sort(hits)
rank(hits)

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