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

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)