IRanges (version 2.0.1)

Ranges-comparison: Comparing and ordering ranges

Description

Methods for comparing and/or ordering Ranges objects.

Usage

## Element-wise (aka "parallel") comparison of 2 Ranges objects ## ------------------------------------------------------------
"compare"(x, y)
rangeComparisonCodeToLetter(code)
## match() ## -------
"match"(x, table, nomatch=NA_integer_, incomparables=NULL, method=c("auto", "quick", "hash"))
## selfmatch() ## -----------
"selfmatch"(x, method=c("auto", "quick", "hash"))
## order() and related methods ## ----------------------------
"order"(..., na.last=TRUE, decreasing=FALSE)
"rank"(x, na.last=TRUE, ties.method=c("average", "first", "random", "max", "min"))

Arguments

x, y, table
Ranges objects.
nomatch
The value to be returned in the case when no match is found. It is coerced to an integer.
incomparables
Not supported.
method
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 been able to determine 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<="" code="">, otherwise the Quicksort-based algorithm.

...
One or more Ranges objects. The additional Ranges objects are used to break ties.
na.last
Ignored.
decreasing
TRUE or FALSE.
ties.method
A character string specifying how ties are treated. Only "first" is supported for now.
code
A vector of codes as returned by compare.

Details

Two ranges are considered equal iff they share the same start and width. Note that with this definition, 2 empty ranges are generally not equal (they need to share the same start to be considered equal). This means that, when it comes to comparing ranges, an empty range is interpreted as a position between its end and start. For example, a typical usecase is comparison of insertion points defined along a string (like a DNA sequence) and represented as empty ranges.

Ranges are ordered by starting position first, and then by width. This way, the space of ranges is totally ordered. On a Ranges object, order, sort, and rank are consistent with this order.

compare(x, y): Performs "generalized range-wise comparison" of x and y, that is, returns an integer vector where the i-th element is a code describing how the i-th element in x is qualitatively positioned relatively to the i-th element in y.

Here is a summary of the 13 predefined codes (and their letter equivalents) and their meanings:

      -6 a: x[i]: .oooo.......         6 m: x[i]: .......oooo.
            y[i]: .......oooo.              y[i]: .oooo.......

-5 b: x[i]: ..oooo...... 5 l: x[i]: ......oooo.. y[i]: ......oooo.. y[i]: ..oooo......

-4 c: x[i]: ...oooo..... 4 k: x[i]: .....oooo... y[i]: .....oooo... y[i]: ...oooo.....

-3 d: x[i]: ...oooooo... 3 j: x[i]: .....oooo... y[i]: .....oooo... y[i]: ...oooooo...

-2 e: x[i]: ..oooooooo.. 2 i: x[i]: ....oooo.... y[i]: ....oooo.... y[i]: ..oooooooo..

-1 f: x[i]: ...oooo..... 1 h: x[i]: ...oooooo... y[i]: ...oooooo... y[i]: ...oooo.....

0 g: x[i]: ...oooooo... y[i]: ...oooooo...

Note that this way of comparing ranges is a refinement over the standard ranges comparison defined by the ==, !=, <=< code="">, >=, < and > operators. In particular a code that is < 0, = 0, or > 0, corresponds to x[i] < y[i], x[i] == y[i], or x[i] > y[i], respectively.

The compare method for Ranges objects is guaranteed to return predefined codes only but methods for other objects (e.g. for GenomicRanges objects) can return non-predefined codes. Like for the predefined codes, the sign of any non-predefined code must tell whether x[i] is less than, or greater than y[i].

rangeComparisonCodeToLetter(x): Translate the codes returned by compare. The 13 predefined codes are translated as follow: -6 -> a; -5 -> b; -4 -> c; -3 -> d; -2 -> e; -1 -> f; 0 -> g; 1 -> h; 2 -> i; 3 -> j; 4 -> k; 5-> l; 6 -> m. Any non-predefined code is translated to X. The translated codes are returned in a factor with 14 levels: a, b, ..., l, m, X.

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 range in table (or nomatch if there is no matching range) for each range in x.

selfmatch(x, method=c("auto", "quick", "hash")): Equivalent to, but more efficient than, match(x, x, method=method).

duplicated(x, fromLast=FALSE, method=c("auto", "quick", "hash")): Determines which elements of x are equal to elements with smaller subscripts, and returns a logical vector indicating which elements are duplicates. duplicated(x) is equivalent to, but more efficient than, duplicated(as.data.frame(x)) on a Ranges object. See duplicated in the base package for more details.

unique(x, fromLast=FALSE, method=c("auto", "quick", "hash")): Removes duplicate ranges from x. unique(x) is equivalent to, but more efficient than, unique(as.data.frame(x)) on a Ranges object. See unique in the base package for more details.

x %in% table: A shortcut for finding the ranges in x that match any of the ranges in table. Returns a logical vector of length equal to the number of ranges in x.

findMatches(x, table, method=c("auto", "quick", "hash")): An enhanced version of match that returns all the matches in a Hits object.

countMatches(x, table, method=c("auto", "quick", "hash")): Returns an integer vector of the length of x containing the number of matches in table for each element in x.

order(...): Returns a permutation which rearranges its first argument (a Ranges object) into ascending order, breaking ties by further arguments (also Ranges objects). See order in the BiocGenerics package for more information.

sort(x): Sorts x. See sort in the base package for more details.

rank(x, na.last=TRUE, ties.method=c("average", "first", "random", "max", "min")): Returns the sample ranks of the ranges in x. See rank in the base package for more details.

See Also

Examples

Run this code
## ---------------------------------------------------------------------
## A. ELEMENT-WISE (AKA "PARALLEL") COMPARISON OF 2 Ranges OBJECTS
## ---------------------------------------------------------------------
x0 <- IRanges(1:11, width=4)
x0
y0 <- IRanges(6, 9)
compare(x0, y0)
compare(IRanges(4:6, width=6), y0)
compare(IRanges(6:8, width=2), y0)
compare(x0, y0) < 0   # equivalent to 'x0 < y0'
compare(x0, y0) == 0  # equivalent to 'x0 == y0'
compare(x0, y0) > 0   # equivalent to 'x0 > y0'

rangeComparisonCodeToLetter(-10:10)
rangeComparisonCodeToLetter(compare(x0, y0))

## Handling of zero-width ranges (a.k.a. empty ranges):
x1 <- IRanges(11:17, width=0)
x1
compare(x1, x1[4])
compare(x1, IRanges(12, 15))

## Note that x1[2] and x1[6] are empty ranges on the edge of non-empty
## range IRanges(12, 15). Even though -1 and 3 could also be considered
## valid codes for describing these configurations, compare()
## considers x1[2] and x1[6] to be *adjacent* to IRanges(12, 15), and
## thus returns codes -5 and 5:
compare(x1[2], IRanges(12, 15))  # -5
compare(x1[6], IRanges(12, 15))  #  5

x2 <- IRanges(start=c(20L, 8L, 20L, 22L, 25L, 20L, 22L, 22L),
              width=c( 4L, 0L, 11L,  5L,  0L,  9L,  5L,  0L))
x2

which(width(x2) == 0)  # 3 empty ranges
x2[2] == x2[2]  # TRUE
x2[2] == x2[5]  # FALSE
x2 == x2[4]
x2 >= x2[3]

## ---------------------------------------------------------------------
## B. match(), selfmatch(), %in%, duplicated(), unique()
## ---------------------------------------------------------------------
table <- x2[c(2:4, 7:8)]
match(x2, table)

x2 %in% table

duplicated(x2)
unique(x2)

## ---------------------------------------------------------------------
## C. findMatches(), countMatches()
## ---------------------------------------------------------------------
findMatches(x2, table)
countMatches(x2, table)

x2_levels <- unique(x2)
countMatches(x2_levels, x2)

## ---------------------------------------------------------------------
## D. order() AND RELATED METHODS
## ---------------------------------------------------------------------
order(x2)
sort(x2)
rank(x2, ties.method="first")

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