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## 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()
## -------
"order"(..., na.last=TRUE, decreasing=FALSE)compare.
integer.
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.
TRUE or FALSE.
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 element-wise (aka "parallel") comparison of 2 Ranges
objects of x and y, that is, returns an integer vector
where the i-th element is a code describing how x[i] is
qualitatively positioned with respect to y[i].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).
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.
findOverlaps for finding overlapping ranges.
## ---------------------------------------------------------------------
## 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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