Ranges-comparison {IRanges} | R Documentation |
Methods for comparing and ordering the elements in one or more Ranges objects.
## ==== Equality and related methods ==== ## -------------------------------------- ## S4 method for signature 'Ranges,Ranges' e1 == e2 ## S4 method for signature 'Ranges,Ranges' e1 != e2 ## S4 method for signature 'Ranges' duplicated(x, incomparables=FALSE, fromLast=FALSE, method=c("auto", "quick", "hash"), ...) ## S4 method for signature 'Ranges' unique(x, incomparables=FALSE, fromLast=FALSE, method=c("auto", "quick", "hash"), ...) ## ==== Ordering and related methods ==== ## -------------------------------------- ## S4 method for signature 'Ranges,Ranges' e1 <= e2 ## S4 method for signature 'Ranges,Ranges' e1 >= e2 ## S4 method for signature 'Ranges,Ranges' e1 < e2 ## S4 method for signature 'Ranges,Ranges' e1 > e2 ## S4 method for signature 'Ranges' order(..., na.last=TRUE, decreasing=FALSE) ## S4 method for signature 'Ranges' sort(x, decreasing=FALSE, ...) ## S4 method for signature 'Ranges' rank(x, na.last=TRUE, ties.method=c("average", "first", "random", "max", "min")) ## ==== Generalized range-wise comparison ==== ## ------------------------------------------- compare(x, y) rangeComparisonCodeToLetter(code)
e1, e2, x, y |
Ranges objects. |
incomparables |
Must be |
fromLast |
See default S3 method for |
method |
Use a Quicksort-based ( |
... |
Ranges objects for |
na.last |
Ignored. |
decreasing |
|
ties.method |
A character string specifying how ties are treated. Only |
code |
A vector of codes as returned by |
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.
The order
, sort
and rank
methods for Ranges
objects are consistent with this order.
duplicated(x)
:
Determines which elements of x
are equal to elements
with smaller subscripts, and returns a logical vector indicating
which elements are duplicates.
It is semantically equivalent to duplicated(as.data.frame(x))
.
See duplicated
in the base package for more details.
unique(x)
:
Removes duplicate ranges from x
.
See unique
in the base package for more details.
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.
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 meanings:
-6: x[i]: .oooo....... 6: x[i]: .......oooo. y[i]: .......oooo. y[i]: .oooo....... -5: x[i]: ..oooo...... 5: x[i]: ......oooo.. y[i]: ......oooo.. y[i]: ..oooo...... -4: x[i]: ...oooo..... 4: x[i]: .....oooo... y[i]: .....oooo... y[i]: ...oooo..... -3: x[i]: ...oooooo... 3: x[i]: .....oooo... y[i]: .....oooo... y[i]: ...oooooo... -2: x[i]: ..oooooooo.. 2: x[i]: ....oooo.... y[i]: ....oooo.... y[i]: ..oooooooo.. -1: x[i]: ...oooo..... 1: x[i]: ...oooooo... y[i]: ...oooooo... y[i]: ...oooo..... 0: x[i]: ...oooooo... y[i]: ...oooooo...Note that this way of comparing ranges is a refinement over the standard ranges comparison defined by the
==
, !=
,
<=
, >=
, <
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.
Ranges-class,
IRanges-class,
duplicated
,
unique
,
order
,
sort
,
rank
x <- IRanges(start=c(20L, 8L, 20L, 22L, 25L, 20L, 22L, 22L), width=c( 4L, 0L, 11L, 5L, 0L, 9L, 5L, 0L)) x ## --------------------------------------------------------------------- ## A. EQUALITY AND RELATED METHODS ## --------------------------------------------------------------------- which(width(x) == 0) # 3 empty ranges x[2] == x[2] # TRUE x[2] == x[5] # FALSE x == x[4] duplicated(x) unique(x) ## --------------------------------------------------------------------- ## B. ORDERING AND RELATED METHODS ## --------------------------------------------------------------------- x >= x[3] order(x) sort(x) rank(x, ties.method="first") ## --------------------------------------------------------------------- ## C. GENERALIZED RANGE-WISE 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))