GenomicRanges-comparison {GenomicRanges} | R Documentation |
Methods for comparing and ordering the elements in one or more GenomicRanges objects.
## duplicated() ## ------------ ## S4 method for signature 'GenomicRanges' duplicated(x, incomparables=FALSE, fromLast=FALSE, nmax=NA, method=c("auto", "quick", "hash")) ## match() & selfmatch() ## --------------------- ## S4 method for signature 'GenomicRanges,GenomicRanges' match(x, table, nomatch=NA_integer_, incomparables=NULL, method=c("auto", "quick", "hash"), ignore.strand=FALSE) ## S4 method for signature 'GenomicRanges' selfmatch(x, method=c("auto", "quick", "hash"), ignore.strand=FALSE) ## order() and related methods ## ---------------------------- ## S4 method for signature 'GenomicRanges' is.unsorted(x, na.rm=FALSE, strictly=FALSE, ignore.strand=FALSE) ## S4 method for signature 'GenomicRanges' order(..., na.last=TRUE, decreasing=FALSE, method=c("shell", "radix")) ## S4 method for signature 'GenomicRanges' sort(x, decreasing=FALSE, ignore.strand=FALSE, by) ## S4 method for signature 'GenomicRanges' rank(x, na.last=TRUE, ties.method=c("average", "first", "last", "random", "max", "min"), ignore.strand=FALSE) ## Generalized parallel comparison of 2 GenomicRanges objects ## ---------------------------------------------------------- ## S4 method for signature 'GenomicRanges,GenomicRanges' pcompare(x, y)
x, table, y |
GenomicRanges objects. |
incomparables |
Not supported. |
fromLast, method, nomatch, nmax |
See |
ignore.strand |
Whether or not the strand should be ignored when comparing 2 genomic ranges. |
na.rm |
Ignored. |
strictly |
Logical indicating if the check should be for strictly increasing values. |
... |
One or more GenomicRanges objects. The GenomicRanges objects after the first one are used to break ties. |
na.last |
Ignored. |
decreasing |
|
ties.method |
A character string specifying how ties are treated. Only |
by |
An optional formula that is resolved against |
Two elements of a GenomicRanges object (i.e. two genomic ranges) are
considered equal iff they are on the same underlying sequence and strand,
and have the same start and width. duplicated()
and unique()
on a GenomicRanges object are conforming to this.
The "natural order" for the elements of a GenomicRanges object is to
order them (a) first by sequence level, (b) then by strand, (c) then by
start, (d) and finally by width.
This way, the space of genomic ranges is totally ordered.
Note that the reduce
method for GenomicRanges uses this
"natural order" implicitly. Also, note that, because we already do (c)
and (d) for regular ranges (see ?`Ranges-comparison`
),
genomic ranges that belong to the same underlying sequence and strand are
ordered like regular ranges.
is.unsorted()
, order()
, sort()
, and rank()
on a
GenomicRanges object behave accordingly to this "natural order".
==
, !=
, <=
, >=
, <
and >
on GenomicRanges objects also behave accordingly to this
"natural order".
H. Pagès, is.unsorted
contributed by Pete Hickey
The GenomicRanges class.
Ranges-comparison in the IRanges package for comparing and ordering genomic ranges.
findOverlaps-methods for finding overlapping genomic ranges.
intra-range-methods and inter-range-methods for intra range and inter range transformations of a GRanges object.
setops-methods for set operations on GenomicRanges objects.
gr0 <- GRanges( Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), IRanges(c(1:9,7L), end=10), strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)), seqlengths=c(chr1=11, chr2=12, chr3=13) ) gr <- c(gr0, gr0[7:3]) names(gr) <- LETTERS[seq_along(gr)] ## --------------------------------------------------------------------- ## A. ELEMENT-WISE (AKA "PARALLEL") COMPARISON OF 2 GenomicRanges OBJECTS ## --------------------------------------------------------------------- gr[2] == gr[2] # TRUE gr[2] == gr[5] # FALSE gr == gr[4] gr >= gr[3] ## --------------------------------------------------------------------- ## B. duplicated(), unique() ## --------------------------------------------------------------------- duplicated(gr) unique(gr) ## --------------------------------------------------------------------- ## C. match(), %in% ## --------------------------------------------------------------------- table <- gr[1:7] match(gr, table) match(gr, table, ignore.strand=TRUE) gr %in% table ## --------------------------------------------------------------------- ## D. findMatches(), countMatches() ## --------------------------------------------------------------------- findMatches(gr, table) countMatches(gr, table) findMatches(gr, table, ignore.strand=TRUE) countMatches(gr, table, ignore.strand=TRUE) gr_levels <- unique(gr) countMatches(gr_levels, gr) ## --------------------------------------------------------------------- ## E. order() AND RELATED METHODS ## --------------------------------------------------------------------- is.unsorted(gr) order(gr) sort(gr) is.unsorted(sort(gr)) is.unsorted(gr, ignore.strand=TRUE) gr2 <- sort(gr, ignore.strand=TRUE) is.unsorted(gr2) # TRUE is.unsorted(gr2, ignore.strand=TRUE) # FALSE ## TODO: Broken. Please fix! #sort(gr, by = ~ seqnames + start + end) # equivalent to (but slower than) above score(gr) <- rev(seq_len(length(gr))) ## TODO: Broken. Please fix! #sort(gr, by = ~ score) rank(gr, ties.method="first") rank(gr, ties.method="first", ignore.strand=TRUE) ## --------------------------------------------------------------------- ## F. GENERALIZED ELEMENT-WISE COMPARISON OF 2 GenomicRanges OBJECTS ## --------------------------------------------------------------------- gr3 <- GRanges(c(rep("chr1", 12), "chr2"), IRanges(c(1:11, 6:7), width=3)) strand(gr3)[12] <- "+" gr4 <- GRanges("chr1", IRanges(5, 9)) pcompare(gr3, gr4) rangeComparisonCodeToLetter(pcompare(gr3, gr4))