Comparing and ordering genomic ranges
Methods for comparing and/or ordering 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("auto", "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, na.rm, strictly, na.last, decreasing |
See |
ignore.strand |
Whether or not the strand should be ignored when comparing 2 genomic ranges. |
... |
One or more GenomicRanges objects. The GenomicRanges objects after the first one are used to break ties. |
ties.method |
A character string specifying how ties are treated. Only |
by |
An optional formula that is resolved against |
Two elements of a GenomicRanges derivative (i.e. two genomic ranges)
are considered equal iff they are on the same underlying sequence and strand,
and share the same start and width. duplicated() and unique()
on a GenomicRanges derivative are conforming to this.
The "natural order" for the elements of a GenomicRanges derivative
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, because we already do (c) and (d) for regular ranges (see
?`IPosRanges-comparison`), genomic ranges that
belong to the same underlying sequence and strand are ordered like regular
ranges.
pcompare(), ==, !=, <=, >=, <
and > on GenomicRanges derivatives behave accordingly to this
"natural order".
is.unsorted(), order(), sort(), rank() on
GenomicRanges derivatives also behave accordingly to this
"natural order".
Finally, note that some inter range transformations like
reduce or disjoin
also use this "natural order" implicitly when operating on
GenomicRanges derivatives.
H. Pagès, is.unsorted contributed by Pete Hickey
The GenomicRanges class.
IPosRanges-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. match(), selfmatch(), %in%, duplicated(), unique()
## ---------------------------------------------------------------------
table <- gr[1:7]
match(gr, table)
match(gr, table, ignore.strand=TRUE)
gr %in% table
duplicated(gr)
unique(gr)
## ---------------------------------------------------------------------
## C. 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)
## ---------------------------------------------------------------------
## D. 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)
## ---------------------------------------------------------------------
## E. 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))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.