Inter range transformations of a GenomicRanges or GRangesList object

Description

See ?`intra-range-methods` and ?`inter-range-methods` in the IRanges package for a quick introduction to intra range and inter range transformations.

This man page documents inter range transformations of a GenomicRanges object (i.e. of an object that belongs to the GenomicRanges class or one of its subclasses, this includes for example GRanges objects).

See ?`intra-range-methods` for intra range transformations of a GenomicRanges object.

Usage

## S4 method for signature 'GenomicRanges'
range(x, ..., ignore.strand=FALSE, na.rm=FALSE)
## S4 method for signature 'GRangesList'
range(x, ..., ignore.strand=FALSE, na.rm=FALSE)

## S4 method for signature 'GenomicRanges'
reduce(x, drop.empty.ranges=FALSE, min.gapwidth=1L, with.revmap=FALSE,
          with.inframe.attrib=FALSE, ignore.strand=FALSE)
## S4 method for signature 'GRangesList'
reduce(x, drop.empty.ranges=FALSE, min.gapwidth=1L,
          with.inframe.attrib=FALSE, ignore.strand=FALSE)

## S4 method for signature 'GenomicRanges'
gaps(x, start=1L, end=seqlengths(x))

## S4 method for signature 'GenomicRanges'
disjoin(x, ignore.strand=FALSE)
## S4 method for signature 'GRangesList'
disjoin(x, ignore.strand=FALSE)

## S4 method for signature 'GenomicRanges'
isDisjoint(x, ignore.strand=FALSE)
## S4 method for signature 'GRangesList'
isDisjoint(x, ignore.strand=FALSE)

## S4 method for signature 'GenomicRanges'
disjointBins(x, ignore.strand=FALSE)

Arguments

Details

On a GRanges object

range returns an object of the same type as x containing range bounds for each distinct (seqname, strand) pairing. The names (names(x)) and the metadata columns in x are dropped.

reduce returns an object of the same type as x containing reduced ranges for each distinct (seqname, strand) pairing. The names (names(x)) and the metadata columns in x are dropped. See ?reduce for more information about range reduction and for a description of the optional arguments.

gaps returns an object of the same type as x containing complemented ranges for each distinct (seqname, strand) pairing. The names (names(x)) and the columns in x are dropped. For the start and end arguments of this gaps method, it is expected that the user will supply a named integer vector (where the names correspond to the appropriate seqlevels). See ?gaps for more information about range complements and for a description of the optional arguments.

disjoin returns an object of the same type as x containing disjoint ranges for each distinct (seqname, strand) pairing. The names (names(x)) and the metadata columns in x are dropped.

isDisjoint returns a logical value indicating whether the ranges in x are disjoint (i.e. non-overlapping).

disjointBins returns bin indexes for the ranges in x, such that ranges in the same bin do not overlap. If ignore.strand=FALSE, the two features cannot overlap if they are on different strands.

On a GRangesList object

When they are supported on GRangesList object x, the above inter range transformations will apply the transformation to each of the list elements in x and return a list-like object parallel to x (i.e. with 1 list element per list element in x). If x has names on it, they're propagated to the returned object.

Author(s)

H. Pagès and P. Aboyoun

See Also

• The GenomicRanges and GRanges classes.

• The Ranges class in the IRanges package.

• The inter-range-methods man page in the IRanges package.

• GenomicRanges-comparison for comparing and ordering genomic ranges.

Examples

gr <- GRanges(
        seqnames=Rle(paste("chr", c(1, 2, 1, 3), sep=""), c(1, 3, 2, 4)),
        ranges=IRanges(1:10, width=10:1, names=letters[1:10]),
        strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
        score=1:10,
        GC=seq(1, 0, length=10)
      )
gr

gr1 <- GRanges(seqnames="chr2", ranges=IRanges(3, 6),
               strand="+", score=5L, GC=0.45)
gr2 <- GRanges(seqnames="chr1",
               ranges=IRanges(c(10, 7, 19), width=5),
               strand=c("+", "-", "+"), score=3:5, GC=c(0.3, 0.5, 0.66))
gr3 <- GRanges(seqnames=c("chr1", "chr2"),
               ranges=IRanges(c(1, 4), c(3, 9)),
               strand=c("-", "-"), score=c(6L, 2L), GC=c(0.4, 0.1))
grl <- GRangesList(gr1=gr1, gr2=gr2, gr3=gr3)
grl

## ---------------------------------------------------------------------
## range()
## ---------------------------------------------------------------------

## On a GRanges object:
range(gr)

## On a GRangesList object:
range(grl)
range(grl, ignore.strand=TRUE)

# ---------------------------------------------------------------------
## reduce()
## ---------------------------------------------------------------------
reduce(gr)

gr2 <- reduce(gr, with.revmap=TRUE)
revmap <- mcols(gr2)$revmap  # an IntegerList

## Use the mapping from reduced to original ranges to group the original
## ranges by reduced range:
relist(gr[unlist(revmap)], revmap)

## Or use it to split the DataFrame of original metadata columns by
## reduced range:
relist(mcols(gr)[unlist(revmap), ], revmap)  # a SplitDataFrameList

## [For advanced users] Use this reverse mapping to compare the reduced
## ranges with the ranges they originate from:
expanded_gr2 <- rep(gr2, elementLengths(revmap))
reordered_gr <- gr[unlist(revmap)]
codes <- compare(expanded_gr2, reordered_gr)
## All the codes should translate to "d", "e", "g", or "h" (the 4 letters
## indicating that the range on the left contains the range on the right):
alphacodes <- rangeComparisonCodeToLetter(compare(expanded_gr2, reordered_gr))
stopifnot(all(alphacodes %in% c("d", "e", "g", "h")))

## On a big GRanges object with a lot of seqlevels:
mcols(gr) <- NULL
biggr <- c(gr, GRanges("chr1", IRanges(c(4, 1), c(5, 2)), strand="+"))
seqlevels(biggr) <- paste0("chr", 1:2000)
biggr <- rep(biggr, 25000)
set.seed(33)
seqnames(biggr) <- sample(factor(seqlevels(biggr), levels=seqlevels(biggr)),
                          length(biggr), replace=TRUE)

biggr2 <- reduce(biggr, with.revmap=TRUE)
revmap <- mcols(biggr2)$revmap
expanded_biggr2 <- rep(biggr2, elementLengths(revmap))
reordered_biggr <- biggr[unlist(revmap)]
codes <- compare(expanded_biggr2, reordered_biggr)
alphacodes <- rangeComparisonCodeToLetter(compare(expanded_biggr2,
                                                  reordered_biggr))
stopifnot(all(alphacodes %in% c("d", "e", "g", "h")))
table(alphacodes)

## On a GRangesList object:
reduce(grl)  # Doesn't really reduce anything but note the reordering
             # of the inner elements in the 2nd and 3rd list elements:
             # the ranges are reordered by sequence name first (which
             # should appear in the same order as in 'seqlevels(grl)'),
             # and then by strand.
reduce(grl, ignore.strand=TRUE)  # 2nd list element got reduced

## ---------------------------------------------------------------------
## gaps()
## ---------------------------------------------------------------------
gaps(gr, start=1, end=10)

## ---------------------------------------------------------------------
## disjoin(), isDisjoint(), disjointBins()
## ---------------------------------------------------------------------
disjoin(gr)
isDisjoint(gr)
stopifnot(isDisjoint(disjoin(gr)))
disjointBins(gr)
stopifnot(all(sapply(split(gr, disjointBins(gr)), isDisjoint)))