Inter range transformations of a RangedSummarizedExperiment object
This man page documents the inter range transformations that are supported on RangedSummarizedExperiment objects.
## S4 method for signature 'RangedSummarizedExperiment' isDisjoint(x, ignore.strand=FALSE) ## S4 method for signature 'RangedSummarizedExperiment' disjointBins(x, ignore.strand=FALSE)
x |
A RangedSummarizedExperiment object. |
ignore.strand |
See |
These transformations operate on the rowRanges component of the
RangedSummarizedExperiment object, which can be a
GenomicRanges or GRangesList
object.
More precisely, any of the above functions performs the following
transformation on RangedSummarizedExperiment object x:
f(rowRanges(x), ...)
where f is the name of the function and ... any additional
arguments passed to it.
See ?isDisjoint in the GenomicRanges
package for the details of how these transformations operate on a
GenomicRanges or GRangesList
object.
See ?isDisjoint in the
GenomicRanges package.
RangedSummarizedExperiment objects.
The isDisjoint man page in the GenomicRanges package where inter range transformations of a GenomicRanges or GRangesList object are documented.
nrows <- 20; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(5, 15)),
IRanges(sample(1000L, 20), width=100),
strand=Rle(c("+", "-"), c(12, 8)))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
rse0 <- SummarizedExperiment(assays=SimpleList(counts=counts),
rowRanges=rowRanges, colData=colData)
rse1 <- shift(rse0, 99*start(rse0))
isDisjoint(rse0) # FALSE
isDisjoint(rse1) # TRUE
bins0 <- disjointBins(rse0)
bins0
stopifnot(identical(bins0, disjointBins(rowRanges(rse0))))
bins1 <- disjointBins(rse1)
bins1
stopifnot(all(bins1 == bins1[1]))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.