Intra range transformations of a RangedSummarizedExperiment object
This man page documents the intra range transformations that are supported on RangedSummarizedExperiment objects.
## S4 method for signature 'RangedSummarizedExperiment'
shift(x, shift=0L, use.names=TRUE)
## S4 method for signature 'RangedSummarizedExperiment'
narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)
## S4 method for signature 'RangedSummarizedExperiment'
resize(x, width, fix="start", use.names=TRUE,
ignore.strand=FALSE)
## S4 method for signature 'RangedSummarizedExperiment'
flank(x, width, start=TRUE, both=FALSE,
use.names=TRUE, ignore.strand=FALSE)
## S4 method for signature 'RangedSummarizedExperiment'
promoters(x, upstream=2000, downstream=200)
## S4 method for signature 'RangedSummarizedExperiment'
restrict(x, start=NA, end=NA, keep.all.ranges=FALSE,
use.names=TRUE)
## S4 method for signature 'RangedSummarizedExperiment'
trim(x, use.names=TRUE)x |
A RangedSummarizedExperiment object. |
shift, use.names |
See |
start, end, width, fix |
See |
ignore.strand, both |
See |
upstream, downstream |
See |
keep.all.ranges |
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:
rowRanges(x) <- f(rowRanges(x), ...)
where f is the name of the function and ... any additional
arguments passed to it.
See ?shift in the IRanges
package for the details of how these transformations operate on a
GenomicRanges or GRangesList
object.
RangedSummarizedExperiment objects.
The shift man page in the IRanges package where intra 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, 1)
stopifnot(identical(
rowRanges(rse1),
shift(rowRanges(rse0), 1)
))
se2 <- narrow(rse0, start=10, end=-15)
stopifnot(identical(
rowRanges(se2),
narrow(rowRanges(rse0), start=10, end=-15)
))
se3 <- resize(rse0, width=75)
stopifnot(identical(
rowRanges(se3),
resize(rowRanges(rse0), width=75)
))
se4 <- flank(rse0, width=20)
stopifnot(identical(
rowRanges(se4),
flank(rowRanges(rse0), width=20)
))
se5 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
stopifnot(identical(
rowRanges(se5),
restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
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