SummarizedExperiment (version 1.2.3)

intra-range-methods: Intra range transformations of a RangedSummarizedExperiment object

Description

This man page documents the intra range transformations that are supported on RangedSummarizedExperiment objects.

Usage

"shift"(x, shift=0L, use.names=TRUE)
"narrow"(x, start=NA, end=NA, width=NA, use.names=TRUE)
"resize"(x, width, fix="start", use.names=TRUE, ignore.strand=FALSE)
"flank"(x, width, start=TRUE, both=FALSE, use.names=TRUE, ignore.strand=FALSE)
"promoters"(x, upstream=2000, downstream=200)
"restrict"(x, start=NA, end=NA, keep.all.ranges=FALSE, use.names=TRUE)
"trim"(x, use.names=TRUE)

Arguments

x

A RangedSummarizedExperiment object.

shift, use.names

See ?shift in the GenomicRanges package.

start, end, width, fix

See ?shift in the GenomicRanges package.

ignore.strand, both

See ?shift in the GenomicRanges package.

upstream, downstream

See ?shift in the GenomicRanges package.

keep.all.ranges

See ?shift in the GenomicRanges package.

Details

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 GenomicRanges package for the details of how these transformations operate on a GenomicRanges or GRangesList object.

See Also

• RangedSummarizedExperiment objects.

• The shift man page in the GenomicRanges package where intra range transformations of a GenomicRanges or GRangesList object are documented.

Examples

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)
))