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

In Bioconductor/SummarizedExperiment: A container (S4 class) for matrix-like assays

Intra range transformations of a RangedSummarizedExperiment object

Description

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

Usage

## 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'
terminators(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)

Arguments

x	A RangedSummarizedExperiment object.
shift, use.names, start, end, width, fix, ignore.strand, both, upstream, downstream, keep.all.ranges	See ?GenomicRanges::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 ?GenomicRanges::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 <- promoters(rse0, upstream=85, downstream=50)
stopifnot(identical(
  rowRanges(se5),
  promoters(rowRanges(rse0), upstream=85, downstream=50)
))

se6 <- terminators(rse0, upstream=85, downstream=50)
stopifnot(identical(
  rowRanges(se6),
  terminators(rowRanges(rse0), upstream=85, downstream=50)
))

se7 <- restrict(rse0, start=200, end=700, keep.all.ranges=TRUE)
stopifnot(identical(
  rowRanges(se7),
  restrict(rowRanges(rse0), start=200, end=700, keep.all.ranges=TRUE)
))

Bioconductor/SummarizedExperiment documentation built on Nov. 2, 2024, 8:20 a.m.