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

intra-range-methodsR Documentation

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'
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

See ?shift in the IRanges package.

start, end, width, fix

See ?shift in the IRanges package.

ignore.strand, both

See ?shift in the IRanges package.

upstream, downstream

See ?shift in the IRanges package.

keep.all.ranges

See ?shift in the IRanges 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 IRanges 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 IRanges 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)
))

Bioconductor/SummarizedExperiment documentation built on Nov. 4, 2022, 11:59 a.m.