Coverage of a RangedSummarizedExperiment object
This man page documents the coverage method for
RangedSummarizedExperiment objects.
## S4 method for signature 'RangedSummarizedExperiment'
coverage(x, shift=0L, width=NULL, weight=1L,
method=c("auto", "sort", "hash"))x |
A RangedSummarizedExperiment object. |
shift, width, weight, method |
See |
This method operates on the rowRanges component of the
RangedSummarizedExperiment object, which can be a
GenomicRanges or GRangesList
object.
More precisely, on RangedSummarizedExperiment object x,
coverage(x, ...) is equivalent to coverage(rowRanges(x), ...).
See ?coverage in the GenomicRanges
package for the details of how coverage operates on a
GenomicRanges or GRangesList
object.
See ?coverage in the GenomicRanges
package.
RangedSummarizedExperiment objects.
The coverage man page in the
GenomicRanges package where the coverage methods
for GenomicRanges and
GRangesList objects 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)),
seqlengths=c(chr1=1800, chr2=1300))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
rowRanges=rowRanges, colData=colData)
cvg <- coverage(rse)
cvg
stopifnot(identical(cvg, coverage(rowRanges(rse))))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.