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### =========================================================================
### Intra-range methods
### -------------------------------------------------------------------------
###
setMethod("shift", "RangedSummarizedExperiment",
function(x, shift=0L, use.names=TRUE)
{
x0 <- x
x <- rowRanges(x)
rowRanges(x0) <- callGeneric()
x0
}
)
setMethod("narrow", "RangedSummarizedExperiment",
function(x, start=NA, end=NA, width=NA, use.names=TRUE)
{
x0 <- x
x <- rowRanges(x)
rowRanges(x0) <- callGeneric()
x0
}
)
setMethod("resize", "RangedSummarizedExperiment",
function(x, width, fix="start", use.names=TRUE, ignore.strand=FALSE)
{
x0 <- x
x <- rowRanges(x)
rowRanges(x0) <- callGeneric()
x0
}
)
setMethod("flank", "RangedSummarizedExperiment",
function(x, width, start=TRUE, both=FALSE, use.names=TRUE,
ignore.strand=FALSE)
{
x0 <- x
x <- rowRanges(x)
rowRanges(x0) <- callGeneric()
x0
}
)
setMethod("promoters", "RangedSummarizedExperiment",
function(x, upstream=2000, downstream=200)
{
x0 <- x
x <- rowRanges(x)
rowRanges(x0) <- callGeneric()
x0
}
)
### Because 'keep.all.ranges' is FALSE by default, it will break if some
### ranges are dropped.
setMethod("restrict", "RangedSummarizedExperiment",
function(x, start=NA, end=NA, keep.all.ranges=FALSE, use.names=TRUE)
{
x0 <- x
x <- rowRanges(x)
rowRanges(x0) <- callGeneric()
x0
}
)
setMethod("trim", "RangedSummarizedExperiment",
function(x, use.names=TRUE)
{
x0 <- x
x <- rowRanges(x)
rowRanges(x0) <- callGeneric()
x0
}
)
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