intra-range-methods: Intra range transformations of a GRanges or GRangesList...

Description Usage Arguments Details Author(s) See Also Examples

Description

This man page documents intra range transformations of a GenomicRanges object (i.e. of an object that belongs to the GenomicRanges class or one of its subclasses, this includes for example GRanges objects), or a GRangesList object.

See ?`intra-range-methods` and ?`inter-range-methods` in the IRanges package for a quick introduction to intra range and inter range transformations.

Intra range methods for GAlignments and GAlignmentsList objects are defined and documented in the GenomicAlignments package.

See ?`inter-range-methods` for inter range transformations of a GenomicRanges or GRangesList object.

Usage

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## S4 method for signature 'GenomicRanges'
shift(x, shift=0L, use.names=TRUE)
## S4 method for signature 'GRangesList'
shift(x, shift=0L, use.names=TRUE)
## S4 method for signature 'GenomicRangesList'
shift(x, shift=0L, use.names=TRUE)

## S4 method for signature 'GenomicRanges'
narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)
## S4 method for signature 'GRangesList'
narrow(x, start=NA, end=NA, width=NA, use.names=TRUE)
## S4 method for signature 'GenomicRangesList'
narrow(x, start=NA, end=NA, width=NA,
       use.names=TRUE)

## S4 method for signature 'GenomicRanges'
resize(x, width, fix="start", use.names=TRUE,
       ignore.strand=FALSE)
## S4 method for signature 'GRangesList'
resize(x, width, fix="start", use.names=TRUE,
       ignore.strand=FALSE)
## S4 method for signature 'GenomicRangesList'
resize(x, width, fix="start", use.names=TRUE,
       ignore.strand=FALSE)

## S4 method for signature 'GenomicRanges'
flank(x, width, start=TRUE, both=FALSE,
      use.names=TRUE, ignore.strand=FALSE)
## S4 method for signature 'GRangesList'
flank(x, width, start=TRUE, both=FALSE,
      use.names=TRUE, ignore.strand=FALSE)
## S4 method for signature 'GenomicRangesList'
flank(x, width, start=TRUE, both=FALSE,
      use.names=TRUE, ignore.strand=FALSE)

## S4 method for signature 'GenomicRanges'
promoters(x, upstream=2000, downstream=200)
## S4 method for signature 'GRangesList'
promoters(x, upstream=2000, downstream=200)
## S4 method for signature 'GenomicRangesList'
promoters(x, upstream=2000, downstream=200)

## S4 method for signature 'GenomicRanges'
restrict(x, start=NA, end=NA, keep.all.ranges=FALSE,
         use.names=TRUE)
## S4 method for signature 'GRangesList'
restrict(x, start=NA, end=NA, keep.all.ranges=FALSE,
         use.names=TRUE)
## S4 method for signature 'GenomicRangesList'
restrict(x, start=NA, end=NA,
      keep.all.ranges=FALSE, use.names=TRUE)

## S4 method for signature 'GenomicRanges'
trim(x, use.names=TRUE)

Arguments

x

A GenomicRanges or GRangesList object.

shift, use.names, start, end, width, both, fix, keep.all.ranges, upstream, downstream

See ?`intra-range-methods`.

ignore.strand

TRUE or FALSE. Whether the strand of the input ranges should be ignored or not. See details below.

...

Additional arguments to methods.

Details

Author(s)

P. Aboyoun and V. Obenchain <vobencha@fhcrc.org>

See Also

Examples

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## ---------------------------------------------------------------------
## A. ON A GRanges OBJECT
## ---------------------------------------------------------------------
gr <- GRanges(
        seqnames=Rle(paste("chr", c(1, 2, 1, 3), sep=""), c(1, 3, 2, 4)),
        ranges=IRanges(1:10, width=10:1, names=letters[1:10]),
        strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
        score=1:10,
        GC=seq(1, 0, length=10)
      )
gr

shift(gr, 1)
narrow(gr[-10], start=2, end=-2)
resize(gr, width=10)
flank(gr, width=10)
restrict(gr, start=3, end=7)

gr <- GRanges("chr1", IRanges(rep(10, 3), width=6), c("+", "-", "*"))
promoters(gr, 2, 2)

## ---------------------------------------------------------------------
## B. ON A GRangesList OBJECT
## ---------------------------------------------------------------------
gr1 <- GRanges("chr2", IRanges(3, 6))
gr2 <- GRanges(c("chr1", "chr1"), IRanges(c(7,13), width=3),
               strand=c("+", "-"))
gr3 <- GRanges(c("chr1", "chr2"), IRanges(c(1, 4), c(3, 9)),
               strand="-")
grl <- GRangesList(gr1= gr1, gr2=gr2, gr3=gr3)
grl

resize(grl, width=20)
flank(grl, width=20)
restrict(grl, start=3)

GenomicRanges documentation built on Sept. 8, 2017, 2:01 a.m.