extendRegions: Extend Regions

In bernatgel/regioneR: Association analysis of genomic regions based on permutation tests

Extend Regions

Description

Extends the regions a number of bases at each end. Negative numbers will reduce the region instead of enlarging it.

Usage

extendRegions(A, extend.start=0, extend.end=0)

Arguments

A	a region set in any of the accepted formats by toGRanges (GenomicRanges, data.frame, etc...)
extend.start	an integer. The number of bases to be subtracted from the start of the region.
extend.end	an integer. The number of bases to be added at the end of the region.

Value

a GenomicRanges object with the extended regions.

Note

If negative values are provided and the new extremes are "flipped", the function will fail. It does not check if the extended regions fit into the genome.

See Also

plotRegions, toDataframe, toGRanges, subtractRegions, splitRegions, overlapRegions, commonRegions, mergeRegions, joinRegions

Examples

A <- data.frame("chr1", c(10, 20, 30), c(13, 28, 40))

extend1 <- extendRegions(A, extend.start=5, extend.end=2)

extend2 <- extendRegions(A, extend.start=15)

extend3 <- extendRegions(A, extend.start=-1)

plotRegions(list(A, extend1, extend2, extend3), chromosome="chr1", regions.labels=c("A", "extend1", "extend2", "extend3"), regions.colors=4:1)

bernatgel/regioneR documentation built on Sept. 10, 2023, 12:03 a.m.