overlapRegions: Overlap Regions

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

Overlap Regions

Description

return overlap between 2 regios set A and B

Usage

overlapRegions(A, B, colA=NULL, colB=NULL, type="any", min.bases=1, min.pctA=NULL, min.pctB=NULL, get.pctA=FALSE, get.pctB=FALSE, get.bases=FALSE, only.boolean=FALSE, only.count=FALSE, ...)

Arguments

A	a region set in any of the accepted formats by toGRanges (GenomicRanges, data.frame, etc...)
B	a region set in any of the accepted formats by toGRanges (GenomicRanges, data.frame, etc...)
colA	numeric vector indicating which columns of A the results will contain (default NULL)
colB	numeric vector indicating which columns of B the results will contain (default NULL)
type	AinB: the region in A is contained in a region in B BinA: the region in B is contained in A within: the region in A or B is contained in a region in the other region set equal: the region in A has the same chromosome, start and end as a region in B AleftB: the end of the region from A overlaps the beginning of a region in B ArightB: the start of a region from A overlaps the end of a region in B any: any kind of overlap is returned
min.bases	numeric minimun number of bp accepted to define a overlap (default 1)
min.pctA	numeric minimun percentage of bases of A accepted to define a overlap (default NULL)
min.pctB	numeric minimun percentage of bases of B accepted to define a overlap (default NULL)
get.pctA	boolean if TRUE add a column in the results indicating the number percentage of A are involved in the overlap (default FALSE)
get.pctB	boolean if TRUE add a column in the results indicating the number percentage of B are involved in the overlap (default FALSE)
get.bases	boolean if TRUE add in the results the number of overlapped bases (default FALSE)
only.boolean	boolean if TRUE devolve as result a boolean vector containing the overlap state of each regions of A (default FALSE)
only.count	boolean if TRUE devolve as result the number of regions of A overlapping with B
...	any additional parameter (are there any left?)

Value

the default results is a data.frame with at least 5 columns "chr" indicating the chromosome of the appartenence of each overlap, "startA", "endA", "startB", "endB", indicating the coordinates of the region A and B for each overlap "type" that describe the nature of the overlap (see arguments "type") eventually other columns can be added (see see arguments "colA", "colB", "get.pctA", "get.pctB", "get.bases")

Note

The implementation uses when possible the countOverlaps function from IRanges package.

See Also

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

Examples

A <- data.frame("chr1", c(1, 5, 20, 30), c(8, 13, 28, 40), x=c(1,2,3,4), y=c("a", "b", "c", "d"))

B <- data.frame("chr1", 25, 35)

overlapRegions(A, B)

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