annotateRegions: Annotate regions.

In fmicompbio/swissknife: Handy code shared in the FMI CompBio group

Annotate regions.

Description

Annotate a GRanges object with sets of reference GRanges or GRangesList objects, with respect to overlaps and nearest neighbors.

Usage

annotateRegions(
  x,
  hasOverlap = list(),
  fracOverlap = list(),
  numOverlap = list(),
  nearest = list(),
  ignore.strand = TRUE
)

Arguments

x	The GRanges object to annotate.
hasOverlap	Named list with GRanges or GRangesList object(s). For each list element, a logical vector "X.hasOverlap" will be added to the mcols of the result, with TRUE for each tile that overlaps any region in that element. "X" is obtained from names(hasOverlap).
fracOverlap	Named list with GRanges or GRangesList object(s). For each list element, a numeric vector "X.fracOverlap" will be added to the mcols of the result, with a value between 0 and 1 giving the fraction of bases in a tile that overlaps with any region in that element. "X" is obtained from names(fracOverlap).
numOverlap	Named list with GRanges or GRangesList object(s). For each list element, two numeric vectors "X.numOverlapWithin" and "X.numOverlapAny" will be added to the mcols of the result, giving the number of ranges in that element that are fully contained within a tile, or that overlap with a tile in any way, respectively. "X" is obtained from names(numOverlap).
nearest	Named list with GRanges or GRangesList object(s). For each list element, two numeric vectors "X.nearestName" and "X.nearestDistance" will be added to the mcols of the result, giving the name and distance of the nearest range in that element for each tile. "X" is obtained from names(nearest), and the values of "X.nearestName" from names(nearest$X). If multiple nearest ranges are at the same distance from a tile, an arbitrary one is reported in "X.nearestName".
ignore.strand	Logical scalar passed to findOverlaps when searching for overlaps between x and reference regions.

Value

A GRanges similar to x, with annotations added to its metadata columns (mcols).

Author(s)

Michael Stadler

See Also

getGenomicTiles that uses this function, findOverlaps and nearest in package GenomicRanges used internally.

Examples

library(GenomicRanges)

x <- GRanges("chr1", IRanges(c(1, 12), width = 10))
tss <- GRanges("chr1", IRanges(c(1, 10, 30), width = 1,
                               names = paste0("t", 1:3)))
blacklist <- GRanges("chr1", IRanges(20, width = 5))
annotateRegions(x, hasOverlap = list(Blacklist = blacklist),
                fracOverlap = list(Blacklist = blacklist),
                numOverlap = list(TSS = tss),
                nearest = list(TSS = tss))

fmicompbio/swissknife documentation built on June 11, 2025, 4:17 p.m.