getGenomicTiles: Get regions tiling a genome.

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

Get regions tiling a genome.

Description

Get sequential, potentially annotated regions of a fixed lengths (tiles) along chromosomes of a genome.

Usage

getGenomicTiles(
  genome,
  tileWidth,
  hasOverlap = list(),
  fracOverlap = list(),
  numOverlap = list(),
  nearest = list(),
  addSeqComp = TRUE
)

Arguments

genome	The genome to work on. Either a BSgenome object, a character scalar with the name of an installed BSgenome or with a file path and name pointing to a fasta file with the genome sequence, or a named numeric vector giving the names and lengths of chromosomes.
tileWidth	numeric scalar with the tile length.
hasOverlap, fracOverlap, numOverlap, nearest	Named lists with GRanges or GRangesList object(s) used to annotate genomic tiles. See annotateRegions for details.
addSeqComp	logical scalar. If TRUE and primary sequence can be obtained from genome, also add sequence composition features for each tile to the annotations. Currently, the following features are included: percent of G+C bases ("percGC"), CpG observed-over-expected ratio ("CpGoe").

Details

The last tile in each chromosome is dropped if it would be shorter than tileWidth. Generated tiles are unstranded (*) and therefore overlaps or searching for nearest neighbors are ignoring strands of annotations (ignore.strand=TRUE).

Value

A GRanges object with genome tiling regions. Optional tile annotations are contained in its metadata columns (mcols).

Author(s)

Michael Stadler

See Also

tileGenome and annotateRegions used by getGenomicTiles internally.

Examples

library(GenomicRanges)

tss <- GRanges("chr1", IRanges(c(1, 10, 30), width = 1,
                               names = paste0("t", 1:3)))
blacklist <- GRanges("chr1", IRanges(20, width = 5))
getGenomicTiles(c(chr1 = 45, chr2 = 12), tileWidth = 10,
                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.