Get regions tiling a genome.

Source: R/getGenomicTiles.R

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

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").

Value

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

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).

See also

tileGenome and annotateRegions used by getGenomicTiles internally.

Author

Michael Stadler

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))
#> Warning: ignoring 'addSeqComp' (sequence not available from 'genome')
#> GRanges object with 5 ranges and 6 metadata columns:
#>       seqnames    ranges strand | Blacklist.hasOverlap Blacklist.fracOverlap
#>          <Rle> <IRanges>  <Rle> |            <logical>             <numeric>
#>   [1]     chr1      1-10      * |                FALSE                   0.0
#>   [2]     chr1     11-20      * |                 TRUE                   0.1
#>   [3]     chr1     21-30      * |                 TRUE                   0.4
#>   [4]     chr1     31-40      * |                FALSE                   0.0
#>   [5]     chr2      1-10      * |                FALSE                   0.0
#>       TSS.numOverlapWithin TSS.numOverlapAny TSS.nearestName
#>                  <integer>         <integer>     <character>
#>   [1]                    2                 2              t1
#>   [2]                    0                 0              t2
#>   [3]                    1                 1              t3
#>   [4]                    0                 0              t3
#>   [5]                    0                 0            <NA>
#>       TSS.nearestDistance
#>                 <integer>
#>   [1]                   0
#>   [2]                   0
#>   [3]                   0
#>   [4]                   0
#>   [5]                <NA>
#>   -------
#>   seqinfo: 2 sequences from an unspecified genome