tileGenome {GenomicRanges} | R Documentation

## Put (virtual) tiles on a given genome

### Description

`tileGenome` returns a set of genomic regions that form a partitioning of the specified genome. Each region is called a "tile".

### Usage

    tileGenome(seqlengths, ntile, tilewidth, cut.last.tile.in.chrom=FALSE)

### Arguments

`seqlengths` | Either a named numeric vector of chromosome lengths or a Seqinfo object. More precisely, if a named numeric vector, it must have a length >= 1, cannot contain NAs or negative values, and cannot have duplicated names. If a Seqinfo object, then it's first replaced with the vector of sequence lengths stored in the object (extracted from the object with the `seqlengths` getter), then the restrictions described previously apply to this vector.
`ntile` | The number of tiles to generate.
`tilewidth` | The desired tile width. The effective tile width might be slightly different but is guaranteed to never be more than the desired width.
`cut.last.tile.in.chrom` | Whether or not to cut the last tile in each chromosome. This is set to `FALSE` by default. Can be set to `TRUE` only when `tilewidth` is specified. In that case, a tile will never overlap with more than 1 chromosome and a GRanges object is returned with one element (i.e. one genomic range) per tile.

### Value

If `cut.last.tile.in.chrom` is `FALSE` (the default), a GRangesList object with one list element per tile, each of them containing a number of genomic ranges equal to the number of chromosomes it overlaps with. Note that when the tiles are small (i.e. much smaller than the chromosomes), most of them only overlap with a single chromosome.

If `cut.last.tile.in.chrom` is `TRUE`, a GRanges object with one element (i.e. one genomic range) per tile.

### Author(s)

H. Pagès, based on a proposal by M. Morgan

### See Also

- genomicvars for an example of how to compute the binned average of a numerical variable defined along a genome.

- GRangesList and GRanges objects.

- Seqinfo objects and the `seqlengths` getter.

- IntegerList objects.

- Views objects.

### Examples

    ## ---------------------------------------------------------------------
    ## A. WITH A TOY GENOME
    ## ---------------------------------------------------------------------

    seqlengths <- c(chr1=60, chr2=20, chr3=25)

    ## Create 5 tiles:
    tiles <- tileGenome(seqlengths, ntile=5)
    tiles
    elementNROWS(tiles)  # tiles 3 and 4 contain 2 ranges

    width(tiles)
    ## Use sum() on this IntegerList object to get the effective tile
    ## widths:
    sum(width(tiles))  # each tile covers exactly 21 genomic positions

    ## Create 9 tiles:
    tiles <- tileGenome(seqlengths, ntile=9)
    elementNROWS(tiles)  # tiles 6 and 7 contain 2 ranges

    table(sum(width(tiles)))  # some tiles cover 12 genomic positions,
                              # others 11

    ## Specify the tile width:
    tiles <- tileGenome(seqlengths, tilewidth=20)
    length(tiles)  # 6 tiles
    table(sum(width(tiles)))  # effective tile width is <= specified

    ## Specify the tile width and cut the last tile in each chromosome:
    tiles <- tileGenome(seqlengths, tilewidth=24,
                        cut.last.tile.in.chrom=TRUE)
    tiles
    width(tiles)  # each tile covers exactly 24 genomic positions, except
                  # the last tile in each chromosome

    ## Partition a genome by chromosome ("natural partitioning"):
    tiles <- tileGenome(seqlengths, tilewidth=max(seqlengths),
                        cut.last.tile.in.chrom=TRUE)
    tiles  # one tile per chromosome

    ## sanity check
    stopifnot(all.equal(setNames(end(tiles), seqnames(tiles)), seqlengths))

    ## ---------------------------------------------------------------------
    ## B. WITH A REAL GENOME
    ## ---------------------------------------------------------------------

    library(BSgenome.Scerevisiae.UCSC.sacCer2)
    tiles <- tileGenome(seqinfo(Scerevisiae), ntile=20)
    tiles

    tiles <- tileGenome(seqinfo(Scerevisiae), tilewidth=50000,
                        cut.last.tile.in.chrom=TRUE)
    tiles

    ## ---------------------------------------------------------------------
    ## C. AN APPLICATION: COMPUTE THE BINNED AVERAGE OF A NUMERICAL VARIABLE
    ##    DEFINED ALONG A GENOME
    ## ---------------------------------------------------------------------

    ## See '?genomicvars' for an example of how to compute the binned
    ## average of a numerical variable defined along a genome.

[Package GenomicRanges version 1.40.0 Index]