tileGenome: Put (virtual) tiles on a given genome

In vjcitn/GenomicRangesGHA: Representation and manipulation of genomic intervals; demo with github actions binary generation

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.

vjcitn/GenomicRangesGHA documentation built on Jan. 18, 2021, 12:39 a.m.