To use the GenomicRanges::tileGenome(seqlengths, ...) function, we need to know what to assign to "seqlengths: Either a named numeric vector of chromosome lengths or a Seqinfo object." This becomes problematic downstream when using annotatr because if we don't use an off-the-shelf Seqinfo object, e.g. hg19, we may get Seqinfo difference errors.
One solution is to use the maximum position of the loci of bs + win_size to build the tiles, and then wipe any Seqinfo object that may get inherited by the returned BSseq-class object.
Function call
tile_by_windows(bs, win_size = 200)
Description
An optional function to aggregate cytosine / CpG level data into regions based on a tiling of the genome with windows having win_size.
Arguments
bs a BSseq object.
win_size the integer size of the windows by which to tile the genome, and group CpGs into.
Values
A BSseq-class object with loci of tiles win_sizebp in width over the genome. Coverage and methylation read count matrices are aggregated by the sums of the cytosines / CpGs in the tiles per sample.
Tests
Test for the correct sums in tiles.
Test for inclusion/exclusion of cytosines / CpGs in regions (left or right closed or open), and include that in the documentation once you're sure of the behavior.
Is it possible for a non-destranded CpG pair to be split among neighboring regions?
Notes
This function will use tile_by_regions() #32, once the GRanges of windows are constructed.
Issues to resolve before implementation
GenomicRanges::tileGenome(seqlengths, ...)function, we need to know what to assign to "seqlengths: Either a named numeric vector of chromosome lengths or a Seqinfo object." This becomes problematic downstream when usingannotatrbecause if we don't use an off-the-shelfSeqinfoobject, e.g. hg19, we may getSeqinfodifference errors.bs+win_sizeto build the tiles, and then wipe anySeqinfoobject that may get inherited by the returnedBSseq-class object.Function call
tile_by_windows(bs, win_size = 200)Description
An optional function to aggregate cytosine / CpG level data into regions based on a tiling of the genome with windows having
win_size.Arguments
bsaBSseqobject.win_sizetheintegersize of the windows by which to tile the genome, and group CpGs into.Values
A
BSseq-class object with loci of tileswin_sizebp in width over the genome. Coverage and methylation read count matrices are aggregated by the sums of the cytosines / CpGs in the tiles per sample.Tests
Notes
tile_by_regions()#32, once theGRangesof windows are constructed.