methods for GenomicRanges.
tile partitions each range
into a set of tiles, which are defined in terms of their number or
slidingWindows generates sliding windows of a specified
width and frequency.
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A GenomicRanges object, like a
The number of tiles to generate.
The (maximum) width of each tile.
The distance between the start positions of the sliding windows.
tile function splits
x into a
each element of which corresponds
to a tile, or partition, of
x. Specify the tile geometry with either
width (not both). Passing
of approximately equal width, truncated by sequence end, while passing
width tiles the region with ranges of the given width, again truncated
by sequence end.
slidingWindows function generates sliding windows within
each range of
x, according to
GRangesList. If the sliding windows do not exactly
cover a range in
x, the last window is partial.
GRangesList object, each element of which corresponds to a window.
tile in the IRanges package.
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gr <- GRanges( seqnames=Rle(c("chr1", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), ranges=IRanges(1:10, end=11), strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)), seqlengths=c(chr1=11, chr2=12, chr3=13)) # split every range in half tiles <- tile(gr, n = 2L) stopifnot(all(elementNROWS(tiles) == 2L)) # split ranges into subranges of width 2 # odd width ranges must contain one subrange of width 1 tiles <- tile(gr, width = 2L) stopifnot(all(all(width(tiles) %in% c(1L, 2L)))) windows <- slidingWindows(gr, width=3L, step=2L) width(windows[[1L]]) # last range is truncated
Loading required package: stats4 Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:base’: expand.grid Loading required package: IRanges Loading required package: GenomeInfoDb  3 3 3 3 3
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