Break region into smaller regions based on cutoff - r

Question

This is I assume a somewhat simple programming issue, but I've been struggling with it. Mostly because I don't know the right words to use, perhaps?
Given a set of "ranges" (in the form of 1-a set of numbers as below, 2-IRanges, or 3-GenomicRanges), I'd like to split it into a set of smaller ranges.
Example Beginning:
Chr Start End
1 1 10000
2 1 5000
Example size of breaks: 2000
New dataset:
Chr Start End
1 1 2000
1 2001 4000
1 4001 6000
1 6001 8000
1 8001 10000
2 1 2000
2 2001 4000
2 4001 5000
I'm doing this in R. I know I could generate these simply with seq, but I'd like to be able to do it based on a list/df of regions instead of having to manually do it every time I have a new list of regions.
Here's an example I've made using seq:
Given 22 chromosomes, loop through them and break each into pieces
# initialize df
Regions <- data.frame(Chromosome = c(), Start = c(), End = c())
# for each row, do the following
for(i in 1:nrow(Chromosomes)){
# create a sequence from the minimum start to the max end by some value
breks <- seq(min(Chromosomes$Start[Chromosomes$Chromosome == i]), max(Chromosomes$End[Chromosomes$Chromosome == i]), by=2000000)
# put this into a dataframe
database <- data.frame(Chromosome = i, Start = breks, End = c(breks[2:length(breks)]-1, max(Chromosomes$End[Chromosomes$Chromosome == i])))
# bind with what we already have
Regions <- rbind(Regions, database)
rm(database)
}
This works fine, I'm wondering if there is something built into a package already to do this as a one-liner OR that is more flexible, as this has its limitations.

Answer 1

Using the R / Bioconductor package GenomicRanges, here are your initial ranges
library(GenomicRanges)
rngs = GRanges(1:2, IRanges(1, c(10000, 5000)))
and then create a sliding window across the genome, generated first as a list (one set of tiles per chromosome) and then unlisted for the format you have in your question
> windows = slidingWindows(rngs, width=2000, step=2000)
> unlist(windows)
GRanges object with 8 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] 1 [ 1, 2000] *
[2] 1 [2001, 4000] *
[3] 1 [4001, 6000] *
[4] 1 [6001, 8000] *
[5] 1 [8001, 10000] *
[6] 2 [ 1, 2000] *
[7] 2 [2001, 4000] *
[8] 2 [4001, 5000] *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
Coerce from / to a data.frame with as(df, "GRanges") or as(unlist(tiles), "data.frame").
Find help at ?"slidingWindows,GenomicRanges-method" (tab completion is your friend, ?"slidingW<tab>).
Embarrassingly, this seems to be implemented only in the 'devel' version of GenomicRanges (v. 1.25.93?); tile does something similar but rounds the width of ranges to be approximately equal while spanning the width of the GRanges. Here is a poor-man's version
windows <- function(gr, width, withMcols=FALSE) {
starts <- Map(seq, start(rngs), end(rngs), by=width)
ends <- Map(function(starts, len) c(tail(starts, -1) - 1L, len),
starts, end(gr))
seq <- rep(seqnames(gr), lengths(starts))
strand <- rep(strand(gr), lengths(starts))
result <- GRanges(seq, IRanges(unlist(starts), unlist(ends)), strand)
seqinfo(result) <- seqinfo(gr)
if (withMcols) {
idx <- rep(seq_len(nrow(gr)), lengths(starts))
mcols(result) = mcols(gr)[idx,,drop=FALSE]
}
result
}
invoked as
> windows(rngs, 2000)
If the approach is useful, consider asking follow-up questions on the Bioconductor support site.