[Bioc-devel] Merging GInteraction/GenomicInteractions ranges
Aaron Lun
|n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Wed Feb 13 12:34:44 CET 2019
Note that your visual won't show up for many (all?) of us. Nonetheless,
I think I know what you want to do.
Your task does not lend itself to vectorization, which makes it
difficult to write efficient R code. It's not impossible, but it would
be quite hard to read and debug, and your maintenance programmer will
be cursing you somewhere down the line.
If speed is truly a concern, I would write this code in C++. This would
probably be several lines' worth of code:
1. Compute a pair of bin IDs for each interaction by dividing each
anchor coordinate by the bin width and truncating the result. (You'll
need to decide if you want to use the midpoint/start/end, etc.)
2. Sort the interactions by the paired bin IDs, e.g., with std::sort.
3. Identify each "run" of interactions with the same paired IDs.
4. Repeat step 1 within each run (you'll need to offset the anchor
coordinate before dividing this time). Append the current quadrant to
the quadrant sequence for return to R at the end of recursion.
Clear, concise, and can be slapped together in less than half an hour
with Rcpp and C++11, if you know what you're doing.
-A
On Tue, 2019-02-12 at 11:34 -0800, Luke Klein wrote:
> Hello. I am planning to develop a new package which extends the
> GenomicInteractions package. I would like some help/advice on
> implementing the following functionality.
>
> Consider the follow GenomicInteractions object
>
> GenomicInteractions object with 10 interactions and 1 metadata
> column:
> seqnames1 ranges1 seqnames2 ranges2 | counts
> <Rle> <IRanges> <Rle> <IRanges> | <integer>
> [1] chrA 1-2 --- chrA 9-10 | 1
> [2] chrA 1-2 --- chrA 15-16 | 1
> [3] chrA 3-4 --- chrA 3-4 | 1
> [4] chrA 5-6 --- chrA 7-8 | 1
> [5] chrA 5-6 --- chrA 9-10 | 1
> [6] chrA 7-8 --- chrA 7-8 | 1
> [7] chrA 7-8 --- chrA 11-12 | 1
> [8] chrA 7-8 --- chrA 17-18 | 1
> [9] chrA 9-10 --- chrA 9-10 | 1
> [10] chrA 9-10 --- chrA 15-16 | 1
> -------
> regions: 8 ranges and 0 metadata columns
> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
>
> Which is visually represented thusly
>
>
>
> I would like to do the following:
>
> 1) I want to group the regions into bins of WxW (in this case, W will
> be 3), as in a quad-tree structure <https://en.wikipedia.org/wiki/Qua
> dtree> with the final group being WxW (instead of 2x2). This will
> involve
> - iteratively dividing the matrix into quadrants {upper-left
> (0), upper-right (1), lower-left (2), lower-right(3)} .
> - labeling each subdivision in a new column until the final WxW
> resolution is reached.
> - sorting by the columns
>
>
>
>
> GenomicInteractions object with 10 interactions and 1 metadata
> column:
> seqnames1 ranges1 seqnames2 ranges2
> | counts quad1 quad2
> <Rle> <IRanges> <Rle> <IRanges> | <integer>
> <integer> <integer>
> [1] chrA 1-2 --- chrA 9-10 | 1
> 0 1
> [2] chrA 1-2 --- chrA 15-16 | 1
> 1 0
> [3] chrA 3-4 --- chrA 3-4 | 1
> 0 0
> [4] chrA 5-6 --- chrA 7-8 | 1
> 0 1
> [5] chrA 5-6 --- chrA 9-10 | 1
> 0 1
> [6] chrA 7-8 --- chrA 7-8 | 1
> 0 3
> [7] chrA 7-8 --- chrA 11-12 | 1
> 0 3
> [8] chrA 7-8 --- chrA 17-18 | 1
> 1 2
> [9] chrA 9-10 --- chrA 9-10 | 1
> 0 3
> [10] chrA 9-10 --- chrA 15-16 | 1
> 1 2
> -------
> regions: 8 ranges and 0 metadata columns
> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
>
> Sorting by the two columns yields what I am after. Of course, I
> include the “quadX” column for illustration only. Upon
> implementation, I would like these columns hidden from the user.
>
> GenomicInteractions object with 10 interactions and 1 metadata
> column:
> seqnames1 ranges1 seqnames2 ranges2
> | counts quad1 quad2
> <Rle> <IRanges> <Rle> <IRanges> | <integer>
> <integer> <integer>
> [1] chrA 3-4 --- chrA 3-4 | 1
> 0 0
> [2] chrA 1-2 --- chrA 9-10 | 1
> 0 1
> [3] chrA 5-6 --- chrA 7-8 | 1
> 0 1
> [4] chrA 5-6 --- chrA 9-10 | 1
> 0 1
> [5] chrA 7-8 --- chrA 7-8 | 1
> 0 3
> [6] chrA 7-8 --- chrA 11-12 | 1
> 0 3
> [7] chrA 9-10 --- chrA 9-10 | 1
> 0 3
> [8] chrA 1-2 --- chrA 15-16 | 1
> 1 0
> [9] chrA 7-8 --- chrA 17-18 | 1
> 1 2
> [10] chrA 9-10 --- chrA 15-16 | 1
> 1 2
> -------
> regions: 8 ranges and 0 metadata columns
> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
> The sorting gives me the quad-tree structure, and each unique
> quadrant sequence defines the group.
>
>
> GenomicInteractions object with 10 interactions and 1 metadata
> column:
> seqnames1 ranges1 seqnames2 ranges2 | counts
> <Rle> <IRanges> <Rle> <IRanges> | <integer>
> [1] chrA 3-4 --- chrA 3-4 | 1
> [2] chrA 1-2 --- chrA 9-10 | 1
> [3] chrA 5-6 --- chrA 7-8 | 1
> [4] chrA 5-6 --- chrA 9-10 | 1
> [5] chrA 7-8 --- chrA 7-8 | 1
> [6] chrA 7-8 --- chrA 11-12 | 1
> [7] chrA 9-10 --- chrA 9-10 | 1
> [8] chrA 1-2 --- chrA 15-16 | 1
> [9] chrA 7-8 --- chrA 17-18 | 1
> [10] chrA 9-10 --- chrA 15-16 | 1
> -------
> regions: 8 ranges and 0 metadata columns
> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
>
> 2) Then I would like to merge the WxW window (i.e. bin the regions),
> expanding the ranges accordingly and adding the counts.. This
> process will
> - ***identify all range-pairs in the same window and merge them
> into a new range pair with appropriately expanded ranges*** (this is
> my primary goal)
> - sum the counts for each of the aforementioned range-pairs (i
> have already figured a way to do this)
>
>
>
> GenomicInteractions object with 5 interactions and 1 metadata column:
> seqnames1 ranges1 seqnames2 ranges2 | counts
> <Rle> <IRanges> <Rle> <IRanges> | <integer>
> [1] chrA 1-6 --- chrA 1-6 | 1
> [2] chrA 1-6 --- chrA 7-12 | 3
> [3] chrA 7-12 --- chrA 7-12 | 3
> [4] chrA 1-6 --- chrA 13-18 | 1
> [5] chrA 7-12 --- chrA 13-18 | 2
> -------
> regions: 3 ranges and 0 metadata columns
> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>
>
> NOTE that ranges1 and ranges2 MUST expand so that the region width is
> 6, though the counts will only change if there exists another
> subrange covered by this bin/expansion that contains a positive
> count.
>
> As always, speed in a concern.
>
> Best,
>
> — Luke Klein
> PhD Student
> Department of Statistics
> University of California, Riverside
> lklei001 using ucr.edu
>
>
>
>
>
>
>
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