[Bioc-devel] Merging GInteraction/GenomicInteractions ranges
Liz Ing-Simmons
||z@|ng@|mmon@ @end|ng |rom gm@||@com
Tue Feb 19 19:00:15 CET 2019
Hi Luke,
If I understand correctly what you want to do, you can use `findOverlaps()`
to create a new GInteractions object from a set of expanded ranges and the
original interactions.
anchor.one <- GRanges(c("chr1", "chr1", "chr1", "chr1"),
IRanges(c(10, 20, 30, 20), width=5))
anchor.two <- GRanges(c("chr1", "chr1", "chr1", "chr2"),
IRanges(c(100, 200, 200, 50), width=5))
interaction_counts <- sample(1:10, 4)
test <- GInteractions(anchor1 = anchor.one,
anchor2 = anchor.two,
counts=interaction_counts)
wider_ranges <- reduce(resize(regions(test), fix = "center", width = 10))
first_ol <- findOverlaps(test, wider_ranges, use.region = "first")
second_ol <- findOverlaps(test, wider_ranges, use.region = "second")
new_gi <- GInteractions(anchor1 = subjectHits(first_ol),
anchor2 = subjectHits(second_ol),
regions = wider_ranges,
counts = test$counts)
This will give you a GInteractions object that's the same length as your
original object. You said you already had a way of summing the counts for
each group of interactions, but you could also incorporate that here. I
would do it with dplyr, but I'm sure there's alternatives that introduce
fewer dependencies...
new_gi_info_df <- data.frame(anchor1 = subjectHits(first_ol),
anchor2 = subjectHits(second_ol),
counts = test$counts) %>%
dplyr::group_by(anchor1, anchor2) %>%
dplyr::summarise(counts = sum(counts))
best wishes,
Liz
On Tue, Feb 19, 2019 at 6:15 PM Luke Klein <lklei001 using ucr.edu> wrote:
> Thank you for the tip, Aaron! I’m working on the sorting step right now.
>
> One thing I’m not clear on is how to expand the ranges from one step to
> the next. The way GenomicInteractions are structured, there is a Granges
> object with all possible ranges, and the GInteractions object is populated
> by reference to said interactions.
>
> What I am going to need is a new GRanges object with the new set of
> (expanded) ranges, and a way to map the prior ranges to the new, wider
> range.
>
> For your edification, I’ve included the images in this email (which is
> addressed directly to you) so that you can see what I’d written in my first
> question.
>
> Best,
>
> — Luke Klein
> PhD Student
> Department of Statistics
> University of California, Riverside
> lklei001 using ucr.edu
>
>
>
>
>
>
>
> > On Feb 13, 2019, at 3:34 AM, Aaron Lun <
> infinite.monkeys.with.keyboards using gmail.com> wrote:
> >
> > 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 <
> 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
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel <
> https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>
> 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/Quadtree>
> 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 <mailto:lklei001 using ucr.edu>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list