[Bioc-devel] Merging GInteraction/GenomicInteractions ranges
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 at 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 at ucr.edu
On Feb 13, 2019, at 3:34 AM, Aaron Lun <
infinite.monkeys.with.keyboards at 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 <
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 at ucr.edu
_______________________________________________ Bioc-devel at r-project.org <mailto:Bioc-devel at 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 at ucr.edu <mailto:lklei001 at ucr.edu> _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel