Find hits of subject that start somewhere in the query by using GRanges / IRanges and findOverlap()
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0
Entering edit mode
svenbioinf • 0
@svenbioinf-11239
Last seen 8 weeks ago
Münster

Using findOverlaps() on a GRanges object I would like to retrive the following hits:

 

Sub:  -------|||||||||||||------------------

Query Ranges:

Hit5: ---------||||||||||||||||||------------

Hit6: -----------|||||||||||||||||||---------

Hit4: ---------|||||||---------------------

.

.

.

That means hits that start in a subject range and may or may not extend over it.

Minimal example:

> sub <- GRanges(c(1),strand=Rle(c("+"),c(1)), IRanges(c(5), c(7)),mcols=data.frame(id=c("T1")))

> sub
GRanges object with 1 range and 1 metadata column:
      seqnames    ranges strand | mcols.id
         <Rle> <IRanges>  <Rle> | <factor>
  [1]        1    [5, 7]      + |       T1
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
> query <- GRanges(c(1,1,1,1,1,1),strand=Rle(c("+","+","+","+","+","+"),c(1,1,1,1,1,1)), IRanges(c(4,4,6,6,7,7), c(5,5,6,6,8,8)),mcols=data.frame(id=c("T8","T9","T10","T11","T12","T13")))
> query
GRanges object with 6 ranges and 1 metadata column:
      seqnames    ranges strand | mcols.id
         <Rle> <IRanges>  <Rle> | <factor>
  [1]        1    [4, 5]      + |       T8
  [2]        1    [4, 5]      + |       T9
  [3]        1    [6, 6]      + |      T10
  [4]        1    [6, 6]      + |      T11
  [5]        1    [7, 8]      + |      T12
  [6]        1    [7, 8]      + |      T13
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

 

I tried with countOverlaps type= "start" but that only gives me hits that start at the exact same position.

> sum(countOverlaps(query,sub))
[1] 6
> sum(countOverlaps(query,sub,type="start"))
[1] 0

 

There must be a way, thanks for looking into that!

IRanges GRanges findoverlaps R • 710 views
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@michael-lawrence-3846
Last seen 5 months ago
United States
findOverlaps(start(query), subject)

 

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Hi Michael! Oh, I understand what you are doing here!
However:

findOverlaps(start(query), subject)

Here, subject has to be a IRanges object that doesnt account for strand information.  So by ranges(sub) I get the IRanges and now I have to take care of the strand information myself.

 

This is a nice solution, thank you very much Michael!

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Entering edit mode

Sorry, here is a better way for GRanges:

findOverlaps(resize(query, 1L), subject)
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