Reducing and aggregating GRanges with gaps using plyranges
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@rapolicastro-24308
Last seen 15 months ago

Hello all,

I am trying to use plyranges to do a strand specific reduction and aggregation of score with gaps allowed. This is conceptually similar to section 4.1 in the HelloRanges tutorial, except with using the max.gapwidth argument in GenomicRanges::reduce. The closest function I see in plyranges is reduce_ranges_directed, but this does not allow gaps.

This question was posted yesterday in Biostars as well, but a consensus could not be reached on a best method.

Example data.

library("plyranges")

df <- data.frame(
  seqnames="chrI", start=c(1, 10, 20), end=c(5, 15, 25), strand=c("+", "+", "-"),
  score=c(8, 3, 6)
)
gr <- as_granges(df)

> gr
GRanges object with 3 ranges and 1 metadata column:
      seqnames    ranges strand |     score
         <Rle> <IRanges>  <Rle> | <integer>
  [1]     chrI       1-5      + |         8
  [2]     chrI     10-15      + |         3
  [3]     chrI     20-25      - |         6
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Example of desired output with max allowed gap width of 10 and summing the scores for the aggregation in this example.

desired_output <- data.frame(
  seqnames="chrI", start=c(1, 20), end=c(15, 25), strand=c("+", "-"),
  score=c(11, 6)
)
desired_output <- as_granges(desired_output)

> desired_output
GRanges object with 2 ranges and 1 metadata column:
      seqnames    ranges strand |     score
         <Rle> <IRanges>  <Rle> | <numeric>
  [1]     chrI      1-15      + |        11
  [2]     chrI     20-25      - |         6
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Cheers!

GenomicRanges plyranges • 266 views
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