findOverlapsOfPeaks() of package ChIPpeakAnno in R

Question

[salamandra]

When running the following code with ChIPpeakAnno package in R:

gr3 = GRanges(seqnames = c("chr1"), strand = c("+","+","+"), ranges = IRanges(start = c(1,3,5), width = 3))
gr3
> gr3
GRanges object with 3 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1    [1, 3]      +
  [2]     chr1    [3, 5]      +
  [3]     chr1    [5, 7]      +
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
gr4 = GRanges(seqnames = c("chr1"), strand = c("+","+","+","+"), ranges = IRanges(start = c(2,4,6,8), width = 3))
gr4
> gr4
GRanges object with 4 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]     chr1   [2,  4]      +
  [2]     chr1   [4,  6]      +
  [3]     chr1   [6,  8]      +
  [4]     chr1   [8, 10]      +
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

In gr4, the interval:

[4]     chr1   [8, 10]      +

doesn't intersect with intervals in gr3, so it's an interval of gr4 alone, but when we do:

ol1 <- findOverlapsOfPeaks(gr3, gr4)
ol1$venn_cnt
> ol1$venn_cnt
     gr3 gr4 Counts
[1,]   0   0      0
[2,]   0   1      0
[3,]   1   0      0
[4,]   1   1      3
attr(,"class")
[1] "VennCounts"

there is no interval in gr4 alone (zero counts in 2nd row) When I do the same inverting the order:

ol2 <- findOverlapsOfPeaks(gr4, gr3)
 ol2$venn_cnt
> ol2$venn_cnt
         gr4 gr3 Counts
    [1,]   0   0      0
    [2,]   0   1      0
    [3,]   1   0      0
    [4,]   1   1      3
    attr(,"class")
    [1] "VennCounts"

the same happens.

Shouldn't there be 1 count for gr4 only? What am I interpreting wrong?

Answer 1

[hukai916]

I agree with your interpretations, actually, the newer versions of ChIPpeakAnno already fix this problem:

library(ChIPpeakAnno)
packageVersion("ChIPpeakAnno")

gr3 = GRanges(seqnames = c("chr1"), strand = c("+","+","+"), ranges = IRanges(start = c(1,3,5), width = 3))
gr4 = GRanges(seqnames = c("chr1"), strand = c("+","+","+","+"), ranges = IRanges(start = c(2,4,6,8), width = 3))

ol1 <- findOverlapsOfPeaks(gr3, gr4)
ol2 <- findOverlapsOfPeaks(gr4, gr3)
ol1$venn_cnt
ol2$venn_cnt

Here are the output:

> packageVersion("ChIPpeakAnno")
[1] '3.25.1'
> ol1$venn_cnt
     gr3 gr4 Counts count.gr3 count.gr4
[1,]   0   0      0         0         0
[2,]   0   1      1         0         1
[3,]   1   0      0         0         0
[4,]   1   1      3         3         3
> ol2$venn_cnt
     gr4 gr3 Counts count.gr4 count.gr3
[1,]   0   0      0         0         0
[2,]   0   1      0         0         0
[3,]   1   0      1         1         0
[4,]   1   1      3         3         3

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