Hello, Does anyone know how number of overlapping peaks are counted when using finOverlapsOfPeaks with connectedPeaks="keepAll" here is the arguments that I used:

```
test.venn <- findOverlapsOfPeaks(atac1, atac2, connectedPeaks="keepAll")
```

and the resulting venn counts:

```
test.venn$venn_cnt
atac1 atac2 Counts count.atac1 count.atac2
[1,] 0 0 0 0 0
[2,] 0 1 42635 0 42635
[3,] 1 0 30492 30492 0
[4,] 1 1 97680 98808 102493
```

I know in `test.venn[4,]`

, `count.atac2`

is the number of overlap using `atac2`

as reference and `count.atac1`

is the number of overlap using `atac1`

as reference. However, I can't figure out where `Counts=97680`

comes from.

Thank you in advance for your help.

Thank you very much for answering my questions. I am very sorry but I'm still confused. What does " the sum of the minimal number of involved peaks in each group of connected/overlapped peaks" means?

For example: If 5 peaks in group1 are overlapping with 2 peaks in group 2, does setting connectedPeaks to "min" will add 2 to the overlapping counts?

Yes, you were right! 2 will be added to the overlapping counts.

Best regards,

Julie

Ah...ok. I think I start to understand.

That means, if 5 peaks in group1 are overlapping with 2 peaks in group 2, setting connectedPeaks to "merge" will add 1 to the overlapping counts? For "keepAll", 5 peaks will be added to count.group1 and 2 will be added to count.group2 and 2 will be added to counts?

Exactly! You nailed it!

Do you mind if we add your examples to the help menus?

Thanks!

Best regards,

Julie

Of course you can add my examples to the help menus. That'd be cool :-)

Thank you so much for all your efforts to keep the documentation clear and up to date. I really appreciate this.

As you may have guessed, I am using your package to analyze ATAC-seq data. Any plan to extend the package for ATAC-seq or at least the

`makeVennDiagram`

? I found test for overlap to be very useful. However, the default`totalTest`

estimate is too small for accessibility regions and I can't figure out a similar estimate for accessible regions.