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.

Yes, you were right about test.venn[4, 4:5]. For test.venn[4,3], i.e., 97680 is the sum of the minimal number of involved peaks in each group of connected/overlapped peaks.

If you run test.venn <- findOverlapsOfPeaks(atac1, atac2, connectedPeaks="min"), you will get 97680.

For more information about this function, please type help(findOverlapsOfPeaks)

We will update the help menu soon as the following. Please let us know if the following help menu is clear. Any suggestions are welcome and appreciated.

connectedPeaks

If multiple peaks are involved in any group of connected/overlapping peaks in any input peak list, set it to "merge" will add 1 to the overlapping counts, while set it to "min" will add the minimal involved peaks in each group of connected/overlapped peaks to the overlapping counts. Set it to "keepAll" will add the number of involved peaks for each peak list to the corresponding overlapping counts. In addition, it will output counts as if connectedPeaks were set to "min".

Thanks!

Best regards,

Julie

Thanks! We will add your example to the help menus and add a link to this post so that you get credit for this.

Please feel free to change totalTest to a large number. I agree with you that it is not easy to come up with a good estimate. Table 1 at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202292 might help you set the totalTest.

Alternatively, you can use the function peakPermTest. Please type help(peakPermTest) for parameter settings and refer the user guide for examples at https://www.bioconductor.org/packages/devel/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.html#perform-permutation-test-to-determine-if-there-is-a-significant-overlap-between-two-sets-of-peaks.

Best,

Julie

Thanks! We will add your example to the help menus and add a link to this post so that you get credit for this.

Please feel free to change totalTest to a large number. I agree with you that it is not easy to come up with a good estimate. Table 1 at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202292 might help you set the totalTest.

Alternatively, you can use the function peakPermTest. Please type help(peakPermTest) for parameter settings and refer the user guide for examples at https://www.bioconductor.org/packages/devel/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.html#perform-permutation-test-to-determine-if-there-is-a-significant-overlap-between-two-sets-of-peaks.

Best,

Julie