I've been trying to generate a set of high-confidence peaks that are common
to my ChIP-seq replicates using ChipPeakAnno. The issue I'm having is
matching the number of overlaping peaks seen on the venn digram resulting
from:
makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1","TF2"),
        totalTest=(Npeaks1 + Npeaks2), useFeature=FALSE, minoverlap = 100,
select= "first")

and the number of peaks ($MergedPeaks) from:
findOverlappingPeaks(peaks1, peaks2, minoverlap = 100, select= "first",
NameOfPeaks1="TF1", NameOfPeaks2="TF2")

I believe the difference is because some of peaks 2 overlap more than peaks
in peaks1. Comparing peaks2 vs peaks one does not solve the problem and
select= "first" is already being used. Also the $MergedPeaks data that is
outputted from makeVennDiagram does not match the number of overlaps:
$MergedPeaks
RangedData with 18650 rows and 0 value columns across 24 spaces

[1] 19039
[1] 21061
$p.value
[1] 0

$vennCounts
     Replicate1 Replicate2 Counts
[1,]          0          0  17300
[2,]          0          1   3761
[3,]          1          0   1739
[4,]          1          1  17300
attr(,"class")
[1] "VennCounts"


I would like to understand from where does this difference arises so that I
ultimately have consistent results in visual and table format.

Cheers,
António


-- 
-- 
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
Pfotenhauerstrasse 108
01307 Dresden
Germany

e-mail: domingue@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

	[[alternative HTML version deleted]]

