findOverlapsOfPeaks in ChIPpeakAnno R package

Question

[salamandra]

In value description of findOverlapsOfPeaks in the ChIPpeakAnno manual (R) it says:

peaklist: a list consists of all overlapping peaks or unique peaks

 uniquePeaks: an object of GRanges consists of all unique peaks

 mergedPeaks: an object of GRanges consists of all merged overlapping peaks

 peaksInMergedPeaks: an object of GRanges consists of all peaks in each samples involved in the overlapping peaks

 overlappingPeaks: a list of data frame consists of the annotation of all the overlapped peaks

 all.peaks: a list of GRanges object which contain the input peaks with formated rownames

What's the difference between "all overlapping peaks" given by the "peaklist", "all merged overlapping peaks" in "mergedPeaks" and "all peaks in each samples involved in the overlapping peaks"? Isn't this just different ways of saying regions of overlap between two groups of peaks?

Answer 1

[cvenkat95]

A late answer but hopefully, it helps:

PeakList --> gives the overall genomic region overlap and the peak IDs within them, but not in separate columns.

overlappingPeaks --> gives the overall genomic region overlap, and the peak names of all involved peaks in separate rows.

For example,

PeakList gives the peakNames for a row as c("Location1__X4344", "Location1__X4346", "Location2__Merged.chr16.89007066.1")

while,

overlappingPeaks gives the peakNames as two different rows, as below:

Merged.chr16.89007066.1_X4344 X4344 Merged.chr16.89007066.1_X4346 X4346

There are a bunch of other information in them too, but I have left them out here. Essentially, both gives the same results, but in different formats, so to speak.

As for the "mergedPeaks", I do not know.