Re: Question about ChipPeaksAnno and intersect

Brad,

Thanks for the feedback! Could you please send us the input files WT312,
WT313?

I assume that you are aware of the two parameters you can tune.

maxgap    
Non-negative integer. Intervals with a separation of maxgap or less are
considered to be overlapping, default 0

Minoverlap
Non-negative integer. Intervals with an overlapping of minoverlap or more
are considered to be overlapping, default to 1

For future correspondence, could you please keep the discussion in the
bioconductor list so others can contribute or benefit? Thanks!

Best regards,

Julie

On 8/13/14 12:55 PM, "Brad Davis" <bdavis-9/[email protected]> wrote:

> Hi Julie,
> 
> I have a question about ChipPeaksAnno and how it calculates the size of an
> intersection between two bed files.  I have read in a few BED files that
> contain the locations of histone mark enriched regions as follows:
> 
> WT312 = 
> BED2RangedData(data.BED="A34082.H3K4me3.WT312.Thyroid.BED.sorted.collapsed.1")
> WT313 = 
> BED2RangedData(data.BED="A34089.H3K4me3.WT313.Thyroid-Adenoma-Follicular.BED.s
> orted.collapsed.1")
> WT340 = 
> BED2RangedData(data.BED="A34381.H3K4me3.WT340.Thyroid.BED.sorted.collapsed.1")
> WT341 = 
> BED2RangedData(data.BED="A34388.H3K4me3.WT341.Thyroid-Adenoma-Follicular.BED.s
> orted.collapsed.1")
> WT354 = 
> BED2RangedData(data.BED="A34707.H3K4me3.WT354.Thyroid.BED.sorted.collapsed.1")
> WT355 = 
> BED2RangedData(data.BED="A34714.H3K4me3.WT355.Thyroid-Goiter.BED.sorted.collap
> sed.1")
> 
> and then I use the makeVennDiagram package to actually display various
> comparisons. for example WT312 vs WT313
> 
> makeVennDiagram(RangedDataList(WT312, WT313), NameOfPeaks=c("WT312", "WT313"),
> totalTest=1000000, fill=brewer.pal(n=3, "Set1")[1:2], col=brewer.pal(n=3,
> "Set1")[1:2])
> 
> However, the size of the overlapping region returned by ChipPeakAnno is
> different than what I get from using
> 
> bedops -i A34082.H3K4me3.WT312.Thyroid.BED.sorted.collapsed.1
> A34089.H3K4me3.WT313.Thyroid-Adenoma-Follicular.BED.sorted.collapsed.1 | wc -l
> 
> or
> 
> bedtools intersect -a A34082.H3K4me3.WT312.Thyroid.BED.sorted.collapsed.1 -b
> A34089.H3K4me3.WT313.Thyroid-Adenoma-Follicular.BED.sorted.collapsed.1 | wc -l
> 
> But I don't understand why that would be.  I know I've seen a bit of a
> discussion about this before, but I can't find it anywhere now.
> 
> Do you have an explanation for this difference in behaviour?  If I recall
> correctly it has something to do with if a region in bed file A intersects
> with multiple regions in bed file B, but I'm not certain.
> 
> Thanks,
> Brad
> 

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