[BioC] Question about ChipPeaksAnno and intersect
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Wed Aug 13 19:26:17 CEST 2014
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 at bcgsc.ca> 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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