[BioC] ChIPpeakAnno findVennCounts

[Zhu, Lihua (Julie)]

Ying,

Thank you so much for putting so much thought into this and for the great
ideas!

It is important to have the numbers add up correctly. For this reason, I
will take your first suggestion.

Best regards,

Julie


On 3/26/12 4:12 PM, "Ying Wu" <daiyingw at usc.edu> wrote:

> Dr Zhu,
> After thinking about this for a couple days, I think the best way is a
> combined approach where more documentation is added to makeVennDiagram
> by such as adding findOverlaps to 'See Also' section and exposing the
> select option in findOverlappingPeaks as well as giving a
> warning/explanation when negative numbers appear. I think making the
> values 0 would simplify things too much for the end-user.
> 
> Personally, I think the following approach would be best for venn
> diagram but would require more calculations and the numbers would not
> add up.
> 100, 010, 001 - regions/peaks exclusive to one bed file (NOT total-overlap)
> 110, 101, 011, 111 - min(overlap) where overlap is calculated both bed1
> -> bed2 and bed2->bed1.
> 
> One case where I think 0s would be appropriate (but are negative numbers
> right now) is when you compare the same file but I have not quite
> figured out why this occurs yet.
> 
> Best,
> Ying
> 
> On 3/23/2012 6:05 AM, Zhu, Lihua (Julie) wrote:
>> Dai-Ying,
>> 
>> Thanks for reporting this bug which happens when some of the peaks in a
>> dataset overlap with multiple peaks in another dataset! What do you think if
>> I set the number to 0 if it becomes negative? Thanks!
>> 
>> Best regards,
>> 
>> Julie
>> 
>> 
>> On 3/22/12 9:49 PM, "Dai-Ying Wu"<daiyingw at usc.edu>  wrote:
>> 
>>> Hi Dr Zhu,
>>> Please disregard the accessing findVennCounts() section of the last email.
>>> I have been able to reproduce the negative values in venn diagram with the
>>> following code
>>> 
>>> p1 = RangedData(IRanges(start=c(100, 500), end=c(199, 599), names=c("s1",
>>> "s2")
>>> p2 = RangedData(IRanges(start=c(110, 190, 320, 650), end=c(150, 199, 340,
>>> 680), names=c("s1", "s0", "s2", "s3")))
>>> p3 = RangedData(IRanges(start=c(130, 330, 530, 800), end=c(150, 350, 550,
>>> 900), names=c("s1", "s2", "s3", "s4")))
>>> vtest = makeVennDiagram(RangedDataList(p3, p2, p1), NameOfPeaks=c("p3",
>>> "p2",
>>> "p1"), totalTest=100)
>>> 
>>> if you flip the order around, it will not show negative numbers but the
>>> venncount will be incorrect
>>> vtest = makeVennDiagram(RangedDataList(p1, p2, p3), NameOfPeaks=c("p1",
>>> "p2",
>>> "p3"), totalTest=100)
>>> in this diagram, the overlap between p1 and p2 (110) should be 1 instead of
>>> 0
>>> and (010) should be 1 instead of 2
>>> 
>>> How do you advise I should proceed? Is there going to be a patch made to
>>> makeVennDiagram to make the counting more consistent? I am currently working
>>> on a dataset where I was looking at two replicates and pooled result and I
>>> was
>>> getting negative numbers in the pooled result which led to very strangely
>>> generated proportional venn diagrams.
>>> 
>>> Best,
>>> Ying
>>> 
>>> ----- Original Message -----
>>> From: Dai-Ying Wu<daiyingw at usc.edu>
>>> Date: Thursday, March 22, 2012 5:30 pm
>>> Subject: ChIPpeakAnno findVennCounts
>>> To: julie.zhu at umassmed.edu
>>> 
>>>> Hi Dr Zhu,
>>>> I have been trying to troubleshoot a venn diagram that I tried to
>>>> create with your very helpful ChIPpeakAnno software. I am trying to
>>>> create a 3-way venn diagram from 3 BED files and the 3rd comparison
>>>> gives a negative number. I have increased totaltest but that does
>>>> not seem to be the issue. I then try and debug it by going into the
>>>> code and try running it step by step, however, when i try to runb
>>>> findVennCounts it gives an "Error: object 'findVennCounts' not
>>>> found" and when I do "ChIPpeakAnno::findVennCounts" it gives not
>>>> exported object from 'namespace:ChIPpeakAnno'
>>>> 
>>>> If I do ?findVennCounts and try and use the example at the end of
>>>> the page but it gives the same error. I am currently using
>>>> ChIPpeakAnno 2.2.0
>>>> 
>>>> Thanks,
>>>> Ying Wu
>>>> 
>> 
>>