ChIPpeakAnno findVennCounts
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
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 >>
ChIPpeakAnno ChIPpeakAnno • 618 views
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Ying Wu ▴ 10
@ying-wu-5193
Last seen 6.4 years ago
United States
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 >>> > >
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
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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 >>>> >> >>
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