User: Brad Davis

gravatar for Brad Davis
Brad Davis20
Reputation:
20
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New User
Location:
Canada
Last seen:
4 years, 8 months ago
Joined:
7 years, 3 months ago
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b**********@gmail.com

Posts by Brad Davis

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Answer: A: Get ChIPpeakAnno to report total number of covered bases in VennDiagrams instead
... That would be perfect. ...
written 4.7 years ago by Brad Davis20
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Answer: A: Get ChIPpeakAnno to report total number of covered bases in VennDiagrams instead
... In the example posted below, the numbers in each of the sections of the venn diagram represent the number of overlapping regions (correct?).  What I would like is to report the total amount of coverage in terms of the number of base pairs in each of those sets of regions.    ...
written 4.7 years ago by Brad Davis20
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Get ChIPpeakAnno to report total number of covered bases in VennDiagrams instead of (or in addition to) regions
... Hi all, I was wondering if there is anyway to get ChIPpeakAnno to report the total number of covered bases (as opposed to the number of overlapping regions) when making use of makeVennDiagram()?  Is this possible? Would it be difficult to add this as a feature? Thanks, Brad  ...
chippeakanno written 4.7 years ago by Brad Davis20 • updated 4.7 years ago by Ou, Jianhong1.1k
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Comment: C: Curious behaviour of ChIPpeakAnno
... Hi Jianhong, I've tried the latest version of the code and worked through your example, but the numbers still do not add up correctly.  The total number of peaks in the two way venn diagram (i.e. both for WT313_WT313_WT355 alone and the intersection between WT313_WT341_WT355 and WT312_WT340_WT354)  ...
written 4.9 years ago by Brad Davis20
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Comment: C: Curious behaviour of ChIPpeakAnno
... Hi Jianhong, Thank you for your quick response. I have installed the latest version of ChIPpeakAnno and I am trying out the example code you have provided me.   What is the best way for me to make the two three-way venn diagrams so that they are comparable with this two-way venn diagram?  My gut r ...
written 4.9 years ago by Brad Davis20
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Comment: C: Curious behaviour of ChIPpeakAnno
... Hi Jianhong, Thanks for pointing me to the latest development version of ChIPpeakAnno.  I am trying to use it but I have encountered what appears to be a bug.  While trying to use the function findOverlappingPeaks I get an error indicating that it cannot find the function .Deprecated.  I've pasted ...
written 4.9 years ago by Brad Davis20
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Answer: A: Curious behaviour of ChIPpeakAnno
... Hi Jianhong, It seems like this behaviour should be related to the 'select' parameter option in findOverlappingPeaks command?  If so, shouldn't there be a way to generate identical venn diagrams by setting the 'select' command to a defined argument, such as 'left'?   Also, would it be possible to ...
written 4.9 years ago by Brad Davis20
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Answer: A: Curious behaviour of ChIPpeakAnno
... Hello Jianhong, Thank you for your reply.  I understand your example and your point. Cheers, Brad ...
written 4.9 years ago by Brad Davis20
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Curious behaviour of ChIPpeakAnno
... Hello everyone, I am getting some surprising behaviour out of the ChIPpeakAnno R package.  The question I’m trying to ask is ‘Which features intersect between samples ‘WT312’, ‘WT340’, and ‘WT354’, that also intersect with the intersection between samples ‘WT313’, ‘WT341’, and ‘WT355’. To visualize ...
chippeakanno written 4.9 years ago by Brad Davis20 • updated 4.9 years ago by Ou, Jianhong1.1k
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Answer: A: ontoCompare
... Hi Oana, I suspect the problem is actually with GO.db rather than goTools. The problems I ran in to involved GO terms that were either deprecated or where alternate IDs for the main GO ID. My workaround for this was to take my list of GO ids and compare it to the list of deprecated GO terms , rem ...
written 7.2 years ago by Brad Davis20

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Popular Question 4.7 years ago, created a question with more than 1,000 views. For Curious behaviour of ChIPpeakAnno

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