User: Stefan Pinter

gravatar for Stefan Pinter
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6 years, 8 months ago
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6 years, 8 months ago
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p*****@molbio.mgh.harvard.edu

Posts by Stefan Pinter

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Comment: C: assignChromosomeRegion in 2.6.0 ChIPpeakAnno
... Hi Julie, maybe I'm misunderstanding something about this function. Below is what I've done as a positive control (using refseq genes as "peaks" compared to ensembl annotation), can you tell me whether these numbers make sense? I was expecting to see close to 100% overlap (according to bedtools clo ...
written 6.7 years ago by Stefan Pinter40
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Comment: C: assignChromosomeRegion in 2.6.0 ChIPpeakAnno
... Hi Julie, well, I was more thinking of something along the lines of either: a.) Over/Under-representation: Percentage of exons in genome = 2% Percentage of peaks overlapping exons = 10% Exons are 5-fold over-represented But I realize now, that will only work with a full annotation, not a custom a ...
written 6.7 years ago by Stefan Pinter40
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Comment: C: assignChromosomeRegion in 2.6.0 ChIPpeakAnno
... Sure, thank you Julie. Yes, that is what I meant. Since all the necessary information (peak locations, feature locations, total count, total length) are already available in RangedData & Annotation, it would be very convenient to calculate enrichment/depletion and possibly even significance sco ...
written 6.7 years ago by Stefan Pinter40
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Comment: C: assignChromosomeRegion in 2.6.0 ChIPpeakAnno
... Hi Julie, yes, that worked! Thank you for the quick help, I very much appreciate it! Thank you and Best wishes, - Stefan. ----- Original Message ----- From: "Lihua Zhu (Julie)" To: "Lihua Zhu (Julie)" , "Stefan Pinter" Cc: "" Sent: Thursday, March 14, 2013 8:50:51 PM Subject: Re: [BioC] assignC ...
written 6.7 years ago by Stefan Pinter40

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