Hi Hua,

I hope that the dev version 1.3.10 now contains the feature both you and Khademul requested.
I have added an option output =c("nearestStart", "overlapping", "both") to annotatePeakInBatch. Default will be "nearestStart" which is compatible to the old version. The option "overlapping" will output the overlapping features. The option "both"  will output the nearest feature, as well as the overlapping features that are not the nearest feature according to the distance between TSS and peak start.

Khademul, per your suggestion, makeVennDiagram is also implemented in the dev version 1.3.10.

Please let me know how it works out for you. Thanks for the great suggestion!

Best regards,

Julie


On 3/15/10 5:42 PM, "Li, Hua" <HUL@stowers.org> wrote:

Julie:

I am guessing that the feature associated with each peak is the one that has the smallest distance between TSS and the peak start.

In the situation that a gene is long, the peak is close to the next gene rather than the it's own gene, the package gives the wrong information. Is there a way that I can get gene names on both sides of the peak?

Here is my testimony:

"ChIPpeakAnno  is a stand alone R package. The batch process of peaks is very useful, which gives the nearby genes associated with the peaks. When comparing peaks from different IP samples, this feature could quickly identify  genes that have peaks for different samples. It greatly facilitates my analysis."

Hua

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