Entering edit mode
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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