[BioC] [ChIPpeakAnno] - What's the "annotatePeakInBatch" function expected running time ?

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Thu Nov 10 19:47:55 CET 2011


For functionalities of ChIPpeakAnno, please refer to
PpeakAnno-BioC2011.pdf and
Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS and Green MR.
(2010)  ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and
ChIP-chip data. BMC Bioinformatics 2010, 11:237 which also gives an overview
of Bioconductor packages for ChIP-seq data analysis

There are several peak calling algorithms available in Bioconductor
http://bioconductor.org/packages/release/bioc/. In addition, there are other
peak calling algorithms outside of Bioconductor
Evaluation of Algorithm Performance in ChIP-Seq Peak Detection (Elizabeth et
al., 2010.PLoS one 5(7):e11471)
Laajala et al., 2009 A practical comparison of methods for detecting
transcription factor binding sites in ChIP-seq experiments. BMC
Bioinformatics 10:618 doi:10.1186/1471-2164-10-618

Best regards,


On 11/10/11 12:56 PM, "Halian Vilela" <halianlian at gmail.com> wrote:

> Julie, thanks for the fast answer.
> Yes, I was using the reads directly. Surely I misunderstood the kind of data
> the function should work with.
> What peak calling algorithm should I use then ? Are there any function to do
> this in your package ? If not, could you suggest me any (package) ?
> Thanks a lot.
> Halian

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