[BioC] ChIPpeakAnno 2.12.2 bug

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Wed Aug 13 23:47:15 CEST 2014


Many thanks for helping us identifying the bug introduced in 2.12.2! The bug has been fixed in version 2.13.1. Please let me know if you have any issues.

For future correspondence, could you please keep the discussion in the bioconductor list so others can contribute or benefit? Thanks!

Best regards,


On 8/13/14 1:18 PM, "Zinkgraf, Matthew S -FS" <mszinkgraf at fs.fed.us> wrote:

Hello Julie
I recently updated ChIPpeakAnno from version 2.10 to 2.12.2 and I am getting incorrect results from annotatePeakInBatch.
More specifically the output column ‘insideFeature’ is not taking feature strand into account when it is assigning peaks to gene features, the function thinks all gene features are on the positive strand even though my genome ranged data contains strand information. Also all other calculations from annotatePeakInBatch gives the same results as in 2.10.

Please let me know if you would like more information about the bug I am getting.



Matthew S. Zinkgraf, PhD
Postdoctoral Researcher
USDA, Forest Service
Davis, CA 95618
mszinkgraf at fs.fed.us <mailto:mszinkgraf at fs.fed.us>

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