[Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called From A Package

[Dario Strbenac]

Hello,

I am writing a package that has a function that uses estimateGLMRobustDisp, leading to an error :

Error in dispBinTrend(y, design, offset = offset, method.trend = "loess",  : 
  could not find function "loessFit"
Calls: edgeRselection ... estimateGLMTrendedDisp -> estimateGLMTrendedDisp.default -> dispBinTrend

I import estimateGLMRobustDisp from edgeR in my NAMESPACE file. This error is because edgeR depends on limma, rather than importing from it. I want to avoid using parent.env<- and .onLoad to get around the problem. Is there any hope of modifying the edgeR description file to have limma in the Imports field ?

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Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia