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

[James W. MacDonald]

Hi Dario,

Isn't an easier fix to simply add

ImportFrom(limma, loessFit)

in your NAMESPACE file?

Best,

Jim


On 6/26/2014 12:00 AM, Dario Strbenac wrote:
> 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 ?
>
> -------------------------------------- Dario Strbenac PhD Student
> University of Sydney Camperdown NSW 2050 Australia
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099