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Using accessor method of DESeq2 in rpy2

I am trying to use DESeq2 package through rpy2. Overall, it works fine, but I am struggling with using accessor function. Specifically, I have a sample data frame tcdf and counts data frame access_tcdf that I convert to R objects by 

rtcdf = pandas2ri.py2ri_pandasdataframe(tcdf)
raccess_tcdf = pandas2ri.py2ri_pandasdataframe(access_tcdf)

and I create a DESeq_DataSet by 

ddsMat = deseq2.DESeqDataSetFromMatrix(countData = raccess_tcdf,
                              colData = rtcdf,
                              design = Formula("~ replicate + strain + time"))

The sticking point is how I can supply predefined normalization factors in rpy2? I have a data frame of per gene normalization factors rnorm_factor and in R I would normally do: 

normalizationFactors( ddsMat ) <- data.matrix(norm_factor)

but I don't understand how and if I can call normalizationFactors function from rpy2.

When I tried:

deseq2.normalizationFactors(ddsMat,bdm)

I got RRuntimeError: 

 Error in .local(object, ...) : 
 unused argument (c(0.401314864917528, 0.375673211527775, ...

I would appreciate suggestions on how to do this.

Solution

  • What is happening in R is that the call

    normalizationFactors( ddsMat ) <- data.matrix(norm_factor)

    is equivalent to

    ddsMat <- `normalizationFactors<-`(ddsMat, data.matrix(norm_factor))

    If this is just setting an attribute in an R S4 class instance you can use the strategy described in the documentation (https://rpy2.github.io/doc/v2.9.x/html/notebooks/s4class.html#class-attributes) otherwise the strategy used by rpy2 itself to implement names(foo) <- bar can be used (see here).