inmoose.deseq2.estimateDispersionsFit

inmoose.deseq2.estimateDispersionsFit(obj, fitType='parametric', minDisp=1e-08, quiet=False)

Low-level function to fit dispersion estimates

Normal users should instead use DESeqDataSet.estimateDispersions(). This low-level function is called by DESeqDataSet.estimateDispersions(), but is exported and documented for non-standard usage. For instance, it is possible to replace fitted values with a custom fit and continue with the maximum a posteriori dispersion estimate.

Parameters:

  • obj (DESeqDataSet) – the input dataset

  • fitType ("parametric", "local", "mean" or "glmGamPoi") – the type of fitting of dispersions to the mean intensity. See DESeqDataSet.estimateDispersions() for description.

  • minDisp (float) – small value for the minimum dispersion, to allow for calculations in log scale, one order of magnitude above this value is used as a test for inclusion in mean-dispersion fitting

  • quiet (bool) – whether to print messages at each step

Returns:

the input obj with fitted dispersion estimates

Return type:

DESeqDataSet