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super-seeded by #151 |
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This is related to #53 :
...arguments to pbDS that are passed to downstreamDESeq2::DESeqoredgeR::glmQLFitshrinkLFCargument to use DESeq2 logFC shrinkage (requires apeglm).edgeR::predFCwasn't included in the end because this isn't different from what the fitting method does, and just offers the option of changing the pseudocount downstream of the fit. This can now anyway be done because...exposes the pseudocount argument.Additionally, the default edgeR normalization was changed to TMMwsp.