DESeq2 on second set of rows using fixed priors

deseq2_fix_priors.R

library(DESeq2)
dds <- makeExampleDESeqDataSet()
dds_leaf <- dds[1:500,]
dds_inner <- dds[501:1000,]
dds_leaf <- DESeq(dds_leaf)
res_leaf <- lfcShrink(dds_leaf, coef="condition_B_vs_A", type="apeglm")

# this runs DESeq2 on inner nodes but using priors from leaves
sizeFactors(dds_inner) <- sizeFactors(dds_leaf)
dds_inner <- estimateDispersionsGeneEst(dds_inner)
dispersionFunction(dds_inner) <- dispersionFunction(dds_leaf) # skipping prior estimation
dds_inner <- estimateDispersionsMAP(dds_inner)
dds_inner <- nbinomWaldTest(dds_inner)

# this runs lfcShrink on inner nodes but using priors from leaves
pc <- attr(res_leaf, "priorInfo")$prior.control
res_inner <- lfcShrink(dds_inner, coef="condition_B_vs_A",
                       type="apeglm", apeAdapt=FALSE, prior.control=pc)