lfcShrink

lfcShrink is a function in the DESeq2 package, a Bioconductor tool for differential expression analysis of count data. It is used to shrink log2 fold-change estimates after fitting a model, with the aim of stabilizing noisy estimates for genes with low counts or high dispersion. By producing more reliable effect sizes, lfcShrink helps improve interpretation and ranking of differential expression results.

Shrinkage works by applying a prior distribution to the true log2 fold changes. Available methods include a normal-prior shrinkage (the default), apeglm shrinkage, and ashr shrinkage. The apeglm and ashr methods rely on external packages (apeglm and ashr) and can provide more accurate shrinkage in heterogeneous data; the normal method is a simpler approach that does not require extra packages.

Usage typically involves calling lfcShrink with a DESeqDataSet on which DESeq has been run, or with a precomputed results object. The user selects which log2 fold change to shrink via the coef parameter or by providing a contrast. The type argument specifies the shrinkage method: "normal", "apeglm", or "ashr". Additional arguments control behavior, but the function centers on shrinking the specified LFC.

Output is a DESeqResults object containing shrunk log2 fold changes in the log2FoldChange column, along with the corresponding lfcSE (standard error), and the existing p-values and padj if available. Shrunk estimates are intended for more stable interpretation of effect sizes and for constructing robust gene rankings.

Limitations include the fact that shrinkage alters LFC estimates and should be interpreted as shrunken effect sizes rather than raw estimates. It is not required for all analyses, and different shrinkage methods may yield different results.

See also: DESeq2, apeglm, ashr.