This is code review for DESeq2 for my personal understanding

• core ........... most of the statistical code (example call below)

• fitNbinomGLMs .. three functions for fitting NB GLMs

• methods ........ the S4 methods (estimateSizeFactors, etc.)

• AllClasses ..... class definitions and object constructors

• AllGenerics .... the generics defined in DESeq2

• results ........ results() function and helpers

• plots .......... all plotting functions

• lfcShrink ...... log2 fold change shrinkage

• helper ......... unmix, collapseReplicates, fpkm, fpm, DESeqParallel

• expanded ....... helpers for dealing with expanded model matrices

• wrappers ....... the R wrappers for the C++ functions (mine)

• RcppExports .... the R wrappers for the C++ functions (auto)

• rlogTransformation ... rlog

• varianceStabilizingTransformation ... VST

• general outline of the internal function calls.

• note: not all of these functions are exported.

• DESeq

  • |- estimateSizeFactors
  • |- estimateSizeFactorsForMatrix
  • |- estimateDispersions
    • |- estimatedispersionsgeneest
    • |- fitnbinomglms
    • |- fitbeta (c++)
    • |- fitdisp (c++)
    • |- estimatedispersionsfit
    • |- estimatedispersionsmap
    • |- estimatedispersionpriorvar
    • |- fitdisp (c++)
    • |- nbinomwaldtest
    • |- fitglmswithprior
    • |- fitnbinomglms
    • |- fitbeta (c++)
    • |- estimatebetapriorvar
    • |- fitnbinomglms
    • |- fitBeta (C++)