voomWithOffset: Implementation of 'limma::voom()' that uses an offset matrix

In DarwinAwardWinner/rctutils: Utility functions by Ryan C. Thompson

Implementation of limma::voom() that uses an offset matrix

Description

Unlike limma::voom(), this function can use an offset matrix instead of normalization factors. This is useful for using limma with gene-level estimated counts from Salmon or Kallisto, for which an offset matrix can be produced from the effective gene lengths.

Usage

voomWithOffset(
  counts,
  design = NULL,
  offset,
  normalize.method = "none",
  span = 0.5,
  plot = FALSE,
  save.plot = FALSE,
  ...
)

Arguments

counts, design, normalize.method, span, plot, save.plot, ...	These arguments have the same meaning as in limma::voom().
offset	An offset matrix to be used in computing log2 CPM values. This is optional only if counts is a edgeR::DGEList().

Value

An EList object like that returned by limma::voom(), but with log2 CPM values computed using the offset matrix.

If counts is a DGEList object that does not contain an offset matrix, one will be generated from the normalized library sizes, yielding identical behavior to limma::voom(). Hence, this is generally usable as a drop-in replacement for limma::voom().

See Also

edgeR::getOffset()

Examples

# TODO: Copy from voom

DarwinAwardWinner/rctutils documentation built on July 22, 2022, 5:19 a.m.