voomWithQualityWeightsAndOffset: Implementation of 'limma::voomWithQualityWeights()' that uses...

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

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

Description

This is a combination of limma::voomWithQualityWeights() and voomWithOffset().

Usage

voomWithQualityWeightsAndOffset(
  counts,
  design = NULL,
  offset,
  normalize.method = "none",
  plot = FALSE,
  span = 0.5,
  var.design = NULL,
  method = "genebygene",
  maxiter = 50,
  tol = 1e-10,
  trace = FALSE,
  replace.weights = TRUE,
  col = NULL,
  ...
)

Arguments

counts, design, normalize.method, span, plot, var.design, method, maxiter, tol, trace, replace.weights, col, ...	These arguments have the same meaning as in limma::voomWithQualityWeights().
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 with weights, like that returned by limma::voomWithQualityWeights(), 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 voomWithQualityWeights

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