limmaDS: Differential expression analysis using limma on the...
In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

limmaDS

R Documentation

Differential expression analysis using limma on the server-side

Description

Performs differential expression analysis using LIMMA

Usage

limmaDS(
  Set,
  variable_names,
  covariable_names,
  type,
  contrasts,
  levels,
  coef,
  sva,
  annotCols,
  method,
  robust,
  normalization,
  voomQualityWeights,
  big,
  sort.by
)

Arguments

`Set`	either a `ExpressionSet` or a `RangedSummarizedExperiment`
`variable_names`	grouping variable used to perform differential expression analysis
`covariable_names`	name of variables used in the adjusted models
`type`	...
`contrasts`	...
`levels`	...
`coef`	...
`sva`	should differential expression analysis be adjusted by SVA?
`annotCols`	variables from the annotation data used in the output
`method`	String indicating the method used in the regression (e.g. lmFit function of limma: "ls" or "robust". (Default: "ls")
`robust`	Logical value indicating whether robust method is applied in the eBayes function of limma. Default is FALSE.
`normalization`	String indicating the normalize method used when using voom for RNAseq data (see normalized.method argument in limma::vomm)
`voomQualityWeights`	Logical value indicating whether limma::voomWithQualityWeights should be used instead of limma::voom.
`big`	Logical value indicating whether SmartSVA should be used instead of SVA (TRUE recommended for methylation or when having large number of samples).