ds.limma: Server-side Differential Gene Expression analysis using limma
In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

ds.limma

R Documentation

Server-side Differential Gene Expression analysis using limma

Description

This function performs a non-disclosive Differential Gene Expression Analysis using limma package from Bioconductor.

Usage

ds.limma(
  model,
  Set,
  type.data = "microarray",
  contrasts = NULL,
  levels = "design",
  coef = 2,
  sva = FALSE,
  annotCols = NULL,
  method = "ls",
  robust = FALSE,
  normalization = "none",
  voomQualityWeights = FALSE,
  big = FALSE,
  sort.by = "none",
  datasources = NULL
)

Arguments

`model`	formula indicating the condition (left side) and other covariates to be adjusted for (i.e. condition ~ covar1 + ... + covar2). The fitted model is: feature ~ condition + covar1 + ... + covarN
`Set`	name of the DataSHIELD object to which the ExpresionSet or RangedSummarizedExperiment has been assigned
`type.data`	optional parameter that allows the user to specify the number of CPU cores to use during
`sva`	logical value
`annotCols`	the column names of the annotation available in the ExpresionSet or RangedSummarizedExperiment (see fData() function)
`method`	String indicating the method used in the regression: "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 for possible values) #' @param voomQualityWeights Logical value indicating whether limma::voomWithQualityWeights should be used instead of limma::voom. Default is FALSE and hence the pipeline uses limma::voom to transform RNAseq data.
`datasources`	a list of `DSConnection-class` objects obtained after login. If the `datasources` argument is not specified the default set of connections will be used: see `datashield.connections_default`.