run_limmaAnalysis {InPAS} | R Documentation

## use limma to analyze the PDUI

### Description

use limma to analyze the PDUI

### Usage

    run_limmaAnalysis(
      UTR3eset,
      design,
      contrast.matrix,
      coef = 1,
      robust = FALSE,
      ...
    )

### Arguments

`UTR3eset` | An object of UTR3eSet, output of `get_UTR3eSet()`
`design` | A design matrix of the experiment, with rows corresponding to arrays and columns to coefficients to be estimated. Defaults to the unit vector meaning that the arrays are treated as replicates. see `stats::model.matrix()`
`contrast.matrix` | A numeric matrix with rows corresponding to coefficients in fit and columns containing contrasts. May be a vector if there is only one contrast. see `limma::makeContrasts()`
`coef` | An integer(1) vector specifying which coefficient or a character(1) vector specifying which contrast of the linear model is to test. see more `limma::topTable()`. Default, 1.
`robust` | A logical(1) vector,indicating whether the estimation of the empirical Bayes prior parameters be robustified against outlier sample variances?
`...` | other arguments which are passed to `limma::lmFit()`

### Value

fit results of eBayes by limma. It is an object of class limma::MArrayLM containing everything found by fit. see `limma::eBayes()`

### Author(s)

Jianhong Ou

### See Also

`run_singleSampleAnalysis()`, `run_singleGroupAnalysis()`, `run_fisherExactTest()`

[Package InPAS version 2.2.0 Index]