run_limmaAnalysis: use limma to analyze the PDUI

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

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()

jianhong/InPAS documentation built on Nov. 5, 2024, 7:45 a.m.