callParameter: Calculate parameters for differential expression test base on...

In ABSSeq: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Description

Calculate parameters for each gene (the moderating basemean, dispersions, moderated fold-change and general sd)

Usage

callParameter(object, replaceOutliers = TRUE, ...)

Arguments

object	a ABSDataSet object.
replaceOutliers	switch for outlier replacement, default is TRUE.
...	parameters past to ReplaceOutliersByMAD

Details

shifted and calculate a set of parameters from normalized counts table before callDEs

Value

A ABSDataSet object with absolute differences, basemean, mean of each group, variance, log2 of foldchange, named as 'absD', 'baseMean', 'Amean', 'Bmean', 'Variance' and 'foldChange', respectively. Use the results to get access it and plotDifftoBase to plot it.

Note

This function should run after normalFactors or providing size factors.

Examples

data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- normalFactors(obj)
obj <- callParameter(obj)
head(results(obj,c("foldChange","absD","baseMean")))
plotDifftoBase(obj)

ABSSeq documentation built on Nov. 8, 2020, 5:07 p.m.