ABSSeq (version 1.8.0)

callParameter: Calculate parameters for differential expression test base on absolute counts differences

Description

Calculate parameters for each gene (the moderating basemean and dispersions)

Usage

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

Arguments

object

a ABSDataSet object.

replaceOutliers

switch for outlier replacement, default is TRUE.

...

parameters past to ReplaceOutliersByMAD

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.

Details

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

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)