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

Description Usage Arguments Details Value Note Examples

Description

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

Usage

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callParameter(object, replaceOutliers = TRUE, qforGeneralSD = 0.75, ...)

Arguments

object

a ABSDataSet object.

replaceOutliers

switch for outlier replacement, default is TRUE.

qforGeneralSD

quantile for estimating general SD of fold-change, default is 0.75.

...

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

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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)


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