callParameter {ABSSeq} | R Documentation |
Calculate parameters for each gene (the moderating basemean, dispersions, moderated fold-change and general sd)
callParameter(object, replaceOutliers = TRUE, ...)
object |
a |
replaceOutliers |
switch for outlier replacement, default is TRUE. |
... |
parameters past to |
shifted and calculate a set of parameters from normalized counts table before callDEs
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.
This function should run after normalFactors
or providing size factors.
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)