The ExonCountSet object has been deprecated and substituted by
the DEXSeqDataSet object. Therefore, all the functions and methods
for the ExonCountSet object were deprecated. These functions have
been subsituted by new functions and methods designed for DEXSeqDataSet objects.
The replacements of defunct functions are summarized in the
following items.
newExonCountSet: DEXseqDataSet
DEUresultTable: DEXseqResults
subsetByGenes:
geneCountTable:
estimateExonDispersionsForModelFrame_BM: estimateDispersions-DEXSeqDataSet
estimateDispersions_BM: estimateDispersions-DEXSeqDataSet
testGeneForDEU_BM: testForDEU
testForDEU_BM: testForDEU
doCompleteDEUAnalysis: DEXSeq
makeCompleteDEUAnalysis_BM: DEXSeq
read.HTSeqCounts: DEXSeqDataSetFromHTSeq
countTableForGene:
fitDispersionFunction: estimateDispersions-DEXSeqDataSet
estimatelog2FoldChange: estimateExonFoldChanges
modelFrameForGene:
buildExonCountSet: DEXSeqDataSetFromSE
constructModelFrame:
getCountVector:
estimateExonDispersion: estimateDispersions-DEXSeqDataSet
testExonForDEU: testForDEU
doCompleteDEUAnalysis: DEXSeq