DEXSeq-defunct:
This functions are deprecated and will become defunct.
Description
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.
Details
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