DEXSeq-defunct {DEXSeq} | R Documentation

## 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`

[Package DEXSeq version 1.38.0 Index]