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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.
● Data Source:
BioConductor
● Keywords:
● Alias: DEXSeq-defunct
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DEXSeq
(Package: DEXSeq) :
Performs the differential exon usage test in a single command
This function is a wrapper that calls the necessary functions to perform a differential exon usage test in a single command.
● Data Source:
BioConductor
● Keywords:
● Alias: DEXSeq
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DEXSeqDataSet-class
(Package: DEXSeq) :
DEXSeqDataSet object and constructors
The DEXSeqDataSet is a subclass of DESeqDataSet, specifically designed to adapt the DESeqDataSet to test for differences in exon usage.
● Data Source:
BioConductor
● Keywords:
● Alias: DEXSeqDataSet, DEXSeqDataSet-class, DEXSeqDataSetFromHTSeq, DEXSeqDataSetFromSE
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DEXSeqHTML
(Package: DEXSeq) :
DEXSeq HTML report writer
This function generates an HTML report from the results of a DEXSeqResults object. Gives an simple report to explore differential exon usage results.
● Data Source:
BioConductor
● Keywords:
● Alias: DEXSeqHTML
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The DEXSeqResults object is a subclass of a DataFrame. It collects relevant information from a DEXSeqDataSet object with the results generated from testing for differences in exon usage.
● Data Source:
BioConductor
● Keywords:
● Alias: DEXSeqResults, DEXSeqResults-class
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featureCounts
(Package: DEXSeq) :
Accessor functions for DEXSeqDataSet details
Accessor functions of the DEXSeqDataSet object.
● Data Source:
BioConductor
● Keywords:
● Alias: exonIDs, exonIDs<-, featureCounts, featureIDs, featureIDs<-, geneIDs, geneIDs<-, groupIDs, groupIDs<-, sampleAnnotation
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counts
(Package: DEXSeq) :
Accessors for the 'counts' slot of a DEXSeqResults object.
The counts slot holds the count data as a matrix of non-negative integer count values, one row for each observational unit (gene or the like), and one column for each sample.
● Data Source:
BioConductor
● Keywords:
● Alias: counts, counts,DEXSeqResults-method
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estimateDispersions
(Package: DEXSeq) :
Estimate the dispersions for a DEXSeqDataSet
This function obtains dispersion estimates for negative binomial distributed data for the specific case for DEXSeq.
● Data Source:
BioConductor
● Keywords:
● Alias: estimateDispersions, estimateDispersions,DEXSeqDataSet-method
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estimateExonFoldChanges
(Package: DEXSeq) :
Estimates exon usage coefficients from the fitted terms of the GLM.
This function calculates the exon usage coefficients and fold changes (on log2 scale) between the different conditions.
● Data Source:
BioConductor
● Keywords:
● Alias: estimateExonFoldChanges
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estimateSizeFactors
(Package: DEXSeq) :
Estimate the size factors for a DEXSeqDataSet
Estimate the size factors for a DEXSeqDataSet
● Data Source:
BioConductor
● Keywords:
● Alias: estimateSizeFactors, estimateSizeFactors,DEXSeqDataSet-method
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