Negative Binomial Models to detect Differential Splicing


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Documentation for package ‘NBSplice’ version 1.11.2

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NBSplice-package NBSplice: Negative Binomial Models to detect Differential Splicing.
buildData GLM fitting and hypothesis testing
buildData-methods GLM fitting and hypothesis testing
buildLowExpIdx IsoDataSet low expressed isoforms detection.
buildLowExpIdx-method IsoDataSet low expressed isoforms detection.
buildLowExpIdx-methods IsoDataSet low expressed isoforms detection.
contrast Getters for an NBSpliceRes object.
contrast-method Getters for an NBSpliceRes object.
contrast-methods Getters for an NBSpliceRes object.
designFormula Getters for an IsoDataSet object.
designFormula-method Getters for an IsoDataSet object.
designFormula-methods Getters for an IsoDataSet object.
designMatrix An example of a design matrix helpful to demonstrate the use of the NBSplice R package.
disp Getters for an NBSpliceRes object.
disp-method Getters for an NBSpliceRes object.
disp-methods Getters for an NBSpliceRes object.
expData Getters for an IsoDataSet object.
expData-method Getters for an IsoDataSet object.
expData-methods Getters for an IsoDataSet object.
fitModel GLM fitting and hypothesis testing
fitModel-methods GLM fitting and hypothesis testing
geneCounts Getters for an IsoDataSet object.
geneCounts-method Getters for an IsoDataSet object.
geneCounts-methods Getters for an IsoDataSet object.
geneIso An example of isoform-gene relationship specification helpful to demonstrate the use of the NBSplice R package.
GetDSGenes Get differentially spliced genes.
GetDSGenes-method Get differentially spliced genes.
GetDSGenes-methods Get differentially spliced genes.
GetDSResults Get differential expression results of significant genes.
GetDSResults-method Get differential expression results of significant genes.
GetDSResults-methods Get differential expression results of significant genes.
GetGeneResults Get differentially spliced genes.
GetGeneResults-method Get differentially spliced genes.
GetGeneResults-methods Get differentially spliced genes.
initialize IsoDataSet object constructor.
initialize-method IsoDataSet object constructor.
initialize-method NBSpliceRes object constructor.
isoCounts Getters for an IsoDataSet object.
isoCounts-method Getters for an IsoDataSet object.
isoCounts-methods Getters for an IsoDataSet object.
isoCountsData An example of an isoform counts matrix helpful to demonstrate the use of the NBSplice R package.
IsoDataSet IsoDataSet constructor
IsoDataSet-class IsoDataSet S4 class implementation in R
IsoDataSet-getters Getters for an IsoDataSet object.
IsoDataSet-methods IsoDataSet constructor
isoGeneRel Getters for an IsoDataSet object.
isoGeneRel-method Getters for an IsoDataSet object.
isoGeneRel-methods Getters for an IsoDataSet object.
lowExpIndex Getters for an IsoDataSet object.
lowExpIndex-method Getters for an IsoDataSet object.
lowExpIndex-method Getters for an NBSpliceRes object.
lowExpIndex-methods Getters for an IsoDataSet object.
myDSResults An example of an NBSpliceRes object.
myIsoDataSet An example of an IsoDataSet object.
NBSpliceRes NBSpliceRes constructor
NBSpliceRes-class NBSpliceRes S4 class implementation in R
NBSpliceRes-getters Getters for an NBSpliceRes object.
NBSpliceRes-initialize NBSpliceRes object constructor.
NBSpliceRes-lowExpIndex Getters for an NBSpliceRes object.
NBSpliceRes-methods NBSpliceRes constructor
NBSpliceRes-print Print an NBSpliceRes object.
NBSpliceRes-show Show method for the NBSpliceRes class.
NBTest Differential splicing analysis.
NBTest-method Differential splicing analysis.
NBTest-methods Differential splicing analysis.
plotGeneResults Method to obtain isoform's relative expression barplot for an specific gene.
plotGeneResults-method Method to obtain isoform's relative expression barplot for an specific gene.
plotGeneResults-methods Method to obtain isoform's relative expression barplot for an specific gene.
plotRatiosDisp Plot the dispersion of isoform's relative expression for significant genes.
plotRatiosDisp-method Plot the dispersion of isoform's relative expression for significant genes.
plotRatiosDisp-methods Plot the dispersion of isoform's relative expression for significant genes.
plotVolcano Method to obtain the Volcano Plot.
plotVolcano-method Method to obtain the Volcano Plot.
plotVolcano-methods Method to obtain the Volcano Plot.
print Print an IsoDataSet object.
print-method Print an IsoDataSet object.
print-method Print an NBSpliceRes object.
results Getters for an NBSpliceRes object.
results-method Getters for an NBSpliceRes object.
results-methods Getters for an NBSpliceRes object.
show Show method for the IsoDataSet class.
show-method Show method for the IsoDataSet class.
show-method Show method for the NBSpliceRes class.
totalGeneCounts Auxiliary function to build gene expression matrix
totalGeneCounts-methods Auxiliary function to build gene expression matrix