# Negative Binomial Models to detect Differential Splicing

## Documentation for package ‘NBSplice’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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