Negative Binomial Models to detect Differential Splicing

Documentation for package ‘NBSplice’ version 1.0.1

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