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 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 |