API for ReportingTools
Tools for making reports in various formats

Global functions
BaseReport-class Man page
CSVFile Man page Source code
CSVFile-class Man page
DGEExact.to.data.frame Source code
DGEExact.to.html Source code
DGELRT.to.data.frame Source code
DGELRT.to.html Source code
DataPackage Man page Source code
DataPackage-class Man page
GOhyperG.to.data.frame Source code Source code
GOhyperG.to.html Source code
GeneSet.to.data.frame Source code
GeneSetCollection.to.data.frame Source code
GeneSetCollection.to.html Source code
GeneSetCollection.to.html2 Source code
HTMLReport Man page Source code
HTMLReport-class Man page
HTMLReportRef-class Man page
Link Man page
Link,HTMLReportRef-method Man page
Link,character-method Man page
Link,list-method Man page
Link-methods Man page
PFAMhyperG.to.data.frame Source code
PFAMhyperG.to.html Source code
PFAMhyperG.to.htmlDF2 Source code
ReportHandlers-class Man page
[[,HTMLReportRef,ANY,ANY-method Man page
[[,HTMLReportRef,ANY-method Man page
[[<-,HTMLReportRef,ANY,ANY,ANY-method Man page
annotate.genes Source code
basePath Man page
basePath,HTMLReport-method Man page
baseUrl Man page
baseUrl,HTMLReport-method Man page
check.eg.ids Source code
check.ids Source code
connectionHandlers Man page Source code
custHeaderPanel Man page Source code
dependencies Man page
dependencies,DataPackage-method Man page
dependencies<- Man page
dependencies<-,DataPackage,character-method Man page
doImage Source code
eSetPlot Source code
entrezGene.link Source code
fileHandlers Man page Source code
fileWIndexHandlers Man page Source code
filename Man page
filename,CSVFile-method Man page
filename,HTMLReport-method Man page
filename-methods Man page
filter.vals Source code
finish Man page
finish,DataPackage-method Man page
finish,HTMLReport-method Man page
finish,HTMLReportRef-method Man page
finish-methods Man page
getNamesAndSymbols Source code
grabScriptAndStyle Source code
hyperG.to.data.frame Source code
hyperGPlot Source code
knitrHandlers Man page Source code
make.gene.plots Source code
makeDESeqDF Man page Source code Source code
makeDESeqFigures Source code
makeGeneListPages Source code
makeGeneListPagesGSC Source code
makeOldHTMLReport Man page Source code
makePageEnd Source code
makePageStart Source code
makeReportPath Source code
makeSplash Source code
marrayLM.to.data.frame Source code
marrayLM.to.html Source code
miniplot Source code
mockRnaSeqData Man page
modifyReportDF Man page
modifyReportDF,ANY,ANY,ANY-method Man page
modifyReportDF,ANY,ANY,DESeqDataSet-method Man page
modifyReportDF,ANY,ANY,DESeqResults-method Man page
modifyReportDF,ANY,ANY,DGEExact-method Man page
modifyReportDF,ANY,ANY,DGELRT-method Man page
modifyReportDF,ANY,ANY,GOHyperGResult-method Man page
modifyReportDF,ANY,ANY,GeneSet-method Man page
modifyReportDF,ANY,ANY,MArrayLM-method Man page
modifyReportDF-methods Man page
name Man page
name,BaseReport-method Man page
name<-,BaseReport,character-method Man page
name<-,CSVFile,character-method Man page
name<-,HTMLReport,character-method Man page
normalizeSubscript Source code
nullFun Source code
objectToHTML Man page
objectToHTML,ANY-method Man page
objectToHTML,XMLInternalNode-method Man page
objectToHTML,character-method Man page
objectToHTML,data.frame-method Man page
objectToHTML,ggbio-method Man page
objectToHTML,ggplot-method Man page
objectToHTML,recordedplot-method Man page
objectToHTML,trellis-method Man page
objectToHTML-methods Man page
page Man page
page,HTMLReport-method Man page
page<- Man page
page<-,HTMLReport,character-method Man page
panel.boxandstrip Source code
path Man page
path,BaseReport-method Man page
path,DataPackage-method Man page
path,HTMLReport-method Man page
path,HTMLReportRef-method Man page
path,ReportHandlers-method Man page
plotGOResults Source code
publish Man page
publish,ANY,DataPackage-method Man page
publish,ANY,HTMLReport-method Man page
publish,ANY,HTMLReportRef-method Man page
publish,ANY,list-method Man page
publish,DESeqDataSet,HTMLReportRef-method Man page
publish,DESeqResults,HTMLReportRef-method Man page
publish,DGEExact,ANY-method Man page
publish,DGEExact,HTMLReport-method Man page
publish,DGEExact,HTMLReportRef-method Man page
publish,DGELRT,ANY-method Man page
publish,DGELRT,HTMLReport-method Man page
publish,DGELRT,HTMLReportRef-method Man page
publish,GOHyperGResult,ANY-method Man page
publish,GOHyperGResult,HTMLReport-method Man page
publish,GOHyperGResult,HTMLReportRef-method Man page
publish,GeneSet,HTMLReport-method Man page
publish,GeneSetCollection,ANY-method Man page
publish,GeneSetCollection,HTMLReport-method Man page
publish,GeneSetCollection,HTMLReportRef-method Man page
publish,HTMLReport,HTMLReport-method Man page
publish,HTMLReport,HTMLReportRef-method Man page
publish,HyperGResultBase,HTMLReport-method Man page
publish,HyperGResultBase,HTMLReportRef-method Man page
publish,MArrayLM,ANY-method Man page
publish,MArrayLM,HTMLReport-method Man page
publish,MArrayLM,HTMLReportRef-method Man page
publish,PFAMHyperGResult,ANY-method Man page
publish,PFAMHyperGResult,HTMLReport-method Man page
publish,PFAMHyperGResult,HTMLReportRef-method Man page
publish,character,DataPackage-method Man page
publish,data.frame,CSVFile-method Man page
publish,data.frame,DataPackage-method Man page
publish,data.frame,HTMLReport-method Man page
publish,data.frame,HTMLReportRef-method Man page
publish,list,HTMLReport-method Man page
publish,list,HTMLReportRef-method Man page
publish,trellis,HTMLReport-method Man page
publish,trellis,HTMLReportRef-method Man page
publish-methods Man page
readReport Man page Source code
remove.axis.and.padding Source code
reportDirectory Man page
reportDirectory,BaseReport-method Man page
reportDirectory<- Man page
reportDirectory<-,BaseReport,character-method Man page
reporting.theme Man page Source code
reporting.theme.alternate Man page Source code
safe.dir.create Source code
save.rda.by.name Source code
save.rda.fn Source code
shinyHandlers Man page Source code
show,BaseReport-method Man page
show,HTMLReport-method Man page
show,HTMLReportRef-method Man page
startHTMLReport Source code
title Man page
title,BaseReport-method Man page
title<- Man page
title<-,BaseReport,character-method Man page
toReportDF Man page
toReportDF,ANY-method Man page
toReportDF,DESeqDataSet-method Man page
toReportDF,DESeqResults-method Man page
toReportDF,DGEExact-method Man page
toReportDF,DGELRT-method Man page
toReportDF,GOHyperGResult-method Man page
toReportDF,GeneSet-method Man page
toReportDF,GeneSetCollection-method Man page
toReportDF,MArrayLM-method Man page
toReportDF,PFAMHyperGResult-method Man page
toReportDF,data.frame-method Man page
toReportDF-methods Man page
url,HTMLReport-method Man page
validConnection Man page Source code
writeHTMLTable Source code
ReportingTools documentation built on Nov. 19, 2017, 2 a.m.