API for Ringo
R Investigation of ChIP-chip Oligoarrays
| Global functions | |
|---|---|
| .onAttach | Source code |
| .onLoad | Source code |
| .onUnload | Source code |
| Cher | Man page |
| [,probeAnno,ANY,ANY,ANY-method | Man page |
| [,probeAnno-method | Man page |
| [<-,probeAnno,ANY,ANY,ANY-method | Man page |
| [<-,probeAnno-method | Man page |
| alongChromTicks | Man page Source code |
| arrayImage | Man page |
| arrayName | Man page |
| arrayName,probeAnno-method | Man page |
| arrayName<- | Man page |
| arrayName<-,probeAnno,character-method | Man page |
| as.data.frame.cherList | Man page Source code |
| asExprSet | Man page Source code |
| asExpressionSet | Man page |
| autocor | Man page Source code |
| autocorr | Man page |
| autocorrelation | Man page |
| cbind2,ExpressionSet,ExpressionSet-method | Man page |
| cellType | Man page |
| cellType,cher-method | Man page |
| cellType<- | Man page |
| cellType<-,cher,character-method | Man page |
| cher | Man page |
| cher-class | Man page |
| cherByThreshold | Man page Source code |
| cherList | Man page |
| cherList-class | Man page |
| cherPlot | Man page |
| chersToBED | Man page Source code |
| chipAlongChrom | Man page Source code |
| chipAlongChrom1 | Man page |
| chipAlongChromOld | Man page |
| chromosomeNames | Man page |
| chromosomeNames,probeAnno-method | Man page |
| clusters | Man page Source code |
| coerce,environment,probeAnno-method | Man page |
| compute.gc | Man page Source code |
| computeRunningMedians | Man page Source code |
| computeSlidingT | Man page Source code |
| corPlot | Man page Source code |
| corrPlot | Man page |
| createProbeAnno | Man page |
| exportCCData | Man page Source code |
| exportCherList | Man page Source code |
| extractProbeAnno | Man page Source code |
| featureColors | Man page Man page Source code |
| features2Probes | Man page Source code |
| findChersOnSmoothed | Man page Source code |
| ftr2xys | Man page Source code |
| gccontent | Man page |
| genome | Man page |
| genome,probeAnno-method | Man page |
| genome<- | Man page |
| genome<-,probeAnno,character-method | Man page |
| get,character,missing,probeAnno-method | Man page |
| getFeats | Man page Source code |
| getFeatures | Man page |
| image,RGList-method | Man page |
| image.RGList | Man page |
| initialize,cher-method | Man page |
| initialize,probeAnno-method | Man page |
| ls,probeAnno,missing,missing,missing,missing-method | Man page |
| merge.RGList | Man page |
| newCher | Man page Source code |
| newVP | Man page Source code |
| nimblegenScale | Man page Source code |
| nonzero | Man page |
| nonzero,dgCMatrix-method | Man page |
| nonzero,matrix-method | Man page |
| nonzero,matrix.csr-method | Man page |
| nonzero-methods | Man page |
| normalizeBetweenArraysVSN | Man page Source code |
| nullUpperBound | Man page |
| oneChannelVSN | Man page Source code |
| pair2xys | Man page Source code |
| panel.cor | Man page Source code |
| panel.scatter | Man page Source code |
| plot,ExpressionSet,probeAnno-method | Man page |
| plot,cher,ExpressionSet-method | Man page |
| plot,cher,missing-method | Man page |
| plot,qop,ANY-method | Man page |
| plot,qop-method | Man page |
| plot.autocor.result | Man page Source code |
| plot.cher | Man page Source code |
| plotAlongChromLegend | Man page Source code |
| plotAutocor | Man page |
| plotBM | Man page Source code |
| plotBinaryMatrix | Man page |
| plotCher | Man page |
| plotFeatures | Source code |
| plotOneChIPSample | Man page Source code |
| posToProbeAnno | Man page Source code |
| posToProbeAnnoEnvironment | Man page |
| preprocess | Man page Source code |
| print.cher | Source code |
| probeAnno | Man page |
| probeAnno-class | Man page |
| probeAnnoFromRGList | Man page |
| probes | Man page |
| probes,cher-method | Man page |
| probes,cherList-method | Man page |
| qop-class | Man page |
| quantilesOverPositions | Man page Source code |
| readNgIntensitiesTxt | Man page Source code |
| readNimblegen | Man page Source code |
| readNimblegenHeader | Man page |
| region.overlap | Man page |
| regionOverlap | Man page Source code |
| relateChers | Man page Source code |
| relateChers2 | Man page |
| show,cher-method | Man page |
| show,probeAnno-method | Man page |
| show,qop-method | Man page |
| sigGOTable | Man page Source code |
| sliding.meansd | Man page Source code |
| sliding.quantile | Man page Source code |
| slidingquantile | Man page |
| splitAndSimplify | Man page Source code |
| takeMeanOverGroups | Man page Source code |
| twoGaussiansNull | Man page Source code |
| update,cher-method | Man page |
| upperBoundNull | Man page Source code |
| validProbeAnno | Man page Source code |
| validateProbeAnno | Man page |
