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| arrayImage | Function to visualize spatial distribution of raw intensities |
| arrayName | Class "probeAnno" |
| arrayName,probeAnno-method | Class "probeAnno" |
| arrayName<- | Class "probeAnno" |
| arrayName<-,probeAnno,character-method | Class "probeAnno" |
| asExpressionSet | converts a Ringo MAList into an ExpressionSet |
| asExprSet | converts a Ringo MAList into an ExpressionSet |
| autocor | Function to compute auto-correlation of probe intensities |
| autocorr | Function to compute auto-correlation of probe intensities |
| autocorrelation | Function to compute auto-correlation of probe intensities |
| cellType | Class "cher" - ChIP-enriched region |
| cellType,cher-method | Class "cher" - ChIP-enriched region |
| cellType<- | Class "cher" - ChIP-enriched region |
| cellType<-,cher,character-method | Class "cher" - ChIP-enriched region |
| Cher | Class "cher" - ChIP-enriched region |
| cher | Class "cher" - ChIP-enriched region |
| cher-class | Class "cher" - ChIP-enriched region |
| cherByThreshold | Function to identify chers based on thresholds |
| cherList | Class "cher" - ChIP-enriched region |
| cherList-class | Class "cher" - ChIP-enriched region |
| cherPlot | Plot identified Chers |
| chipAlongChrom | Visualize ChIP intensities along the chromosome |
| chromosomeNames | Class "probeAnno" |
| chromosomeNames,probeAnno-method | Class "probeAnno" |
| coerce,environment,probeAnno-method | Class "probeAnno" |
| compute.gc | Compute the GC content of DNA and probe sequences |
| computeRunningMedians | Function to compute running medians on a tiling expression set |
| computeSlidingT | Function to compute sliding T statistics on a tiling expression set |
| corPlot | Function to plot correlation of different samples |
| corrPlot | Function to plot correlation of different samples |
| createProbeAnno | Function for creating a probeAnno environment |
| exportCherList | Function to export cherList into a file |
| extractProbeAnno | Build probeAnno from match positions in an RGList |
| features2Probes | Function for mapping genomic features to probes |
| findChersOnSmoothed | Find ChIP-enriched regions on smoothed ExpressionSet |
| ftr2xys | Convert a NimbleScan ftr-file into a xys-file |
| gccontent | Compute the GC content of DNA and probe sequences |
| genome | Class "probeAnno" |
| genome,probeAnno-method | Class "probeAnno" |
| genome<- | Class "probeAnno" |
| genome<-,probeAnno,character-method | Class "probeAnno" |
| get,character,missing,probeAnno,missing,missing-method | Class "probeAnno" |
| getFeats | Utility function to extract all features from a cherList |
| getFeatures | Utility function to extract all features from a cherList |
| image,RGList-method | Function to visualize spatial distribution of raw intensities |
| image.RGList | Function to visualize spatial distribution of raw intensities |
| initialize,cher-method | Class "cher" - ChIP-enriched region |
| initialize,probeAnno-method | Class "probeAnno" |
| ls,probeAnno,missing,missing,missing,missing-method | Class "probeAnno" |
| nonzero | Methods for Function nonzero |
| nonzero,dgCMatrix-method | Methods for Function nonzero |
| nonzero,matrix-method | Methods for Function nonzero |
| nonzero,matrix.csr-method | Methods for Function nonzero |
| nonzero-methods | Methods for Function nonzero |
| nullUpperBound | function to estimate upper limit of null distribution |
| plot,cher,ExpressionSet-method | Plot identified Chers |
| plot,cher,missing-method | Plot identified Chers |
| plot,ExpressionSet,probeAnno-method | Visualize ChIP intensities along the chromosome |
| plot.autocor.result | Plots auto-correlation of probe intensities |
| plot.cher | Plot identified Chers |
| plotAutocor | Plots auto-correlation of probe intensities |
| plotBinaryMatrix | Visualization of a binary matrix |
| plotBM | Visualization of a binary matrix |
| plotCher | Plot identified Chers |
| posToProbeAnno | Function for creating a probeAnno environment |
| posToProbeAnnoEnvironment | Function for creating a probeAnno environment |
| preprocess | Preprocess Raw ChIP-chip Intensities |
| probeAnno | Class "probeAnno" |
| probeAnno-class | Class "probeAnno" |
| probeAnnoFromRGList | Build probeAnno from match positions in an RGList |
| probes | Class "cher" - ChIP-enriched region |
| probes,cher-method | Class "cher" - ChIP-enriched region |
| probes,cherList-method | Class "cher" - ChIP-enriched region |
| quantilesOverPositions | show ChIP-chip data aligned over genome features, e.g. TSSs |
| readNimblegen | Function to read in Nimblegen Intensity Text Files |
| region.overlap | Function to compute overlap of genomic regions |
| regionOverlap | Function to compute overlap of genomic regions |
| relateChers | Relate found Chers to genomic features |
| show,cher-method | Class "cher" - ChIP-enriched region |
| show,probeAnno-method | Class "probeAnno" |
| sliding.meansd | Compute mean and standard deviation of scores in a sliding window |
| sliding.quantile | Compute quantile of scores in a sliding window |
| slidingquantile | Compute quantile of scores in a sliding window |
| twoGaussiansNull | Estimate a threshold from Gaussian mixture distribution |
| update,cher-method | Class "cher" - ChIP-enriched region |
| upperBoundNull | function to estimate upper limit of null distribution |
| [,probeAnno,ANY,ANY,ANY-method | Class "probeAnno" |
| [,probeAnno-method | Class "probeAnno" |
| [<-,probeAnno,ANY,ANY,ANY-method | Class "probeAnno" |
| [<-,probeAnno-method | Class "probeAnno" |