Entry: Ringo-internal
Aliases: clusters panel.scatter panel.cor merge.RGList takeMeanOverGroups as.data.frame.cherList splitAndSimplify readNimblegenHeader readNgIntensitiesTxt normalizeBetweenArraysVSN relateChers2 whichCsr oneChannelVSN
Keywords: internal
Description: Internal Ringo functions
URL: ../../../library/Ringo/html/Ringo-internal.html

Entry: image.RGList
Aliases: arrayImage image.RGList
Keywords: hplot
Description: Function to visualize spatial distribution of raw intensities
URL: ../../../library/Ringo/html/arrayImage.html

Entry: asExprSet
Aliases: asExprSet asExpressionSet
Keywords: manip
Description: converts a Ringo MAList into an ExpressionSet
URL: ../../../library/Ringo/html/asExprSet.html

Entry: autocor
Aliases: autocorr autocor autocorrelation
Keywords: manip
Description: Function to compute auto-correlation of probe intensities
URL: ../../../library/Ringo/html/autocorr.html

Entry: cherByThreshold
Aliases: cherByThreshold
Keywords: manip
Description: Function to identify chers based on thresholds
URL: ../../../library/Ringo/html/cherByThreshold.html

Entry: cher-class
Aliases: cher-class initialize,cher-method show,cher-method update,cher-method cher Cher cherList cherList-class cellType<-,cher,character-method cellType,cher-method cellType cellType<-
Keywords: classes
Description: Class "cher" - ChIP-enriched region
URL: ../../../library/Ringo/html/cherClass.html

Entry: chipAlongChrom
Aliases: chipAlongChrom
Keywords: hplot
Description: Visualize ChIP intensities along the chromosome
URL: ../../../library/Ringo/html/chipAlongChrom.html

Entry: computeRunningMedians
Aliases: computeRunningMedians
Keywords: manip
Description: Function to compute running medians on a tiling expression set
URL: ../../../library/Ringo/html/computeRunningMedians.html

Entry: compute.gc
Aliases: compute.gc gccontent
Keywords: manip
Description: Compute the GC content of DNA and probe sequences
URL: ../../../library/Ringo/html/compute_gc.html

Entry: computeSlidingT
Aliases: computeSlidingT
Keywords: manip
Description: Function to compute sliding T statistics on a tiling expression set
URL: ../../../library/Ringo/html/compute_sliding_t.html

Entry: corPlot
Aliases: corrPlot corPlot
Keywords: hplot
Description: Function to plot correlation of different samples
URL: ../../../library/Ringo/html/corrPlot.html

Entry: features2Probes
Aliases: features2Probes
Keywords: manip
Description: Function for mapping genomic features to probes
URL: ../../../library/Ringo/html/features2Probes.html

Entry: findChersOnSmoothed
Aliases: findChersOnSmoothed
Keywords: manip
Description: Find ChIP-enriched regions on smoothed ExpressionSet
URL: ../../../library/Ringo/html/findChersOnSmoothed.html

Entry: ftr2xys
Aliases: ftr2xys
Keywords: file IO
Description: Convert a NimbleScan ftr-file into a xys-file
URL: ../../../library/Ringo/html/ftr2xys.html

Entry: getFeats
Aliases: getFeats getFeatures
Keywords: manip
Description: Utility function to extract all features from a cherList
URL: ../../../library/Ringo/html/getFeats.html

Entry: newCher
Aliases: newCher
Keywords: internal
Description: Create a list object of class cher
URL: ../../../library/Ringo/html/newCER.html

Entry: nimblegenScale
Aliases: nimblegenScale
Keywords: manip internal
Description: Function to compute scaled log-ratios
URL: ../../../library/Ringo/html/nimblegenNorm.html

Entry: plot.autocor.result
Aliases: plotAutocor plot.autocor.result
Keywords: hplot
Description: Plots auto-correlation of probe intensities
URL: ../../../library/Ringo/html/plotAutocorr.html

Entry: plot.cher
Aliases: plot.cher plotCher cherPlot plot,cher,missing-method plot,cher,ExpressionSet-method
Keywords: hplot
Description: Plot identified Chers
URL: ../../../library/Ringo/html/plot_cher.html

Entry: posToProbeAnno
Aliases: posToProbeAnno posToProbeAnnoEnvironment createProbeAnno
Keywords: manip
Description: Function for creating a probeAnno environment
URL: ../../../library/Ringo/html/posToProbeAnnoEnvironment.html

Entry: preprocess
Aliases: preprocess
Keywords: manip
Description: Preprocess Nimblegen Raw Intensities
URL: ../../../library/Ringo/html/preprocess.html

Entry: probeAnno-class
Aliases: probeAnno-class probeAnno arrayName<-,probeAnno,character-method arrayName,probeAnno-method arrayName<- arrayName genome<- genome chromosomeNames [<-,probeAnno-method [,probeAnno-method chromosomeNames,probeAnno-method get,character,missing,probeAnno,missing,missing-method initialize,probeAnno-method ls,probeAnno,missing,missing,missing,missing-method show,probeAnno-method genome<-,probeAnno,character-method genome,probeAnno-method coerce,environment,probeAnno-method
Keywords: classes
Description: Class "probeAnno"
URL: ../../../library/Ringo/html/probeAnnoClass.html

Entry: readNimblegen
Aliases: readNimblegen
Keywords: file IO
Description: Function to read in Nimblegen Intensity Text Files
URL: ../../../library/Ringo/html/readNimblegen.html

Entry: regionOverlap
Aliases: regionOverlap region.overlap
Keywords: manip
Description: Function to compute overlap of genomic regions
URL: ../../../library/Ringo/html/regionoverlap.html

Entry: relateChers
Aliases: relateChers
Keywords: manip
Description: Relate found Chers to genomic features
URL: ../../../library/Ringo/html/relateCERs.html

Entry: sliding.meansd
Aliases: sliding.meansd
Keywords: manip
Description: Compute mean and standard deviation of scores in a sliding window
URL: ../../../library/Ringo/html/sliding_meansd.html

Entry: sliding.quantile
Aliases: sliding.quantile slidingquantile
Keywords: manip
Description: Compute quantile of scores in a sliding window
URL: ../../../library/Ringo/html/sliding_quantile.html

Entry: upperBoundNull
Aliases: upperBoundNull nullUpperBound
Keywords: manip
Description: function to estimate upper limit of null distribution
URL: ../../../library/Ringo/html/upperBoundNull.html

Entry: validProbeAnno
Aliases: validProbeAnno validateProbeAnno
Keywords: internal
Description: Function to check a probeAnno environment
URL: ../../../library/Ringo/html/validProbeAnno.html
