Entry: Ringo-internal
Aliases: clusters panel.scatter panel.cor merge.RGList takeMeanOverGroups addTypes typifyList getGeneToTranscriptMap getTranscriptToGeneMap combine.tables calcOverlapDfVsDf as.data.frame.peakList generatePeakList splitAndSimplify readNimblegenHeader readNgIntensitiesTxt
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
Keywords: internal
Description: converts MAList into an exprSet
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: 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: corPlot
Aliases: corrPlot corPlot
Keywords: hplot
Description: Function to plot correlation of different samples
URL: ../../../library/Ringo/html/corrPlot.html

Entry: findPeaksOnSmoothed
Aliases: findPeaksOnSmoothed
Keywords: manip
Description: Find peaks on smoothed ExpressionSet
URL: ../../../library/Ringo/html/findPeaksOnSmoothed.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: newPeak
Aliases: newPeak
Keywords: internal
Description: Create a list object of class peak
URL: ../../../library/Ringo/html/newPeak.html

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

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

Entry: peak
Aliases: peak peak-class print.peak peakList-class peakList
Keywords: classes data
Description: Class peak - A list holding ChIP-chip peak characteristics
URL: ../../../library/Ringo/html/peakClass.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.peak
Aliases: plot.peak plotPeak peakPlot
Keywords: hplot
Description: Plot identified peaks
URL: ../../../library/Ringo/html/plot_peak.html

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

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

Entry: relatePeaks
Aliases: relatePeaks
Keywords: manip
Description: Relate found peaks to genomic features
URL: ../../../library/Ringo/html/relatePeaks.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
