R Investigation of NimbleGen Oligoarrays


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Documentation for package ‘Ringo’ version 1.2.0

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arrayImage Function to visualize spatial distribution of raw intensities
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
chipAlongChrom Visualize ChIP intensities along the chromosome
compute.gc Compute the GC content of DNA and probe sequences
computeRunningMedians Function to compute running medians on a tiling expression set
corPlot Function to plot correlation of different samples
corrPlot Function to plot correlation of different samples
findPeaksOnSmoothed Find peaks on smoothed ExpressionSet
ftr2xys Convert a NimbleScan ftr-file into a xys-file
gccontent Compute the GC content of DNA and probe sequences
image.RGList Function to visualize spatial distribution of raw intensities
peak Class peak - A list holding ChIP-chip peak characteristics
peak-class Class peak - A list holding ChIP-chip peak characteristics
peakByThreshold Function to identify peaks based on thresholds
peakList Class peak - A list holding ChIP-chip peak characteristics
peakList-class Class peak - A list holding ChIP-chip peak characteristics
peakPlot Plot identified peaks
plot.autocor.result Plots auto-correlation of probe intensities
plot.peak Plot identified peaks
plotAutocor Plots auto-correlation of probe intensities
plotPeak Plot identified peaks
preprocess Preprocess Nimblegen Raw Intensities
print.peak Class peak - A list holding ChIP-chip peak characteristics
readNimblegen Function to read in Nimblegen Intensity Text Files
relatePeaks Relate found peaks to genomic features
sliding.quantile Compute quantile of scores in a sliding window
slidingquantile Compute quantile of scores in a sliding window