Man pages for Ringo
R Investigation of ChIP-chip Oligoarrays

arrayImageFunction to visualize spatial distribution of raw intensities
asExprSetconverts a Ringo MAList into an ExpressionSet
autocorrFunction to compute auto-correlation of probe intensities
cherByThresholdFunction to identify chers based on thresholds
cherClassClass "cher" - ChIP-enriched region
chipAlongChromVisualize ChIP intensities along the chromosome
chipAlongChromOldVisualize ChIP intensities along the chromosome
compute_gcCompute the GC content of DNA and probe sequences
computeRunningMediansFunction to compute running medians on a tiling expression...
compute_sliding_tFunction to compute sliding T statistics on a tiling...
corrPlotFunction to plot correlation of different samples
exportCherListFunction to export cherList into a file
extractProbeAnnoBuild probeAnno from match positions in an RGList
features2ProbesFunction for mapping genomic features to probes
findChersOnSmoothedFind ChIP-enriched regions on smoothed ExpressionSet
ftr2xysConvert a NimbleScan ftr-file into a xys-file
getFeatsUtility function to extract all features from a cherList
newCERCreate a list object of class cher
nimblegenNormFunction to compute scaled log-ratios
nonzeroMethods for Function nonzero
plotAutocorrPlots auto-correlation of probe intensities
plotBMVisualization of a binary matrix
plot_cherPlot identified Chers
posToProbeAnnoEnvironmentFunction for creating a probeAnno environment
preprocessPreprocess Raw ChIP-chip Intensities
probeAnnoClassClass "probeAnno"
qopS4Class "qop" Quantiles Over Positions
quantilesOverPositionsshow ChIP-chip data aligned over genome features, e.g. TSSs
readNimblegenFunction to read in Nimblegen Intensity Text Files
regionoverlapFunction to compute overlap of genomic regions
relateCERsRelate found Chers to genomic features
Ringo-internalInternal Ringo functions
sigGOTableObtain significant GO terms for a list of genes
sliding_meansdCompute mean and standard deviation of scores in a sliding...
sliding_quantileCompute quantile of scores in a sliding window
twoGaussiansNullEstimate a threshold from Gaussian mixture distribution
upperBoundNullfunction to estimate upper limit of null distribution
validProbeAnnoFunction to check a probeAnno environment
Ringo documentation built on Nov. 1, 2018, 3:44 a.m.