R Investigation of ChIP-chip Oligoarrays

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Documentation for package ‘Ringo’ version 1.64.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

arrayImage	Function to visualize spatial distribution of raw intensities
arrayName	Class "probeAnno"
arrayName-method	Class "probeAnno"
arrayName<-	Class "probeAnno"
arrayName<--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-method	Class "cher" - ChIP-enriched region
cellType<-	Class "cher" - ChIP-enriched region
cellType<--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
chersToBED	Class "cher" - ChIP-enriched region
chipAlongChrom	Visualize ChIP intensities along the chromosome
chromosomeNames	Class "probeAnno"
chromosomeNames-method	Class "probeAnno"
coerce-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-method	Class "probeAnno"
genome<-	Class "probeAnno"
genome<--method	Class "probeAnno"
get-method	Class "probeAnno"
getFeats	Utility function to extract all features from a cherList
getFeatures	Utility function to extract all features from a cherList
image-method	Function to visualize spatial distribution of raw intensities
image.RGList	Function to visualize spatial distribution of raw intensities
initialize-method	Class "cher" - ChIP-enriched region
initialize-method	Class "probeAnno"
ls-method	Class "probeAnno"
nonzero	Methods for Function nonzero
nonzero-method	Methods for Function nonzero
nonzero-methods	Methods for Function nonzero
nullUpperBound	function to estimate upper limit of null distribution
plot-method	Visualize ChIP intensities along the chromosome
plot-method	Plot identified Chers
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-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-method	Class "cher" - ChIP-enriched region
show-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-method	Class "cher" - ChIP-enriched region
upperBoundNull	function to estimate upper limit of null distribution
[-method	Class "probeAnno"
[<--method	Class "probeAnno"