# R Investigation of ChIP-chip Oligoarrays

## Documentation for package ‘Ringo’ version 1.14.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## 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
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"