R Investigation of ChIP-chip Oligoarrays


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Documentation for package ‘Ringo’ version 1.6.0

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arrayImage Function to visualize spatial distribution of raw intensities
arrayName Class "probeAnno"
arrayName,probeAnno-method Class "probeAnno"
arrayName<-,probeAnno,character-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,cher-method Class "cher" - ChIP-enriched region
cellType<-,cher,character-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,probeAnno-method Class "probeAnno"
coerce,environment,probeAnno-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
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,probeAnno-method Class "probeAnno"
genome<-,probeAnno,character-method Class "probeAnno"
get,character,missing,probeAnno,missing,missing-method Class "probeAnno"
getFeats Utility function to extract all features from a cherList
getFeatures Utility function to extract all features from a cherList
image.RGList Function to visualize spatial distribution of raw intensities
initialize,cher-method Class "cher" - ChIP-enriched region
initialize,probeAnno-method Class "probeAnno"
ls,probeAnno,missing,missing,missing,missing-method Class "probeAnno"
nullUpperBound function to estimate upper limit of null distribution
plot,cher,ExpressionSet-method Plot identified Chers
plot,cher,missing-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
plotCher Plot identified Chers
posToProbeAnno Function for creating a probeAnno environment
posToProbeAnnoEnvironment Function for creating a probeAnno environment
preprocess Preprocess Nimblegen Raw Intensities
probeAnno Class "probeAnno"
probeAnno-class Class "probeAnno"
probeAnnoFromRGList Build probeAnno from match positions in an RGList
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,cher-method Class "cher" - ChIP-enriched region
show,probeAnno-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
update,cher-method Class "cher" - ChIP-enriched region
upperBoundNull function to estimate upper limit of null distribution
[,probeAnno-method Class "probeAnno"
[<-,probeAnno-method Class "probeAnno"