asExprSet               converts a Ringo MAList into an ExpressionSet
autocor                 Function to compute auto-correlation of probe
                        intensities
cher-class              Class "cher" - ChIP-enriched region
cherByThreshold         Function to identify chers based on thresholds
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
computeSlidingT         Function to compute sliding T statistics on a
                        tiling expression set
corPlot                 Function to plot correlation of different
                        samples
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
getFeats                Utility function to extract all features from a
                        cherList
image.RGList            Function to visualize spatial distribution of
                        raw intensities
nonzero-methods         Methods for Function nonzero
plot.autocor.result     Plots auto-correlation of probe intensities
plot.cher               Plot identified Chers
plotBM                  Visualization of a binary matrix
posToProbeAnno          Function for creating a probeAnno environment
preprocess              Preprocess Raw ChIP-chip Intensities
probeAnno-class         Class "probeAnno"
quantilesOverPositions
                        show ChIP-chip data aligned over genome
                        features, e.g. TSSs
readNimblegen           Function to read in Nimblegen Intensity Text
                        Files
regionOverlap           Function to compute overlap of genomic regions
relateChers             Relate found Chers to genomic features
sliding.meansd          Compute mean and standard deviation of scores
                        in a sliding window
sliding.quantile        Compute quantile of scores in a sliding window
twoGaussiansNull        Estimate a threshold from Gaussian mixture
                        distribution
upperBoundNull          function to estimate upper limit of null
                        distribution
