bpmapToProbeAnno        Creating a probeAnno object
cmarrt.ma               Compute moving average statistics by
                        incorporating the correlation
cmarrt.peak             Obtain bound regions for a given error rate
                        control
correlationPlot         correlation of ChIP signals to other data
densityscatter          Compute density of a scatterplot
expressionByFeature     Getting expression value by feature from an
                        ExpressionSet
filterGenes             Filter Features/Genes
getMeans                Get mean ChIP-signal over annotated features
getProfiles             Get profiles of ChIP-signal over annotated
                        features
getRatio                Building ratio over experiments
heatmapplot             heatmapplot
list2matrix             Convert profile list to matrix
makeProbeAnno           Creating a probeAnno object
makeSplines             Fit splines to profiles
normalize.Probes        Normalization of probes
plotBoxes               boxplots of experiments
plotDensity             density plots of experiments
plotGCbias              Visualize GC-Bias of Hybridization
plotImage               Reconstruct the array image
plotMA                  M versus A plot
plotPosBias             Bias of hybridzation, depending on base
                        position in sequence.
plotProfiles            Plotting ChIP profiles of one or more clusters
plotRatioScatter        Plot ratios of all possible combinations of IP
                        and CONTROL
plotScatter             High level scatterplot of experiments
plotcmarrt              Histogram of p-values and normal QQ plots for
                        standardized MA
profileplot             Vizualize clusters
read.gffAnno            Reading gff annotation
readCelFile             Read raw intensities from CEL files
remap                   Remap reporter sequences to the genome and
                        create a new bpmap file
writeGFF                write ChIP-chip data to a gff file
writePosFile            Creating a pos file
