| bpmapToProbeAnno | Creating a probeAnno object |
| cmarrt.ma | Compute moving average statistics by incorporating the correlation structure |
| 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 |
| plotcmarrt | Histogram of p-values and normal QQ plots for standardized MA statistics |
| 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 |
| 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 |
| writeWIG | write ChIP-chip data to a *.wig file |