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 |
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 |