# Simple tiling array analysis of Affymetrix ChIP-chip data

## Documentation for package ‘Starr’ version 1.6.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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
plotcmarrt | Histogram of p-values and normal QQ plots for standardized MA
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