Simple tiling array analysis of Affymetrix ChIP-chip data

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Documentation for package ‘Starr’ version 1.8.1

Help Pages

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