AdjustedCopyEstimate    Container for results of GC adjusted copy
                        number estimation.
AffymetrixCdfFile       Placeholder For AffymetrixCdfFile Documentation
BAM2GRanges             Read in a (list of) BAM file(s) into a
                        GRanges(List) object.
ChromaBlocks            A function to find areas of enrichment in
                        sequencing data
ChromaResults-class     ChromaResults class
ClusteredScoresList     Container for coverage matrices with clustering
                        results.
CopyEstimate            Container for results of fold change copy
                        number estimation.
FastQC-class            FastQC and associated classes
GCAdjustParams          Container for parameters for mappability and GC
                        content adjusted absolute copy number
                        estimation.
GCadjustCopy            Calculate Absolute Copy Number from Sequencing
                        Counts
GCbiasPlots             Plot GC content vs. Read Counts Before
                        Normalising, and GC content vs. Copy Estimates
                        After Normalising.
GDL2GRL                 Utility function to covert a GenomeDataList
                        object into GRangesList objects.
ScoresList              Container for 'featureScores()' output.
absoluteCN              Calculate and Segment Absolute Copy Number from
                        Sequencing Counts
annoDF2GR               Convert a 'data.frame' to a 'GRanges'.
annoGR2DF               Convert an annotated 'GRanges' to a
                        'data.frame'.
annotationBlocksCounts
                        Counts the number of sequencing reads within
                        supplied genomic blocks.
annotationBlocksLookup
                        Forms a mapping between probe locations and
                        chromosomal blocks (regions).
annotationCounts        Counts the number of sequencing reads
                        surrounding supplied annotations
annotationLookup        Forms a mapping between probes on a tiling
                        array and windows surrounding the TSSs of
                        genes.
binPlots                Create line plots of averaged signal across a
                        promoter
blocksStats             Calculate statistics for regions in the genome
checkProbes             Check Probe Specificity for Some Regions
chr21genes              Positions of Genes on Human Chromosome 21
chromosomeCNplots       Plot copy number by chromosome
clusterPlots            Visualisation of tables of feature coverages.
cpgBoxplots             Boxplots of intensity, binned by Cpg Density
cpgDensityCalc          Calculate CpG Density in a Window
cpgDensityPlot          Plot the distribution of sequencing reads CpG
                        densities.
enrichmentCalc          Calculate sequencing enrichment
enrichmentPlot          Plot the distribution of sequencing enrichment.
expr                    Vector of expression differences
featureBlocks           Make windows for distances around a reference
                        point.
featureScores           Get scores at regular sample points around
                        genomic features.
findClusters            Find Clusters Epigenetically Modified Genes
gcContentCalc           Calculate The gcContent of a Region
genQC                   Plot Quality Checking Information for
                        Sequencing Data
genomeBlocks            Creates bins across a genome.
getProbePositionsDf     Translate Affymetrix probe information in a
                        table.
loadPairFile            A routine to read Nimblegen tiling array
                        intensities
loadSampleDirectory     A routine to read Nimblegen tiling array
                        intensities
makeWindowLookupTable   Using the output of 'annotationLookup', create
                        a tabular storage of the indices
mappabilityCalc         Calculate The Mappability of a Region
mergeReplicates         Merge GRanges that are of replicate
                        experiments.
multiHeatmap            Superfigure plots
plotClusters            Plot Scores of Cluster Regions
processNDF              Reads in a Nimblegen microarray design file
                        (NDF)
profilePlots            Create line plots of averaged signal across a
                        promoter for gene sets, compared to random
                        sampling.
regionStats             Find Regions of significance in microarray data
relativeCN              Calculate and Segment Relative Copy Number From
                        Sequencing Counts
samplesList             Short Reads from Cancer and Normal
sequenceCalc            Find occurences of a DNA pattern
summarizeScores         Subtract scores of different samples.
writeWig                Writes sequencing data out into wiggle files
