abcdDNA                 A wrapper for fitting the offset-adjusted
                        ABCD-DNA GLM
absoluteCN              Calculate and Segment Absolute Copy Number from
                        Sequencing Counts
AdjustedCopyEstimate    Container for results of GC adjusted copy
                        number estimation.
AffymetrixCdfFile       Placeholder For AffymetrixCdfFile Documentation
AffymetrixCelSet        Placeholder For AffymetrixCelSet Documentation
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.
BAM2GRanges             Read in a (list of) BAM file(s) into a
                        GRanges(List) object.
BayMethList             Class '"BayMethList"'
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
ChromaBlocks            A function to find areas of enrichment in
                        sequencing data
ChromaResults-class     ChromaResults class
chromosomeCNplots       Plot copy number by chromosome
ClusteredScoresList     Container for coverage matrices with clustering
                        results.
clusterPlots            Visualisation of tables of feature coverages.
CopyEstimate            Container for results of fold change copy
                        number estimation.
cpgBoxplots             Boxplots of intensity, binned by Cpg Density
cpgDensityCalc          Calculate CpG Density in a Window
cpgDensityPlot          Plot the distribution of sequencing reads CpG
                        densities.
determineOffset         Function to determine the normalising offset f
                        that accounts for the relative sequencing
                        depth.
empBayes                Function to calculate prior parameters using
                        empirical Bayes.
enrichmentCalc          Calculate sequencing enrichment
enrichmentPlot          Plot the distribution of sequencing enrichment.
expr                    Vector of expression differences
FastQC-class            FastQC and associated classes
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
GCadjustCopy            Calculate Absolute Copy Number from Sequencing
                        Counts
GCAdjustParams          Container for parameters for mappability and GC
                        content adjusted absolute copy number
                        estimation.
GCbiasPlots             Plot GC content vs. Read Counts Before
                        Normalising, and GC content vs. Copy Estimates
                        After Normalising.
gcContentCalc           Calculate The gcContent of a Region
genomeBlocks            Creates bins across a genome.
genQC                   Plot Quality Checking Information for
                        Sequencing Data
getProbePositionsDf     Translate Affymetrix probe information in a
                        table.
getSampleOffsets        Calculates the sample-specific offsets, using
                        the neutral state
hcRegions               Masking files for hg19
hyperg2F1_vec           Gaussian hypergeometric function for vectorial
                        arguments
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
MappabilitySource       Superclass for datatypes that can refer to
                        genome mappability data.
maskOut                 Function to mask suspicious regions.
mergeReplicates         Merge GRanges that are of replicate
                        experiments.
methylEst               Function to derive regional methylation
                        estimates.
multiHeatmap            Superfigure plots
plotClusters            Plot Scores of Cluster Regions
plotQdnaByCN            Plotting the response of qDNA-seq data by CNV
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.
QdnaData                A container for quantitative DNA sequencing
                        data for ABCD-DNA analyses
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
ScoresList              Container for 'featureScores()' output.
sequenceCalc            Find occurences of a DNA pattern
setCNVOffsets           Set the CNVOffsets of a 'QdnaData' object
summarizeScores         Subtract scores of different samples.
writeWig                Writes sequencing data out into wiggle files
