callSummarize           Defines which variables should be written back
                        when calling a cn.farms run
cn.farms                cn.farms
cnLibrary               This function was taken from snowfall and
                        edited due to some deprecated function calls.
combineData             Combine two ExpressionSet objects
createAnnotation        Creation of annotation files
createMatrix            Creates the needed matrix
distributionDistance    Computes the distribution distance
dnaCopySf               Runs DNAcopy in parallel mode
doCnFarmsSingle         Does the whole cn.farms process in one call
flcSnp6Std              Does a fragment length correction on
                        intensities
flcStd                  Does a fragment length correction on
                        intensities
fragLengCorr            Does a fragment length correction
getFragmentSet          Finds SNPs which belong to one fragment
getSingleProbeSetSize   Combines data for probeset summarization
mlSummarization         Method for computation of the multi-loci
                        summarization
normAdd                 Extracts info from the package name
normalizeAverage        Scales the range of the non-polymorphic data to
                        the range of a given array.
normalizeCels           Wrapper for the normalization functions
normalizeNone           Runs the SOR normalization on microarray data
normalizeNpData         Processes the non-polymorphic data
normalizeQuantiles      Normalization Quantiles
normalizeSequenceEffect
                        Correction for probe sequence effects
normalizeSor            Runs the SOR normalization on microarray data
plotDendrogram          Plots a dendrogram
plotDensity             Function to create a density plot
plotEvalIc              Creates a plot with known regions and a numeric
                        vector
plotRegions             Plots given regions by segments
plotSmoothScatter       Creates a smooth scatter plot
plotViolines            Create a violine plot
slSummarization         Method for computation of the single-locus
                        summarization
sparseFarmsC            Normalizes the data with SOR
summarizeFarmsExact     Summarization Laplacian approach with exact
                        computation
summarizeFarmsExact2    Summarization Laplacian approach with exact
                        computation
summarizeFarmsExact3    Summarization Laplacian approach with exact
                        computation
summarizeFarmsGaussian
                        Summarization Gaussian approach
summarizeFarmsMethods   Lists methods for possible FARMS summarization
summarizeFarmsStatistics
                        Mean or median instead of the FARMS model
summarizeFarmsVariational
                        Summarization variational Laplacian approach
summarizeWindowBps      Combines neighbouring locations to windows
summarizeWindowMethods
                        Lists methods for possible window methods
summarizeWindowStd      Combines neighbouring locations to windows
