ACE-package             ACE package
ACEcall                 Categorize and plot subclonal, single, and
                        double gains / losses
analyzegenomiclocations
                        Retrieve adjusted copy number information for
                        specific genomic locations
compresstemplate        Reduce the size of a template data frame
copyNumbersSegmented    Segmented data of two tumor samples
correlationmatrix       Create a correlation matrix of all samples in a
                        QDNAseq-object
forcesegmentsontemplate
                        Custom resegmentation with user-defined segment
                        information
getadjustedsegments     Create a data frame with segment information
                        corresponding to a model
linkvariants            Append columns with total genomic copies and
                        mutant copies to a file with variant/mutation
                        data
loopsquaremodel         Create 'squaremodel' summaries for all samples
                        in a QDNAseq-object
objectsampletotemplate
                        Converts data of a sample in a QDNAseq-object
                        to a template for ACE functions
postanalysisloop        Batch analysis of samples in a QDNAseq-object
                        for which models have been chosen
runACE                  Absolute Copy number Estimation
segmentstotemplate      Create a template data frame from input that
                        only provides segment information
singlemodel             Calculate potential fits for a single sample
singleplot              Plot an absolute copy number profile for a
                        single sample
squaremodel             Calculate potential fits for a single sample
                        using ploidy as a variable
squaremodelsummary      Create a graphical summary of the result of
                        squaremodel fitting
templatefromequalsegments
                        Create a template data frame with artificial
                        segments of equal length
twosamplecompare        Overlay copy number data of two samples and
                        compare segment values
