addVar                  Plot vector of a quantitative variable over a
                        MDS map.
adjustPeaks             Adjust peak width so that samples obtained
                        under different conditions become comparable.
bg3                     Sample binding site and related data from BG3
                        cell line in Drosophila melanogaster.
boostMDS                Improve goodness-of-fit of a given MDS solution
                        in terms of R-square.
clusGPS                 Computation of cluster density estimates for
                        cluster contour representation and
                        correct-classification rates (cluster
                        robustness). A pre-computed clustering of
                        elements used in the map has to be given as an
                        input, which is useful to explore results using
                        different clustering algorithms and
                        methodologies (top-down, bottom-up, etc).
clusGPS-class           Class '"clusGPS"'
combineGenesMatrix      Combine two datasets with epigenetic factor
                        profiles at gene level in order to produce a
                        differential chroGPS-genes map.
diffFactors             Performs differential analysis of
                        chroGPS-factors maps based on Procrustes
                        analysis.
diffGenes               Performs differential analysis of chroGPS-genes
                        maps based on Bayesian Correct Classification
                        Rates.
distGPS                 Compute matrix with pairwise distances between
                        objects. Several GPS metrics are available.
distGPS-class           Class '"distGPS"'
domainDist              Overview of intra and inter-domain distances.
geneSetGPS              Highlight point (gene) position over a
                        Multi-dimensional Scaling plot.
getURL                  Retrieve file from URL.
gff2RDList              Retrieve binding site information from GFF3
                        files.
gps2xgmml               Export an 'mds' object to Cytoscape .xgmml
                        format
mds                     Metric and non-metric Multidimensional Scaling
                        for a distGPS object.
mds-class               Class '"mds"'
mergeClusters           Unsupervised cluster merging based on their
                        observed overlap with automatic changepoint
                        detection.
mergeReplicates         Merges information from epigenetic replicates
                        at factor, gene and chroGPS MDS map level.
procrustesAdj           Use Procrustes to adjust an MDS map containing
                        samples obtained under different conditions,
                        e.g. technology or genetic backgrounds.
profileClusters         Assess epigenetic profiles for genes present in
                        each cluster as obtained by the 'clusGPS'
                        function.
rankFactorsbyDomain     Function to help selecting candidate epigenetic
                        factors based on Epigenetic Domain
                        cohesion/separation.
rankFactorsbyProfile    Function to help selecting candidate epigenetic
                        factors based on their predictive capabilities.
s2                      Sample binding site and related data from S2
                        and BG3 cell lines in Drosophila melanogaster.
splidDistGPS-class      Class '"splitDistGPS"'
