.n_approx               n_tilde in AC
.p_approx               p_tilde in AC
.z                      Normal alpha/2 quantile
agrestiCoullCI          Agresti-Coull confidence interval for a
                        binomial proportion
bootstrapCompartments   Non-parametric bootstrapping of compartments
                        and summarization of bootstraps/compute
                        confidence intervals
checkAssayType          Check if the assay is a SummarizedExperiment
condenseRE              Condense a RaggedExperiment to a list of
                        SummarizedExperiments
condenseSE              Condense the output of condenseRE to
                        reconstruct per-sample GRanges objects to plot
estRMT                  Denoising of Covariance matrix using Random
                        Matrix Theory
extractOpenClosed       Get the open and closed compartment calls based
                        on sign of singular values
fexpit                  Helper function: expanded expit
filterCompartments      Filter compartments using confidence estimates
                        and eigenvalue thresholds
fisherZ                 Fisher's Z transformation
fixCompartments         Invert, or "fix", compartments that have a
                        minimum confidence score (1-min.conf)
flogit                  Helper function: squeezed logit
getABSignal             Calculate Pearson correlations of smoothed
                        eigenvectors
getATACABsignal         Estimate A/B compartments from ATAC-seq data
getAssayNames           Get the assay names from a SummarizedExperiment
                        object
getBinMatrix            Generate bins for A/B compartment estimation
getChrs                 Get the chromosomes from an object
getCorMatrix            Calculate Pearson correlations of a binned
                        matrix
getDenoisedMatrix       Wrapper to denoise a correlation matrix using a
                        Random Matrix Theory approach
getDomainInflections    A wrapper function to generate a GRanges object
                        of chromatin domain inflection points
getGlobalMeans          Get the global means of a matrix
getMatrixBlocks         Get chunked sets of row-wise or column-wise
                        indices of a matrix
getSVD                  Compute the SVD of a matrix using irlba
getSeqLengths           Get the seqlengths of a chromosome
getShrinkageTargets     Get the specified samples to shrink towards
                        instead of the global mean
hdf5TFIDF               Transform/normalize compartment calls using
                        TF-IDF on HDF5-backed objects
hg19.gr                 hg19 seqlengths as a GRanges object
hg38.gr                 hg38 seqlengths as a GRanges object
ifisherZ                Fisher's Z transformation
importBigWig            Import and optionally summarize a bigwig at a
                        given resolution
k562_scatac_chr14       Example scATAC-seq data for compartmap
k562_scrna_chr14        Example scRNA-seq data for compartmap
k562_scrna_se_chr14     Example scRNA-seq data for compartmap
meanSmoother            Windowed mean smoother
mm10.gr                 mm10 seqlengths as a GRanges object
mm9.gr                  mm9 seqlengths as a GRanges object
plotAB                  Plots A/B compartment estimates on a per
                        chromosome basis
plotCorMatrix           Plot a denoised correlation matrix
precomputeBootstrapMeans
                        Pre-compute the global means for bootstrapping
                        compartments
removeEmptyBoots        Remove bootstrap estimates that failed
scCompartments          Estimate A/B compartments from single-cell
                        sequencing data
shrinkBins              Employ an eBayes shrinkage approach for
                        bin-level estimates for A/B inference
sparseToDenseMatrix     Convert a sparse matrix to a dense matrix in a
                        block-wise fashion
ss3_umi_sce             Example SMART-seq3 scRNA-seq data for
                        compartmap
summarizeBootstraps     Summarize the bootstrap compartment estimates
                        and compute Agresti-Coull confidence intervals
transformTFIDF          Transform/normalize compartment calls using
                        TF-IDF
