# Higher-order chromatin domain inference in single cells from scRNA-seq and scATAC-seq

## Documentation for package ‘compartmap’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

.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
getAssayNames | Get the assay names from a SummarizedExperiment object
getATACABsignal | Estimate A/B compartments from ATAC-seq data
getBinMatrix | Generate bins for A/B compartment estimation
getChrs | Get the chromosomes from an object
getCorMatrix | Calculate Pearson correlations of a binned matrix
getDenoisedCorMatrix | Wrapper to denoise a correlation matrix using a Random Matrix Theory approach
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
getRNAABsignal | Estimate A/B compartments from ATAC-seq data
getSeqLengths | Get the seqlengths of a chromosome
getShrinkageTargets | Get the specified samples to shrink towards instead of the global mean
getSVD | Compute the SVD of a matrix using irlba
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