Package index • compartmap

Compartment mapping

scCompartments(): Estimate A/B compartments from single-cell RNA or ATAC sequencing data
arrayCompartments(): Estimate A/B compartments from methylation array data

filterCompartments(): Filter compartments using confidence estimates and eigenvalue thresholds
fixCompartments(): Invert, or "fix", compartments that have a minimum confidence score (1-min.conf)
extractOpenClosed(): Get the open and closed compartment calls based on sign of singular values
getABSignal(): Calculate Pearson correlations of smoothed eigenvectors

estRMT(): Denoising of Covariance matrix using Random Matrix Theory
getCorMatrix(): Calculate Pearson correlations of a binned matrix
getDenoisedCorMatrix(): Wrapper to denoise a correlation matrix using a Random Matrix Theory approach

transformTFIDF(): Transform/normalize counts using TF-IDF
hdf5TFIDF(): Transform/normalize compartment calls using TF-IDF on HDF5-backed objects

precomputeBootstrapMeans(): Pre-compute the global means for bootstrapping compartments
bootstrapCompartments(): Non-parametric bootstrapping of compartments and summarization of bootstraps/compute confidence intervals
summarizeBootstraps(): Summarize the bootstrap compartment estimates and compute Agresti-Coull confidence intervals

importBigWig(): Import and optionally summarize a bigwig at a given resolution
filterOpenSea(): Filter to open sea CpG loci
getOpenSeas(): Gather open sea CpG from a GRanges of CpG islands
preprocessArrays(): Preprocess arrays for compartment inference

condenseRE(): Condense a RaggedExperiment to a list of SummarizedExperiments
condenseSE(): Condense the output of condenseRE to reconstruct per-sample GRanges objects to plot
getAssayNames(): Get the assay names from a SummarizedExperiment object
getSeqLengths(): Get the seqlengths of a chromosome from a given genome's GRanges
getChrs(): Get the chromosomes from an object

agrestiCoullCI(): Agresti-Coull confidence interval for a binomial proportion
fexpit(): Helper function: expanded expit
fisherZ(): Fisher's Z transformation
flogit(): Helper function: squeezed logit
getBinMatrix(): Generate bins for A/B compartment estimation
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
getShrinkageTargets(): Get the specified samples to shrink towards instead of the global mean
ifisherZ(): Inverse Fisher's Z transformation
imputeKNN(): Impute missing values/NAs with KNN
meanSmoother(): Windowed mean smoother
precomputeBootstrapMeans(): Pre-compute the global means for bootstrapping compartments
preprocessArrays(): Preprocess arrays for compartment inference
removeEmptyBoots(): Remove bootstrap estimates that failed
scCompartments(): Estimate A/B compartments from single-cell RNA or ATAC 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

cleanAssayCols(): Remove columns/cells/samples with NAs exceeding a threshold. See cleanAssay()
cleanAssayRows(): Remove rows with NAs exceeding a threshold. See cleanAssay()
.n_approx(): n_tilde in AC
.p_approx(): p_tilde in AC
.z(): Normal alpha/2 quantile

array_data_chr14: Example Illumina 450k methylation array data for compartmap
hg19.gr: hg19 seqlengths as a GRanges object
hg19.tx.gr: hg19 genes as a GRanges object
hg38.gr: hg38 seqlengths as a GRanges object
hg38.tx.gr: hg38 genes as a GRanges object
k562_scatac_chr14: Example scATAC-seq data for compartmap
k562_scrna_chr14: Example scRNA-seq data for compartmap
k562_scrna_raw: Example scRNA-seq data for compartmap
mm10.gr: mm10 seqlengths as a GRanges object
mm10.tx.gr: mm10 genes as a GRanges object
mm9.gr: mm9 seqlengths as a GRanges object
mm9.tx.gr: mm9 genes as a GRanges object
openSeas.hg19: hg19 open sea CpG as a GRanges object
openSeas.hg38: hg38 open sea CpG as a GRanges object
openSeas.mm10: mm10 open sea CpG as a GRanges object
openSeas.mm9: mm9 open sea CpG as a GRanges object
ss3_umi_sce: Example SMART-seq3 scRNA-seq data for compartmap