Package index • compartmap

Compartment mapping

scCompartments(): Estimate A/B compartments from single-cell sequencing data

getArrayABsignal(): Estimate A/B compartments from methylation array data

Compartment helper

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

getATACABsignal() getRNAABsignal(): Estimate A/B compartments from ATAC-seq data

Correlation matrix

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

Data transformation

transformTFIDF(): Transform/normalize counts using TF-IDF

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

Bootstrapping

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

Data import

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

Bioconductor helpers

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

Stat functions

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 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

Plotting

plotAB(): Plots A/B compartment estimates on a per chromosome basis

plotCorMatrix(): Plot a denoised correlation matrix

Helpers

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

Datasets

hg19.gr: hg19 seqlengths as a GRanges object

hg38.gr: hg38 seqlengths as a GRanges object

mm10.gr: mm10 seqlengths as a GRanges object

mm9.gr: mm9 seqlengths 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

array_data_chr14: Example Illumina 450k methylation array data for compartmap

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

ss3_umi_sce: Example SMART-seq3 scRNA-seq data for compartmap