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

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Documentation for package ‘compartmap’ version 1.18.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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