.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 |