Man pages for biobenkj/compartmentalizer
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq
| agrestiCoullCI | Agresti-Coull confidence interval for a binomial proportion |
| array.data.chr14 | Example Illumina 450k methylation array data for compartmap |
| bootstrapCompartments | Non-parametric bootstrapping of compartments and... |
| checkAssayType | Check if the assay is a SummarizedExperiment |
| cleanAssayCols | Remove columns/cells/samples with NAs exceeding a threshold |
| cleanAssayRows | Remove rows with NAs exceeding a threshold |
| condenseRE | Condense a RaggedExperiment to a list of... |
| condenseSE | Condense the output of condenseRE to reconstruct per-sample... |
| dot-n_approx | n_tilde in AC |
| dot-p_approx | p_tilde in AC |
| dot-z | Normal alpha/2 quantile |
| estRMT | Denoising of Covariance matrix using Random Matrix Theory |
| extractOpenClosed | Get the open and closed compartment calls based on sign of... |
| fexpit | Helper function: expanded expit |
| filterCompartments | Filter compartments using confidence estimates and eigenvalue... |
| filterOpenSea | Filter to open sea CpG loci |
| fisherZ | Fisher's Z transformation |
| fixCompartments | Invert, or "fix", compartments that have a minimum confidence... |
| flogit | Helper function: squeezed logit |
| getABSignal | Calculate Pearson correlations of smoothed eigenvectors |
| getArrayABsignal | Estimate A/B compartments from methylation array data |
| 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 |
| getDenoisedMatrix | Wrapper to denoise a correlation matrix using a Random Matrix... |
| getDomainInflections | A wrapper function to generate a GRanges object of chromatin... |
| getGlobalMeans | Get the global means of a matrix |
| getMatrixBlocks | Get chunked sets of row-wise or column-wise indices of a... |
| getSeqLengths | Get the seqlengths of a chromosome |
| getShrinkageTargets | Get the specified samples to shrink towards instead of the... |
| getSVD | Compute the SVD of a matrix using irlba |
| hdf5TFIDF | Transform/normalize compartment calls using TF-IDF on... |
| 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... |
| imputeKNN | Impute missing values/NAs with KNN |
| 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 |
| 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 |
| 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 |
| 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... |
| sparseToDenseMatrix | Convert a sparse matrix to a dense matrix in a block-wise... |
| ss3_umi_sce | Example SMART-seq3 scRNA-seq data for compartmap |
| summarizeBootstraps | Summarize the bootstrap compartment estimates and compute... |
| transformTFIDF | Transform/normalize compartment calls using TF-IDF |
