Man pages for JordanVeldboom/compartmap
A/B compartment inference from ATAC-seq and methylation array data
| 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 |
| extractOpenClosed | Get the open and closed compartment calls based on sign of... |
| fexpit | Helper function: expanded expit |
| filterCells | Filter cells using either k-means or Dirichlet process means... |
| filterCompartments | Filter compartments using confidence estimates and eigenvalue... |
| filtered.data.chr14 | Example ATAC-seq data for compartmap |
| 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 |
| getBSABsignal | Estimate A/B compartments from BS-seq data |
| getChrs | Get the chromosomes from an object |
| getCorMatrix | Calculate Pearson correlations of a binned matrix |
| 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... |
| ifisherZ | Fisher's Z transformation |
| imputeKNN | Impute missing values/NAs with KNN |
| meanSmoother | Windowed mean smoother |
| plotAB | Plots A/B compartment estimates on a per chromosome basis |
| precomputeBootstrapMeans | Pre-compute the global means for bootstrapping compartments |
| preprocessArrays | Preprocess arrays for compartment inference |
| preprocessBSseq | Preprocess BS-seq for compartment inference |
| removeEmptyBoots | Remove bootstrap estimates that failed |
| scCompartments | Estimate A/B compartments from ATAC-seq data |
| shrinkBins | Employ an eBayes shrinkage approach for bin-level estimates... |
| smoothBSCounts | Dirichlet smoothing of BS-seq counts prior to compartment... |
| sparseToDenseMatrix | Convert a sparse matrix to a dense matrix in a block-wise... |
| summarizeBootstraps | Summarize the bootstrap compartment estimates and compute... |
| transformTFIDF | Transform/normalize compartment calls using TF-IDF |
