Man pages for rz6/CopulaHiC
Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models
| aggregate_diagonals | Aggregates diagonals of based on similarity of XY... |
| balance | Inserts 0 columns and rows after last row/column to... |
| best_fit_bilinear | Fits bilinear model to set of x,y points. |
| bootstrap_dataset | Bootstraps interactions from given Hi-C dataset. |
| bootstrap_interactions | Hi-C interactions bootstrapping. |
| bootstrap_sparse | Bootstraps interactions from contact map given in sparse... |
| compartment_ranges | Calculates ranges of each consecutive compartment along given... |
| constructGLM | Constructs GLM to model per-diagonal Hi-C contact dependancy |
| decay_correlation.HiCcomparator | Calculates correlations between diagonals. |
| dense2sparse | Converts matrix given in dense format to sparse format data... |
| differential_interactions.HiCglm | Finds significantly interacting rectangle-like regions. |
| dominating_signal.HiCcomparator | Calculates coverage or decay of Hi-C maps. |
| do_pca | PCA analysis of Hi-C contact maps. |
| HiCcomparator | An S3 class to represent object for Hi-C maps comparisons. |
| hicdiff2mtx | Converts significance maps to dense matrices. |
| hicdiff.HiCglm | Computes differential (p-value/q-value) map. |
| HiCglm | An S3 object to represent differential GLM Hi-C model. |
| image_plot_na | Wrapper for fields::image.plot function. |
| interactions2tads | Maps interactions to TADs. |
| interactions2zscores | Convert interactions into zscores |
| intersect_tads | Finds intersection between 2 sets of TADs. |
| left.max | Find first local maximum. |
| local.max | Finds local maximas indices. |
| local.min | Finds local minimas indices. |
| map2tads | Determines TAD boundaries using Insulation Score. |
| mean_expected | Constructs Toeplitz matrix with means on diagonals... |
| merge.HiCcomparator | Finds regions, which interacts in both experiments (maps). |
| move_contacts | Move contacts to given pair of interacting regions |
| neighborhood | Extracts neighborhood around i,j cells of given matrix. |
| pc2mtx | Matches compartment with entries of contact map given in... |
| pipe | Pipe operator |
| plot_contact_map | Plots simple contact map or fold-change contact map with log2... |
| plot_diff_map | Plots differential map. |
| plot_pc_vector | Plots A/B compartment vector. |
| plot_regions | Plots regions (TADs or Long Range interactions) on contact... |
| plot_with_inset | Plots contact map or diff map with inset. |
| proportions | Calculate proportion of interactions |
| read_dense | Reads given npz file and returns list with dense matrices. |
| read_npz | Reads npz file with matrices and converts them sparse... |
| read_size | Reads dimension of every matrix in npz file. |
| remove_unmappable | Removes unmappable regions (all zeros columns and rows) from... |
| restore_unmappable_mtx | Restores unmappable regions (all zeros columns and rows) in... |
| restore_unmappable_vec | Restores deleted regions (cells) in vector, for example... |
| right.min | Find first local minimum. |
| sample_alri | Randomly selects cells for artificial long range... |
| sample_hic_data | Sample data containing Hi-C contact maps as well as... |
| save_npz | Saves list with dense matrices to npz compressed file. |
| significance | Computes significance of data given the model |
| simulate_contacts | Simulate corresponding interactions based on given... |
| simulate_map.HiCglm | Simulates maps based on background model. |
| simulate_null.HiCglm | Samples interactions based on background model. |
| sparse2dense | Converts sparse matrix to dense matrix. |
| sparse2interactions | Convert sparse contact map to atomic interactions. |
| superdiag | Efficiently slices k-th diagonal from matrix A. |
