Man pages for qenvio/dryhic
Some Functions to Handle HiC Data
| correct_mat_from_b | Apply a bias correction to a HiC contact matrix |
| evec_dist | Compute the distance between two eigenvectors. |
| first_max | Find first local minimum |
| first_min | Find first local minimum |
| fitcnv | Estimate copy number |
| get_contacts_matrix | Make a contact matrix from HiC data |
| get_contacts_per_bin | Retrieve HiC data per genomic bin |
| get_distance_decay | Compute distance decay of a contact matrix |
| get_expected_matrix | Compute expected matrix (by distance decay). |
| ICE | Quick and dirty implementation of ICE matrix normalization |
| kr_sparse | Perform the Knight-Ruiz normalization. |
| laplacian_matrix | Get the associated laplacian matrix. |
| logfinite | Log-transform a vector and substitute infinite values by 'NA' |
| logpseudo | Add pseudo counts to a vector and Log-transform it |
| make_bins | Bin the genome |
| mat2df | Transform the contacts of a 'dgTMatrix' into a 'data.frame' |
| oned | Compute oned correction |
| paste_matrices | Create a 'data.frame' with the contacts of two matrices... |
| plot_matrix | Plot HiC contact matrix |
| reduce_resolution | Reduce resolution (incrrease bin size) of a HiC contact... |
| reproducibility_score | Compute the reproducibility score between two contact... |
| scc | Compute the stratum adjusted correlation coefficient (SCC)... |
| subsample_matrix | Subsample a HiC contact matrix |
| subset_matrix | Extract the contacts associated to a region form a acontact... |
| symmetrize_matrix | Get the full symmetric matrix from a upper triangular contact... |
| upper_tri | Get upper triangular matrix from a HiC contact matrix |
