Man pages for jdreyf/PANTS
Pathway analysis via network smoothing
| diag_kernel | Make diagonal kernel matrix |
| edgelist2graph | Transform a data frame edge list into an 'igraph' graph |
| ezpermutations | Resample sample labels for permutation testing |
| Gmat2gmt | Transform analyte-by-pathway matrix into list compatible with... |
| gmt2Gmat | Transform list from GMT into feature-by-pathway matrix |
| graph2kernel | Transform an 'igraph' graph into a p-step random walk kernel |
| match_mats | Expand kernel to match features in object and pathway matrix |
| mat_pow | Calculate power of a matrix |
| neighbor_nms | Get names of nodes' neighbors |
| opt_binom_n | Find minimal binomial N that ensures 'ezpermutations' obtains... |
| pants | Pathway analysis via network smoothing (Pants) |
| p_ecdf | Estimate p-value from simulations |
| plot_pwy | Plot network diagram for a pathway |
| sapply_by_ncores | Sapply by number of cores |
| score_features | Score features using ezlimma and score_fcn |
| select_ntop_per_pwy | Select top drivers for a pathway |
| sif2edgelist | Clean Pathway Commons SIF file |
| sim_pants | Simulate 'pants' to estimate size & power |
| sim_pants_mediation | Simulate 'pants' with mediation to estimate size & power |
| SMPDB2Gmat | Transform SMPDB protein and/or metabolite pathway data frames... |
| subset_gmat | Subset pathway inclusion matrix based on size |
| write_pants_xl | Write Excel XLSX file with links to CSVs |
