Man pages for ash129/LAPP
Ligand Analysis with Physicochemical Properties
| convmat.23 | Amino acid conversion matrix with 23 properties |
| hla.name | Simplify two-position HLA allotype names |
| LAPP | LAPP |
| LAPP.arr.to.df | Convert list of 3D arrays into a 2D data.frame |
| LAPP.heatmap | Plot or save heatmap for a matrix |
| LAPP.PCA | Perform PCA on HLA features |
| LAPP.plot.PCA | Plot LAPP PCA |
| LAPP.plot.PCA.con | Plot PCA contributions |
| LAPP.plot.PCA.var | Plot variances for LAPP PCA |
| LAPP.plot.tSNE | Plot LAPP tSNE |
| LAPP.tSNE | Perform tSNE on HLA features |
| LAPP.wass.1 | Calculate the cumulative first Wasserstein metric over... |
| make.features | Create a converted three-dimensional feature array using a... |
| make.features.list | Create list of feature arrays using a list of list of ligands... |
| normalize | Normalize feature data and remove uninformative features |
| rand.9mers | Randomly selected nonamer sequences from Uniprot |
| read.ligand.files | Read in all .txt files in a folder as ligands |
| renormalize | Normalize feature data and drop features according to how... |
| wass.1 | Calculate the first Wasserstein metric (Earth Mover's... |
