Man pages for evanamartin/TopPICR
What the Package Does (One Line, Title Case)
| align_rt | Align retention times to a reference data set |
| apply_evalue_cutoff | Filter the data by E-value |
| augment_annotation | Include additional variables and UniProt accessions |
| calc_error | Calculate ppm and retention time error |
| cluster | Cluster data based on mass and retention time |
| compute_fdr | Compute the FDR |
| create_mdata | Create feature metadata |
| create_pcg | Combines clusters based on mass and retention time |
| data_pf | ... |
| filter_by_count | Filter low count proteoforms |
| find_evalue_cutoff | Calculate E-value cutoff |
| find_ref_ds | Find reference data set |
| form_model | Use 'loess' to create a model between data sets |
| infer_prot | Protein inference |
| map_proteoform | Map proteoforms to proteins |
| match_features | Extract feature intensity values from unidentified feature... |
| plot_acc | Plot PTMs with associated spectral counts |
| plot_accession_ptm | ... |
| plot_fragments | Plot all fragments for a given UniProt accession |
| read_toppic | Read in TopPIC files |
| recalibrate_mass | Recalibrate the mass |
| remove_decoys | Remove decoy proteins |
| rm_false_gene | Select one gene per feature |
| set_pf_level | Determine the proteoform level for each 'Proteoform' |
| to_msnset | Convert TopPICR output to an MSnSet object |
