Man pages for bioinform/ecTMB
Esitmation and Classification of TMB
| assignClass | AssignClass |
| calMut | calMut provide observed and predicted mutation rate |
| CalTMB | CalTMB |
| checkMutC | check each sample have at least one mutation. |
| CM | CM |
| ConvertExtraType | ConvertExtraType |
| count_Mut | Count mutatin per patient or per mutation tri-nuclear... |
| ExGMM | ExGMM |
| fit_model | fit_model |
| getBgMRtri | Calculate the relative mutation frequency for each... |
| getEnsemblID | getEnsemblID |
| get_exomeGene | Get exomeGene |
| getGeneBgProb | getGeneBgProb |
| getGeneSymbol | getGeneSymbol |
| get_genewise_dispersion_mle_mu | MLE to estimate genewise dispersion ### |
| get_glen | get_glen |
| Get_incon_mut | Get_incon_mut Get Variants with incosistant gene annotation... |
| get_muhat | get data mu for each gene ##### |
| get_mu_hat_mle | get_mu_hat_mle |
| get_mu_phi | get_mu_phi |
| getmu_post_optimize | getmu_post_optimize |
| getsigma | get sigma ### |
| getsubData | getsubData |
| getTMBs | getTMBs |
| getzero_p | get zero_p ### |
| get_zip_pairparam_mle | Calculate mu and zero_p by MLE for ZIP model # |
| loadfile | loadfile |
| mafCleanup | maf.cleanup |
| maf_dnp_converter | maf_dnp_converter |
| MutSet | MutSet class |
| OverLap | OverLap |
| pred_TMB | pred_TMB |
| readData | read and load maf file and necessary reference file |
| remove_outliers | remove_outliers |
| retrieve_context | retrieve_context |
| zipMLE | Calculate mu and zero_p by MLE for ZIP model # |
