Man pages for biospi/bayesprot
Bayesian Protein-level Quantification for Proteomics
| bayesprot | Fit the BayesProt Bayesian Protein-level quantification model |
| bayesprot_fit | Interrogating the 'bayesprot' fit object |
| dea_limma | Univariate differential expression analysis with... |
| dea_MCMCglmm | Mixed-effects univariate differential expression analysis... |
| dea_metafor | Mixed-effects univariate differential expression analysis... |
| dist_invchisq | fit scaled inverse chi squared distribution with fitdistrplus |
| dist_invchisq_mcmc | fit scaled inverse chi squared distribution |
| dist_lst | fit location-scale t distribution with fitdistrplus |
| dist_lst_mcmc | fit location-scale t distribution |
| dist_normal | fit normal distribution with fitdistrplus |
| dist_normal_mcmc | fit normal distribution with fitdistrplus |
| dist_sf_with_fixed_df1_fitdistrplus | fit scaled F distribution with per-datapoint fixed df1 with... |
| execute_model | execute_model (internal) |
| fdr_ash | False Discovery Rate correction with ash |
| fdr_BH | False Discovery Rate correction with the Benjamini-Hochberg... |
| import_MSstats | Import data outputed by an MSstats import routine |
| import_OpenSwath_PyProphet | Import OpenSWATH - PyProphet data |
| import_Progenesis | Import Waters Progenesis data |
| import_ProteinPilot | Import SCIEX ProteinPilot data |
| import_ProteomeDiscoverer | Import Thermo ProteomeDiscoverer data |
| new_control | Control parameters for the BayesProt Bayesian model |
| new_design | Specify study design for imported dataset |
| norm_median | Median normalisation |
| plot_exposures | Add together two numbers. |
| plot_fdr | Add together two numbers. |
| plot_fits | Add together two numbers. |
| plot_pca | Add together two numbers. |
| process_model | process_model (internal) |
| process_model0 | process_model0 (internal) |
| process_plots | process_plots (internal) |
| rhat | rhat |
| runs | Imported dataset run information |
| squeeze_var | Our squeezeVar function - works for small DF unlike Limma... |
| squeeze_var_limma | Limma squeezeVar function |
| summarise_normal_robust | summarise using median/mad |
| summarise_normal_robust_mcmc | fit normal distribution with fitdistrplus |
