Man pages for vladpetyuk/vp.misc
Miscellaneous functions used by Vlad Petyuk for proteomics data analysis
| colorschemes | Favorite Colorschemes |
| concatenate_by_features | Concatenate MSnSet Objects by Features |
| dist | Customized Distance Function |
| eset_lm | Nested Linear Model Analysis |
| eset_presence_absence | Presence/Absence Testing |
| exhaustive_ratios | Exhaustive Ratios |
| heatmap.3 | Heatmap |
| heatmap.plus.2 | Tweak of "heatmap.plus" |
| image_msnset | Visualize MSnSet |
| keep_longest_isoform_per_gene | Resolving ambiguity in PTM mapping. |
| knn_imputation | Customized K-NN Imputation |
| limma_a_b | Wrapper for Limma |
| longitudinal_biomarker_study | Example of Longitudinal Biomarker Study |
| lr_modeling | Logistic Regression Predictive Models |
| make.unique.2 | Custom Make Unique |
| map_PTM_sites | PTM Mapping Utilities |
| mixed_effects_anova | Mixed Effects ANOVA |
| msnset | SRM proteomics data from human CSF |
| msnset2txt | Exporting MSnSet as text file |
| normalize_by_feature_property | Normalization of LC-MS/MS Data |
| normalizeByGlob | Basic Normalization Routines |
| normalizeByRef | Normalization of SRM Data |
| oca.set | CPTAC Ovarian Cancer Proteomics Dataset |
| plot_annHeatmap2 | Tweaks of plot.annHeatmap |
| plotAUC | Plot AUC |
| plot_feature | Plotting Individual Protein (Feature) |
| plot_pca_v1 | PCA Plot |
| plot_umap | UMAP Plot |
| protein_inference | Protein Inference |
| readMaxQuantPeptides | Reading MaxQuant Output |
| readMaxQuantProtGroups | Reading MaxQuant Output |
| readMaxQuantSummary | Reading MaxQuant Output |
| readSkyLinePRR | Read SkyLine Results |
| remove_covariate | Removing Covariate Effect form Expression Data |
| rf_modeling | Random Forest Predictive Models |
| rrollup | Rolling-Up Features Abundance Measurements |
| subset_by_size | Filter of ontology enrichment results by size |
| volcano_plot | Volcano Plot |
| xtable2 | Customized xtable |
