Man pages for XikunHan/metabolomicsR
Tools for Metabolomics Data
| anno_hmdb | Query metabolite ID in HMDB database |
| assayData | get assayData |
| assayData_set | set assayData |
| batch_norm | batch normalization |
| batch_norm_df | batch normalization for a data.frame |
| bridge | bridge different data sets based on conversion factors |
| column_missing_rate | column missing rate |
| correlation | correlation of features between two Metabolite objects |
| create_Metabolite | Create a Metabolite object |
| df_plasma | Example data. |
| featureData | get featureData |
| featureData_set | set featureData |
| filter_column_constant | filter columns if values are constant |
| filter_column_missing_rate | filter columns using missing rate |
| filter_row_missing_rate | filter rows using missing rate |
| fit_lm | available regression methods |
| genuMet_makefeature | distinguish genuine untargeted metabolic features without QC... |
| impute | impute missing values |
| inverse_rank_transform | rank-based inverse normal transformation |
| is_outlier | is outlier |
| load_data | Load metabolite data from three separate files |
| load_excel | Load metabolite data from an excel file |
| maplet2Metabolite | Convert maplet data to a Metabolite object |
| merge_data | merge two Metabolite objects |
| Metabolite2maplet | Convert a Metabolite object to maplet data |
| Metabolite-class | The Metabolite class |
| modelling_norm | LOESS normalization |
| nearestQC_norm | nearest QC sample normalization |
| outlier_rate | outlier rate |
| pareto_scale | pareto scale transformation |
| plot_injection_order | injection order scatterplot |
| plot_Metabolite | plot a Metabolite object |
| plot_PCA | plot PCA |
| plot_QC | quality control visualization |
| plot_ROC | ROC |
| plot_tsne | plot tSNE |
| plot_UMAP | Plot UMAP |
| plot_volcano | volcano plot for regression results |
| QCmatrix_norm | QCmatrix normalization |
| QC_pipeline | quality control pipeline |
| QC_pipeline_df | quality control pipeline for a simplified data.frame. |
| regression | regression analysis |
| replace_outlier | change outlier values as NA or winsorize |
| row_missing_rate | row missing rate |
| RSD | RSD |
| run_PCA | Principal Components Analysis |
| sampleData | get sampleData |
| sampleData_set | set sampleData |
| save_data_txt | Save metabolite data in txt files |
| save_data_xls | Save metabolite data in an Excel file |
| show-Metabolite-method | Print a Metabolite class object |
| subset | subset a Metabolite object. |
| transformation | apply transformation to a Metabolite object |
| update_Metabolite | Update a Metabolite object |
