Man pages for zhuchcn/Metabase
Data container, handling, and visualization for high through-put quantitative experiment data.
| as_ExpressionSet | Convert to an mSet object to ExpressionSet |
| as_phyloseq | convert a MicrobiomeSet object to phyloseq |
| assign_lipid_class | Assign lipid class based on lipid annotation name |
| calibrate_lipidomics_wcmc | Calculate concentration by calibrating from internal... |
| collapse_QC | Collapse QC samples from a MetabolomcisSet object |
| conc_table | Construct or assess a conc_table object |
| conc_table-class | S4 class for concentration table |
| conc_table-set | Assign a conc_table slot to a mSet object |
| data-lipid | (Data) Lipidomics dataset |
| dim-mSet-method | Get dimemsions of the conc_table of a mSet object |
| experiment_data | Access the experiment_data slot from a mSet object |
| ExperimentData-class | Deprecated A virtual S4 class for experiment data |
| experiment_data-set | Assign a experiment_data slot to a mSet object |
| export_excel | Export mSet object into a excel sheet |
| export_txt | Export mSet object to separate text files |
| Extract | Extract or Replace A Slot of An mSet or ExperimentData object |
| feature_data | Construct or access a feature_data object |
| feature_data-class | S4 class for feature data. |
| feature_data-set | Assign a feature_data slot to a mSet object |
| featureNames-mSet-method | Get the feature names of a mSet object |
| filter_by_cv | Filter features by QC CV |
| GlycomicsExperimentData | Deprecated Construction method for the S4 class... |
| GlycomicsExperimentData-class | Deprecated S4 class to store experiment data for glycomics... |
| GlycomicsSet | Construct a GlycomicsSet object |
| GlycomicsSet-class | S4 class to store glycomics experiment data |
| hello | Hello, World! |
| import_wcmc_excel | Import West Coast Metabolomics Center data spreadsheet to a... |
| lipid_name_formater | Lipid annotation formater for lipidblast |
| LipidomcisSet-class | S4 class to store lipidomics dataset |
| LipidomicsExperimentData | Construction method for LipidomicsExperimentData-class |
| LipidomicsExperimentData-class | Deprecated S4 class to store experiment data for metabolomics... |
| LipidomicsSet | Construct a LipidomicsSet object |
| MetabolomicsExperimentData | Deprecated Construction method for... |
| MetabolomicsExperimentData-class | Deprecated S4 class to store experiment data for metabolomics... |
| MetabolomicsSet | Construct a MetabolomicsSet object |
| MetabolomicsSet-class | S4 class to store metabolomics experiment data |
| MicrobiomeExperimentData | Deprecated Construct a MicrobiomeExperimentData object |
| MicrobiomeExperimentData-class | Deprecated S4 class to store the experiment data of a... |
| MicrobiomeSet | Main constructor for MicrobiomeSet class |
| MicrobiomeSet-class | S4 class to store Micorbiome Data |
| mSet-class | A virtual S4 class to store an quantitative experiment data. |
| mSet_deseq | Run negative bionomial bistribution based differential... |
| mSet_limma | Run linear model with the limma package |
| MultiExperimentData | S4 class to store experiment data for MultxSet |
| MultxSet | Construct a MultxSet class object |
| MultxSet-class | S4 class for mutiple experiment types |
| mz2molwt | calculate molecular weight from m/z |
| nCarbons | Extract the carbon chain length from lipidome annotation |
| nDoubleBonds | Get the number of double bonds |
| nFattyAcyls | Get the number of fatty acyls of a given lipid annotation. |
| nfeatures-mSet-method | Get number of features from a mSet object |
| nsamples-mSet-method | Get number of samples from a mSet object |
| plot_boxplot | Make a boxplot of a feature |
| plot_heatmap | Create a heatmap of an mSet object |
| plot_hist_NA | Plot Histogram of Missing Values |
| plot_median_hist | Histogram of medians of all features after scaling. |
| plot_normality_boxplot | Plot normality boxplot of each individual feature |
| plot_normality_ridges | Normality density plot of each feature |
| plot_pca | Create a PCA plot |
| plot_qc | Plot quality control from a MetabolomcisSet object |
| ProteomicsExperimentData | Deprecated Construction method for the S4 class... |
| ProteomicsExperimentData-class | Deprecated S4 class to store experiment data for proteomics... |
| ProteomicsSet | Construct a ProteomicsSet object |
| ProteomicsSet-class | S4 class to store proteomics experiment data |
| sampleNames-mSet-method | Get or set the sample names of a mSet object |
| sample_table | Construction or access a sample_table object |
| sample_table-class | S4 class for sample metadata. |
| sample_table-set | Assign a sample_table slot to a mSet object |
| subset_samples-mSet-method | Subset an mSet object |
| summarize_ACL | Calculate the average carbon chain length |
| summarize_EOD | Calculate the Equivalent Double Bond per 18 carbons |
| summarize_features | Summarize mSet by a feature variable |
| summarize_lipid_ratios | Calculate lipid classes ratios |
| summarize_odd_chain | Calculate odd chain lipids abundance |
| summarize_samples | Summarize mSet by sample variables |
| transform_by_feature | Transform an mSet object by features |
| transform_by_sample | Transform an mSet object by sample |
