Man pages for samWieczorek/DAPAR2
Tools for the Differential Analysis of Proteins Abundance with R
| Add_Item_to_Dataset | xxx |
| adjacency-matrix-filter | Filter a peptide assay on the basis of its adjacency matrix. |
| aggregateIter | xxxx |
| aggregateIterParallel | xxxx |
| aggregateMean | Compute the intensity of proteins as the mean of the... |
| AggregateMetacell | Symbolic product of matrices |
| aggregateSum | Compute the intensity of proteins with the sum of the... |
| aggregateTopn | Compute the intensity of proteins as the sum of the... |
| BuildAdjacencyMatrix | Function matrix of appartenance group |
| BuildColumnToProteinDataset | creates a column for the protein dataset after agregation by... |
| build-design | xxxx |
| buildGraph | Display a CC |
| BuildMetaCell | metacell function which xxx |
| check.conditions | Check if the design is valid |
| check.design | Check if the design is valid |
| Children | Names of all chidren of a node |
| ConvertListToHtml | Convert a list to unnumbered HTML list |
| CountPep | Compute the number of peptides used to aggregate proteins |
| create-example | Creates an example dataset |
| DaparToolshed | DaparToolshed: A package for computating the notorious bar... |
| DaparToolshed-aggregate | Aggregate an assay's quantitative features |
| design-example | xxxx |
| display.CC.visNet | Display a CC |
| dl | mod_dl |
| ExtendPalette | Extends a base-palette of the package RColorBrewer to n... |
| finalizeAggregation | Finalizes the aggregation process |
| ft | ft dataset |
| ft_na | ft_na dataset |
| fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge... |
| GetColorsForConditions | Builds a complete color palette for the conditions given in... |
| GetDetailedNbPeptides | Computes the detailed number of peptides for each protein |
| GetDetailedNbPeptidesUsed | Computes the detailed number of peptides used for aggregating... |
| getExtension | Extension of a file |
| getListNbValuesInLines | Returns the possible number of values in lines in the data |
| GetMetacell | xxxx |
| GetNbPeptidesUsed | Computes the number of peptides used for aggregating each... |
| get.pep.prot.cc | Build the list of connex composant of the adjacency matrix |
| getProteinsStats | Computes the number of proteins that are only defined by... |
| GetSoftAvailables | The set of available softwares to convert from |
| GraphPepProt | Function to create a histogram that shows the repartition of... |
| import-export-QFeatures | Creates an object of class 'QFeatures' from text file. |
| inner.aggregate.iter | xxxx |
| inner.aggregate.topn | xxxx |
| inner.mean | xxxx |
| inner.sum | xxxx |
| is.OfType | Similar to the function 'is.na()' but focused on the equality... |
| Keep_Items_from_Dataset | xxx |
| LH0 | xxxxxx |
| LH0.lm | xxxxxx |
| LH1 | xxxxxx |
| LH1.lm | xxxxxx |
| match.metacell | Similar to the function 'is.na()' but focused on the equality... |
| Metacell_DIA_NN | Sets the metacell dataframe for datasets which are from... |
| Metacell_maxquant | Sets the metacell dataframe |
| metacell-plots | Displays a correlation matrix of the quantitative data of a... |
| Metacell_proline | Sets the metacell dataframe for datasets which are from... |
| metacell-tree | Displays a correlation matrix of the quantitative data of a... |
| mod_Agregation | Module agregation |
| mod_convert | xxx |
| mod_filterExample | xxx |
| mod_Filtering | Module Filtering |
| mod_format_DT | mod_format_DT_ui and mod_format_DT_server |
| mod_helpPopover | Help popover windows |
| mod_infos_dataset | mod_infos_dataset_ui and mod_infos_dataset_server |
| mod_inputGroup | Help popover windows |
| mod_open_dataset | mod_open_dataset_ui and mod_open_dataset_server |
| mod_open_demo_dataset | mod_open_demo_dataset_ui and mod_open_demo_dataset_server |
| mod_settings | mod_settings_ui and mod_settings_server |
| my_hc_chart | Customised resetZoomButton of highcharts plots |
| my_hc_ExportMenu | Customised contextual menu of highcharts plots |
| nEmptyLines | Number of empty lines in the data |
| nonzero | Retrieve the indices of non-zero elements in sparse matrices |
| Parent | Parent name of a node |
| pepa.test | PEptide based Protein differential Abundance test |
| pipeline-protein | Module of Protein pipeline |
| Pipelines | xxx |
| pkgs.require | Loads packages |
| plotJitter | Jitter plot of CC |
| plotJitter_rCharts | Display a a jitter plot for CC |
| ProstarVersions | Version number of Prostar suite |
| QFeatures-accessors | List of metacell tags |
| QFeatures-excel | Exports a 'QFeatures' object to a Excel file. |
| QFeatures-filtering-oneSE | Filter features of one SE based on their rowData |
| QFeatures-utils | Utility funcitons to dela with QFeatures objects. |
| q_metacell | Quantitative metadata vocabulary for entities |
| qMetacell-filter | Search lines which respects request on one or more... |
| query-metacell | xxxx |
| query_qMetacell | Build queries for filtering quantitative metadata |
| ReplaceSpecialChars | Standardize names |
| samLRT | xxxxxx |
| splitAdjacencyMat | splits an adjacency matrix into specific and shared |
| test.design | Check if xxxxxx |
| tracking | Tracking of entities within plots |
