Man pages for HenrikBengtsson/aroma.Base
A generic R plugin dispatcher for BASE
| addColumn.BaseFileSection | Adds a column to the other column names |
| appendSection.BaseFile | Adds a section to this BASE file structure |
| aroma.Base-package | Package aroma.Base |
| as.character.BaseFile | Gets a string description of object |
| as.character.BaseFileAssays | Gets a string description of object |
| as.character.BaseFileBioassaysetinfo | Gets a string description of object |
| as.character.BaseFileParameters | Gets a string description of BASE parameters |
| as.character.BaseFileSection | Gets a string description of object |
| as.character.BaseFileSpots | Gets a string description of object |
| as.list.BaseFile | Gets a list representation of object |
| as.list.BaseFileSection | Gets a list representation of object |
| attachParameters.BaseFileParameters | Assigns the parameters of a BASE parameters section locally |
| BaseFile | The BaseFile class |
| BaseFileAssays | The BaseFileAssays class extending BaseFileSection |
| BaseFileBioassaysetinfo | The BaseFileBioassaysetinfo class extending BaseFileSection |
| BaseFileParameters | The BaseFileParameters class extending BaseFileSection |
| BaseFileSection | The BaseFileSection class |
| BaseFileSpots | The BaseFileSpots class extending BaseFileSection |
| BasePluginDispatcher | The BasePluginDispatcher class |
| buildReports.BasePluginDispatcher | Build reports from RSP templates |
| equals.BaseFile | Checks if this object equals another |
| equals.BaseFileSection | Checks if a BASE file section equals another |
| extractBaseFileSpotsData | Low-level function to extract assay data and save it to file... |
| getAllDataFiles.BaseFile | Gets the names of a external data files used by a BASE file |
| getAnnotationColumns.BaseFileAssays | Gets the names of the annotation columns |
| getAssayFields.BaseFileSpots | Gets the names of the assay-field data columns |
| getAssays.BaseFileSpots | Gets the ids of the assays in this section |
| getColumns.BaseFileSection | Gets the column names of the data table |
| getColumns.BaseFileSpots | Gets the names of the non-assay-field data columns |
| getCount.BaseFileAssays | Gets the (expected) number of assays in the data table |
| getData.BaseFileSection | Gets all or a subset of data of a BASE file section |
| getData.BaseFileSpots | Gets a subset of or the complete data table |
| getDataByIds.BaseFileAssays | Gets a subset of data for one or all bioassays in the... |
| getDataByKeys.BaseFileSection | Gets a subset of data for one or all bioassays in the... |
| getDataFiles.BaseFileSpots | Gets the filenames where data of an assay-field section is... |
| getHeader.BaseFileSection | Gets one header of a BASE section |
| getHeaders.BaseFileSection | Gets the headers of a BASE section |
| getId.BaseFileAssays | Gets the id of all bioassays in the bioassay set |
| getName.BaseFileAssays | Gets the name of all bioassays in the bioassay set |
| getName.BaseFileBioassaysetinfo | Gets the name of the bioassay set |
| getParameter.BaseFileParameters | Gets one parameter from a BASE parameters section |
| getParameters.BaseFileParameters | Gets parameters from a BASE parameters section |
| getParents.BaseFileAssays | Gets the ids of the assay parents of all bioassays in the... |
| getPluginVersion.BaseFileParameters | Gets the plugin version of a BASE parameters section |
| getSection.BaseFile | Gets one section of this BASE file structure |
| getSections.BaseFile | Gets a subset or all BASE sections |
| getType.BaseFileSection | Gets the type of a BASE section |
| hasColumns.BaseFileSection | Checks if certain columns exists or not |
| hasData.BaseFileSection | Checks if section has a data table |
| hasDataFiles.BaseFileSpots | Checks if data of an assay-field section is stored on file |
| hasHeaders.BaseFileSection | Checks if specified headers exists in a BASE section |
| hasSerialBioAssaySets.BaseFile | Checks if the bioassay sets have data in serial format |
| isSerial.BaseFile | Checks if a BASE file is in serial format or not |
| main.BasePluginDispatcher | Static method to start a BASE plugin |
| nbrOfAssays.BaseFileAssays | Gets the (expected) number of assays in the data table |
| nbrOfAssays.BaseFileSpots | Gets the number of assays in this section |
| nbrOfHeaders.BaseFileSection | Gets the number of headers in a BASE section |
| nbrOfParameters.BaseFileParameters | Gets the number of parameters in a BASE parameters section |
| nbrOfSections.BaseFile | Gets the number of sections in this BASE file structure |
| Non-documented_objects | Non-documented objects |
| patchCode.BasePluginDispatcher | Sources all R source files in the patch directory |
| print.BaseFileSection | Prints a BASE file section to stdout |
| readBaseFile | Low-level function to read a BASE file (stream) from a... |
| read.BaseFile | Static method to read a BASE file structure |
| readBaseFileSection | Low-level function to read a BASE file section from a... |
| removeAllDataFiles.BaseFile | Removes all external data files used by a BASE file structure |
| removeSection.BaseFile | Removes a section from a BASE file structure |
| replaceSection.BaseFile | Replaces a section in a BASE file structure |
| seq.BaseFile | Gets an index sequence for the sections in this BASE file... |
| setAnnotationColumns.BaseFileAssays | Sets the names of the annotation columns |
| setAssays.BaseFileSpots | Sets the ids of the assays in this section |
| setColumns.BaseFileSection | Sets the column names of the data table |
| setColumns.BaseFileSpots | Sets the column names of the data table |
| setCount.BaseFileAssays | Sets (or update) the number of assays in the data table |
| setData.BaseFileAssays | Sets data of a BASE file section |
| setData.BaseFileSection | Sets data of a BASE file section |
| setDataFieldByIds.BaseFileAssays | Sets a field of one or all bioassays in the bioassay set |
| setDataFieldByKeys.BaseFileSection | Sets a data field by another key field |
| setDataFields.BaseFileSpots | Sets data field for an assay in a BASE file spots section |
| setDataFiles.BaseFileSpots | Sets the filenames where data of an assay-field section is... |
| setHeader.BaseFileSection | Sets a header of a BASE section |
| setName.BaseFileAssays | Sets the names of one or all bioassays in the bioassay set |
| setParents.BaseFileAssays | Sets the ids of the assay parents of one or all bioassays in... |
| setType.BaseFileSection | Sets the type of a BASE section |
| sizeOfData.BaseFileSection | Gets the dimension of the data table |
| validate.BaseFileAssays | Validates assays section |
| validate.BaseFileBioassaysetinfo | Validates bioassay-set information section |
| validate.BaseFileSection | Validates BASE file section |
| writeBaseFile | Low-level function to write a BASE file structure to a... |
| write.BaseFile | Writes this BASE file structure |
| writeBaseFileSection | Low-level function to write a BASE file section to a... |
