Man pages for nbenn/singleCellFeatures
Analyze single cell features stored in an openBIS instance
| analyzeSeparation | Find a hyperplane separating the sample points |
| augmentAggregate | Augment PlateData with Aggregates |
| augmentBscore | Augment PlateData with B-scores |
| augmentCordinateFeatures | Augment all features involving locations |
| augmentImageLocation | Augment the image location within a well |
| augmentMars | Augment PlateData with MARS residuals |
| checkCompletenessFeature | Check completeness of data |
| checkCompletenessImage | Check if the set of images is complete |
| checkCompletenessWell | Check if the set of wells is complete |
| checkConsistency | Check consistency of Data object |
| cleanData | Remove some bad image data |
| compareModeltoTruth | Compare result of binary classification to truth |
| configGet | Loads the config object |
| configInit | Creates a config file template |
| configPathGet | Get the config file path |
| configPathSet | Set the config file path |
| configSet | Overwrites the config file |
| convertToPlateLocation | Covert compatible objects to PlateLocation |
| convertToWellLocation | Covert compatible objects to WellLocation |
| deleteAllMetadataCaches | Remove all metadata caches |
| deleteAllWellCaches | Remove all local well caches |
| extractCells | Extract cells from Data objects |
| extractFeatures | Extract features from Data objects |
| extractImages | Extract data for images from Data objects |
| extractWells | Extract WellData objects form a PlateData object |
| findPlates | Find PlateLocations |
| findWells | Find WellLocations |
| getAllLocalPlates | Get all local plates |
| getBarcode | Get the barcode of a PlateLocation/WellLocation object |
| getCacheFilenameData | Get path/filename of a PlateLocation/WellLocation object... |
| getCacheFilenameMeta | Get the path/filename of the metadata chache for a... |
| getFeatureNames | List feature names of a Data object |
| getLocalPath | Get the local path of a PlateLocation/WellLocation object |
| getNoImgPerWell | Get the number of images per Well |
| getNumCores | Get the number of available cores |
| getOpenBisPath | Get the path of a PlateLocation/WellLocation object on... |
| getPathogen | Get the pathogen name of a PlateLocation/WellLocation object |
| getSingleCellData | Read all single cell features for wells/plates |
| getWellIndex1D | Linearize the index of a well on a 16x24 well plate |
| getWellIndex2D | Get the 2D index of a well on a 16x24 well plate |
| getWellName | Get the well name of a WellLocation object |
| glmBootstrapStability | Analyze stability of top n coefficients |
| ImageData | Constructor for ImageData objects |
| makeFeatureCompatible | Enforce equal feature sets |
| makeRankFull | Enforce full rank design matrix |
| MatData | Constructor for MatData objects |
| meltData | Combine all data in a given Data object |
| moveFeatures | Move feature(s) to different group |
| normalizeData | Normalize Datasets |
| normalizeMoltenData | Normalize data |
| PlateAggregate | Constructor for PlateAggregate objects |
| plateBoxplot | Boxpolot of feature per well |
| PlateData | Constructor for PlateData objects |
| plateHeatmap | Plot a plate heatmap |
| PlateLocation | Constructor for PlateLocation objects |
| PlateMetadata | Constructor for PlateMetadata objects |
| prepareDataforGlm | Prepare a dataset for GLM analysis |
| processSingleCellDataPlate | Read all single cell features for wells/a plate |
| readRDSMC | A wrapper around readRDS for faster reading of compressed... |
| rebuildAllMatDataCaches | Rebuild all local plates |
| rebuildCache | Rebuild cache files for certain Data objects |
| reloadSingleCellFeatures | Reload the singleCellFeatures package |
| saveRDSMC | A wrapper around saveRDS to enable multicore compression |
| saveToCache | Build cache files for certain Data objects |
| size | Get amount of storage used by an object |
| updateDatabaseFeatures | Update the featureDatabase object |
| updateDatabasePlate | Generate the plateDatabase object |
| updateDatabaseWells | Generate the wellDatabasePathogen objects |
| WellData | Constructor for WellData objects |
| wellDatabaseCoverage | Assess the coverage provided by available metadata |
| WellLocation | Constructor for WellLocation objects |
| WellMetadata | Constructor for WellMetadata objects |
