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| cellHTS2-package | cellHTS2 Package Overview |
| annotate | Annotates the reagents (probes) of a cellHTS object |
| annotate,cellHTS-method | Annotates the reagents (probes) of a cellHTS object |
| batch | Access and replace the batch slot of a cellHTS object |
| batch,cellHTS-method | Access and replace the batch slot of a cellHTS object |
| batch<-,cellHTS,array-method | Access and replace the batch slot of a cellHTS object |
| bdgpbiomart | Dataset with annotation of CG identifiers |
| Bscore | B score normalization |
| cellHTS | A class for data from cell-based high-throughput assays performed in plate format. |
| cellHTS-class | A class for data from cell-based high-throughput assays performed in plate format. |
| cellHTS2 | cellHTS2 Package Overview |
| class.cellHTS | A class for data from cell-based high-throughput assays performed in plate format. |
| compare2cellHTS | A class for data from cell-based high-throughput assays performed in plate format. |
| compare2cellHTS,cellHTS,cellHTS-method | A class for data from cell-based high-throughput assays performed in plate format. |
| configurationAsScreenPlot | Screen plot of the plate configuration of a cellHTS object |
| configure | Configures the plates and plate result files |
| configure,cellHTS-method | Configures the plates and plate result files |
| convertOldCellHTS | Convert an old S3 class cellHTS object to the new S4 class cellHTS object |
| convertWellCoordinates | Converts different well identifiers |
| Data | Access and replace the assayData slot of a cellHTS object |
| Data,cellHTS-method | Access and replace the assayData slot of a cellHTS object |
| Data<-,cellHTS,array-method | Access and replace the assayData slot of a cellHTS object |
| dualCh | A sample cellHTS object containing dual channel data |
| geneAnno | Access the annotation from a cellHTS object. |
| geneAnno,cellHTS-method | Access the annotation from a cellHTS object. |
| getDynamicRange | Per-plate dynamic range of a cellHTS object |
| getEnVisionCrosstalkCorrectedData | Read a plate file obtain from EnVision Plate Reader |
| getEnVisionRawData | Read a plate file obtain from EnVision Plate Reader |
| getMeasureRepAgreement | Measures of agreement between plate replicates from a cellHTS object |
| getTopTable | Generate the hit list from a scored cellHTS object |
| getZfactor | Per-experiment Z'-factor of a cellHTS object |
| imageScreen | Experiment-wide quality control plot of a cellHTS object |
| initialize,cellHTS-method | A class for data from cell-based high-throughput assays performed in plate format. |
| intensityFiles | Retrieve the contents of the input files used to generate a given cellHTS object. |
| intensityFiles,cellHTS-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
| KcViab | A sample cellHTS object - D. melanogaster genome-wide RNAi screen |
| KcViabSmall | A sample cellHTS object - D. melanogaster genome-wide RNAi screen |
| lines,ROC-method | Creates an object of class "ROC" which can be plotted as a ROC curve |
| meanSdPlot | A class for data from cell-based high-throughput assays performed in plate format. |
| meanSdPlot,cellHTS-method | A class for data from cell-based high-throughput assays performed in plate format. |
| name | A class for data from cell-based high-throughput assays performed in plate format. |
| name,cellHTS-method | A class for data from cell-based high-throughput assays performed in plate format. |
| name<-,cellHTS,character-method | A class for data from cell-based high-throughput assays performed in plate format. |
| nbatch | A class for data from cell-based high-throughput assays performed in plate format. |
| nbatch,cellHTS-method | A class for data from cell-based high-throughput assays performed in plate format. |
| normalizePlates | Per-plate data transformation, normalization and variance adjustment |
| oldKcViabSmall | A sample S3 class cellHTS object - D. melanogaster genome-wide RNAi screen |
| oneRowPerId | Rearrange dataframe entries such that there is exactly one row per ID. |
| pdim | Retrieve information related with the format of a RNAi experiment |
| pdim,cellHTS-method | Retrieve information related with the format of a RNAi experiment |
| plate | Retrieve information related with the format of a RNAi experiment |
| plate effects | Per-plate data transformation, normalization and variance adjustment |
| plate,cellHTS-method | Retrieve information related with the format of a RNAi experiment |
| plateConf | Retrieve the contents of the input files used to generate a given cellHTS object. |
| plateConf,cellHTS-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
| plateEffects | Access plate effects stored in a cellHTS object. |
| plateEffects,cellHTS-method | Access plate effects stored in a cellHTS object. |
| plateList | Retrieve the contents of the input files used to generate a given cellHTS object. |
| plateList,cellHTS-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
| plot,ROC,missing-method | Creates an object of class "ROC" which can be plotted as a ROC curve |
| plotSpatialEffects | Plate plot with the row and column offsets estimated by the a spatial normalization method |
| position | Retrieve information related with the format of a RNAi experiment |
| position,cellHTS-method | Retrieve information related with the format of a RNAi experiment |
| readHTAnalystData | Read a set of plate results obtained from a HTanalyser plate reader |
| readPlateList | Read a collection of plate reader data files |
| ROC | Creates an object of class "ROC" which can be plotted as a ROC curve |
| ROC,cellHTS-method | Creates an object of class "ROC" which can be plotted as a ROC curve |
| ROC-class | Class that contain data that can be plotted as a ROC curve. |
| scoreReplicates | Scores normalized replicate values given in a cellHTS object |
| scores2calls | Sigmoidal transformation of the score values stored in a cellHTS object obtaining the call values for each probe. |
| screenDesc | Retrieve the contents of the input files used to generate a given cellHTS object. |
| screenDesc,cellHTS-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
| screenLog | Retrieve the contents of the input files used to generate a given cellHTS object. |
| screenLog,cellHTS-method | Retrieve the contents of the input files used to generate a given cellHTS object. |
| show,cellHTS-method | A class for data from cell-based high-throughput assays performed in plate format. |
| show,ROC-method | Class that contain data that can be plotted as a ROC curve. |
| spatialNormalization | Spatial normalization |
| state | Retrieve the state of a cellHTS object. |
| state,cellHTS-method | Retrieve the state of a cellHTS object. |
| summarizeChannels | Summarization of dual-channel data |
| summarizeReplicates | Summarize between scored replicate values given in a cellHTS object to obtain a single value for each probe |
| templateDescriptionFile | Creates a template description file for an RNAi experiment |
| well | Retrieve information related with the format of a RNAi experiment |
| well,cellHTS-method | Retrieve information related with the format of a RNAi experiment |
| wellAnno | Access the annotation from a cellHTS object. |
| wellAnno,cellHTS-method | Access the annotation from a cellHTS object. |
| write.tabdel | Wrapper to function 'write.table' used to write data to a tab-delimited file |
| writeReport | Create a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS experiment |
| writeTab | Write the data from a cellHTS object to a tab-delimited file |
| writeTab,cellHTS-method | Write the data from a cellHTS object to a tab-delimited file |