# Analysis of cell-based screens - revised version of cellHTS

## Documentation for package ‘cellHTS2’ version 2.10.5

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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 information of a cellHTS object
batch,cellHTS-method | Access and replace the batch information of a cellHTS object
batch<- | Access and replace the batch information of a cellHTS object
batch<-,cellHTS,data.frame-method | Access and replace the batch information 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.
coerce,chtsImage,data.frame-method | 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<- | 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
getSettings | cellHTS2 HTML report settings
getTopTable | Generate the hit list from a scored cellHTS object
getZfactor | Per-experiment Z'-factor of a cellHTS object
gseaModule | Constructor for an object of class gseaModule
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
length,GeneSet-method | Constructor for an object of class gseaModule
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<- | 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.
setSettings | cellHTS2 HTML report settings
settings | cellHTS2 HTML report settings
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
updateCellHTS | Update old serialized cellHTS objects.
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