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

## Documentation for package ‘cellHTS2’ version 2.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D G I K L M N O P R S T U W

cellHTS2-package | cellHTS2 Package Overview

## -- A --

annotate | Annotates the reagents (probes) of a cellHTS object
annotate-method | Annotates the reagents (probes) of a cellHTS object

## -- B --

batch | Access and replace the batch information of a cellHTS object
batch-method | Access and replace the batch information of a cellHTS object
batch<- | Access and replace the batch information of a cellHTS object
batch<--method | Access and replace the batch information of a cellHTS object
bdgpbiomart | Dataset with annotation of CG identifiers
Bscore | B score normalization
buildCellHTS2 | Build a cellHTS2 object from a data frame containing measurements

## -- C --

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-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-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-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

## -- D --

Data | Access and replace the assayData slot of a cellHTS object
Data-method | Access and replace the assayData slot of a cellHTS object
Data<- | Access and replace the assayData slot of a cellHTS object
Data<--method | Access and replace the assayData slot of a cellHTS object
dualCh | A sample cellHTS object containing dual channel data

## -- G --

geneAnno | Access the annotation from a cellHTS object.
geneAnno-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

## -- I --

imageScreen | Experiment-wide quality control plot of a cellHTS object
initialize-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-method | Retrieve the contents of the input files used to generate a given cellHTS object.

## -- K --

KcViab | A sample cellHTS object - D. melanogaster genome-wide RNAi screen
KcViabSmall | A sample cellHTS object - D. melanogaster genome-wide RNAi screen

## -- L --

length-method | Constructor for an object of class gseaModule
lines-method | Creates an object of class "ROC" which can be plotted as a ROC curve

## -- M --

meanSdPlot | A class for data from cell-based high-throughput assays performed in plate format.
meanSdPlot-method | A class for data from cell-based high-throughput assays performed in plate format.

## -- N --

name | A class for data from cell-based high-throughput assays performed in plate format.
name-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<--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-method | A class for data from cell-based high-throughput assays performed in plate format.
normalizePlates | Per-plate data transformation, normalization and variance adjustment

## -- O --

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.

## -- P --

pdim | Retrieve information related with the format of a RNAi experiment
pdim-method | Retrieve information related with the format of a RNAi experiment
plate | Retrieve information related with the format of a RNAi experiment
plate-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-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-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-method | Retrieve the contents of the input files used to generate a given cellHTS object.
plot-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-method | Retrieve information related with the format of a RNAi experiment

## -- R --

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-class | Class that contain data that can be plotted as a ROC curve.
ROC-method | Creates an object of class "ROC" which can be plotted as a ROC curve
rsa | Perform RSA ranking on the screening results.

## -- S --

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-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-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-method | Class that contain data that can be plotted as a ROC curve.
show-method | A class for data from cell-based high-throughput assays performed in plate format.
spatialNormalization | Spatial normalization
state | Retrieve the state of a cellHTS object.
state-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

## -- T --

templateDescriptionFile | Creates a template description file for an RNAi experiment

## -- U --

updateCellHTS | Update old serialized cellHTS objects.

## -- W --

well | Retrieve information related with the format of a RNAi experiment
well-method | Retrieve information related with the format of a RNAi experiment
wellAnno | Access the annotation from a cellHTS object.
wellAnno-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-method | Write the data from a cellHTS object to a tab-delimited file