Analysis of cell-based screens - revised version of cellHTS


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Documentation for package ‘cellHTS2’ version 2.6.0

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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