Analysis of cell-based screens - revised version of cellHTS

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Documentation for package ‘cellHTS2’ version 2.42.0

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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