cellHTS2: cellHTS2 Package Overview
In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

Description Details Author(s) References See Also

cellHTS2 Package Overview

This package provides data structures and algorithms for cell-based high-throughput assays performed in plate format. Typical applications are RNA interference or small molecular compound screens. The most important data class is cellHTS, which extends the NChannelSet class.

Full help on methods and associated functions is available from within class help pages.

Data sets: KcViab, KcViabSmall, oldKcViabSmall, dualCh, bdgpbiomart.

Introductory information is available from vignettes, type openVignette().

Class-specific methods: annotate, batch, batch<-, compare2cellHTS, configure, Data, Data<-, geneAnno, intensityFiles, name, name<-, nbatch, pdim, plate, plateConf, plateEffects, plateList, position, screenDesc, screenLog, state, well, wellAnno, writeTab, ROC.

Generic functions: show, initialize, validObject.

Other functions: oneRowPerId, write.tabdel, readPlateList, readHTAnalystData, normalizePlates, Bscore, spatialNormalization, plotSpatialEffects, summarizeChannels, scoreReplicates, summarizeReplicates, imageScreen, configurationAsScreenPlot, getEnVisionRawData, getEnVisionCrosstalkCorrectedData, getTopTable, getMeasureRepAgreement. getDynamicRange, getZfactor, writeReport, convertOldCellHTS, scores2calls, and templateDescriptionFile.

A full listing of documented topics is available in HTML view by typing help.start() and selecting the cellHTS2 package from the Packages menu or via library(help="cellHTS2").

Ligia P. Bras

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

Below, we present a list of ‘high level’ functions in the celHTS2 package together with a brief description of what they do.

Data import:

readPlateList read a collection of plate reader data files.

readHTAnalystData read input files from a HTanalyser plate reader containing data for a set of plate replicates.

getEnVisionRawData this function can be used as an import function when calling readPlateList to read plate result files obtained from EnVision Plate Reader.

getEnVisionCrosstalkCorrectedData this function can be used as an import function when calling readPlateList to read plate result files obtained from EnVision Plate Reader.

Screen configuration and annotation:

annotate annotates the reagents (e.g. siRNAs, molecular compounds) of a cellHTS object.

configure annotates the plates and the plate result files of a gcellHTS object.

Accessors:

batch accesses and replaces the batch slot of a cellHTS object.

Data accesses and replaces the assayData slot of a cellHTS object. It returns a 3D array with dimensions number of features (product between the number of wells per plates and the number of plates) x number of samples (or replicates) x number of channels.

geneAnno returns the reagent IDs used in the screen (i.e. the contents of fData(object)[,"GeneID"].

intensityFiles returns a list, where each component contains a copy of the imported input data files.

name obtains the name(s) of the assay, or multiple assays, stored in the object. This corresponds to the contents of column assay of the phenoData slot of the cellHTS object.

pdim obtains the plate dimensions (number of rows and columns) for the data stored in object.

plate plate identifier for each feature (well).

plateConf returns a data.frame that contains what was read from the plate configuration input file (except the first two header rows) during the screen configuration step.

plateList returns a data.frame containing what was read from the plate list file, plus a column status of type character that contains the string "OK" if the data import appeared to have gone well, and the respective error or warning message otherwise.

plateEffects accesses the slots rowcol.effects and overall.effects.

position gives the well number for each feature (well) within each plate.

screenDesc returns an object of class character that contains what was read from the screen description input file during the configuration of the cellHTS object.

screenLog returns a data.frame containing what was read from the screen log input file during the screen configuration step.

state This generic function accesses the state of an object derived from the cellHTS class.

well gives the alphanumeric identifier (e.g. A01, A02, ...) for each well and plate.

wellAnno accesses the plate annotation stored in fData(object)[,"controlStatus"].

Data preprocessing:

All the following methods work on the data stored in the slot assayData of a cellHTS object.

normalizePlates per-plate data transformation, normalization and variance adjustment.

Bscore correction of plate and spatial effects using the B score method (without variance adjustment of the residuals).

spatialNormalization correction of spatial effects by fitting a polynomial surface within each plate using local regression (loess or robust local fit). Uses a second degree polynomial (local quadratic fit). Only wells containing "sample" are considered to fit the models.

summarizeChannels combines intensities from a dual-channel assay by applying the function defined in fun.

scoreReplicates transform per-replicate values into scores.

summarizeReplicates summarizes between normalized and scored replicate values, obtaining a single value for each probe.

scores2calls applies a sigmoidal transformation to the z-score values stored in a cellHTS object mapping them to the range [0,1].

Miscellaneous:

compare2cellHTS compares two cellHTS objects to see whether they derive from the same initial cellHTS object.

convertOldCellHTS converts an old S3 class cellHTS object obtained using cellHTS package to new S4 class cellHTS object(s) to use with package cellHTS2.

convertWellCoordinates converts between different ways of specifying well coordinates within a plate. For example, wells can be identified by an alphanumeric character (e.g. "B02" or c("B", "02")) or by an integer value (e.g. 26).

ROC creates an object of class ROC from a scored cellHTS object which can be plotted as a ROC curve.

getTopTable generates the hit list from a scored cellHTS object and write it to a tab-delimited file.

getMeasureRepAgreement calculates the agreement between plate replicates using raw data or normalized data stored in a cellHTS object.

getDynamicRange calculates per-plate dynamic range of data stored in a cellHTS object.

getZfactor calculates per-experiment Z'-factor of data stored in a cellHTS object. The Z'-factor is a measure that quantifies the separation between the distribution of positive and negative controls.

plotSpatialEffects this function plots the per-plate row and column effects estimated by the B score method or by the spatial normalization.

imageScreen creates an image plot that gives an overview of the whole set of score values stored in a scored cellHTS object.

writeReport creates a directory with HTML pages of linked tables and plots documenting the contents of the preprocessing of a cellHTS object.

oneRowPerId rearranges dataframe entries such that there is exactly one row per ID.

nbatch gives the total number of batches in a cellHTS object.

templateDescriptionFile creates a template description file for an RNAi experiment with default entries compliant with MIAME class and with additional entries specific for a cellHTS object.

writeTab this function is a wrapper for the function write.table to write the contents of assayData slot of a cellHTS object to a tab-delimited file. If the object is already annotated, the probe information (fData(object)@GeneID) is also added.

write.tabdel a wrapper for the function write.table used to write data to a tab-delimited file.

meanSdPlot method for meanSdPlot (from the vsn package) to construct the standard deviation versus mean plot of data stored in a cellHTS object.

cellHTS2 documentation built on Nov. 8, 2020, 6 p.m.