cellHTS2              package:cellHTS2              R Documentation

_c_e_l_l_H_T_S_2 _P_a_c_k_a_g_e _O_v_e_r_v_i_e_w

_D_e_s_c_r_i_p_t_i_o_n:

     cellHTS2 Package Overview

_D_e_t_a_i_l_s:

     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")'.

_A_u_t_h_o_r(_s):

     Ligia P. Bras ligia@ebi.ac.uk

_R_e_f_e_r_e_n_c_e_s:

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

_S_e_e _A_l_s_o:

     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
     g'cellHTS' 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.

