cellHTS2 {cellHTS2} | R Documentation

## cellHTS2 Package Overview

### Description

cellHTS2 Package Overview

### Details

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")`.

### Author(s)

Ligia P. Bras

### References

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

### See Also

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.

[Package cellHTS2 version 2.50.0 Index]