cellHTS2 {cellHTS2} | R Documentation |
cellHTS2 Package Overview
Important data class: cellHTS
.
This class is a container for cell-based high-throughput RNA
interference assays performed in plate format and it 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
,
and scores2calls
.
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 ligia@ebi.ac.uk
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 gene IDs of a given cellHTS
object.
configure
annotates the plates and the plate result files of a given 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 gene 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 of the assay stored in the object
. This corresponds to the contents of column assay
of the phenoData
slot of the cellHTS
object.
pdim
obtains the plate dimension 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:
normalizePlates
Per-plate data transformation, normalization and variance adjustment.
Bscore
correction of plate and spatial effects of data stored in slot assayData
of a cellHTS
object using the B score method (without variance adjustment of the residuals).
spatialNormalization
correction of spatial plate effects of data stored in slot assayData
of a cellHTS
object 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 plate-corrected intensities from dual-channel data stored in slot assayData
of a cellHTS
instance by applying the function defined in fun
.
scoreReplicates
scores normalized replicate values given in a cellHTS object.
summarizeReplicates
summarizes between normalized and scored replicate values given in a cellHTS object 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.
writeTab
this function is a wrapper for 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
wrapper to function 'write.table' used to write data to a tab-delimited file.
meanSdPlot
wrapper of function meanSdPlot
to construct the standard deviation vs mean plot of data stored in a cellHTS
object.