| cellHTS-class {cellHTS2} | R Documentation |
Container for data and experimental meta-data from cell-based
high-throughput assays performed in plate format.
Typical applications are RNA interference or small molecular compound screens.
The class extends the NChannelSet class.
Data are from experiments where the same set of reagents (probes) where used.
The class can represent data from multi-channel assays.
The data can be thought of as being organised in a two- or three-dimensional array as follows:
cellHTS object
keeps track of plate ID, row, and column associated with each element.
For historic reasons, and because we are using infrastructure that
was developed for microarray experiments, the following terms are
used synonymously for the elements of the first dimension: reagents,
features, probes, genes.
phenoData.
This is because we are using infrastructure
(the NChannelSet class) that
uses this unfortunate term for this purpose.
Objects can be created by calls of the form new("cellHTS",
assayData, phenoData, ...). See the examples below.
plateList:data.frame containing what was read from input measurement data files
plus a column status of type character containing the string "OK" if the data import
appeared to have gone well, and the respective error or warning
message otherwise.intensityFiles:plateList.
state:plateConf:data.frame containing what was read from the configuration file for the experiment (except the first two header rows). It contains at least three columns named Plate, Well and Content.
Columns Plate and Well are allowed to contain regular expressions.
screenLog:data.frame containing what was read from the screen log file for the experiment, in case it exists. Contains at least three columns, and column names Plate, Well,
and Flag. Additional columns are Sample (when there are replicates or more than one sample or condition) and Channel (when there are multiple channels).
screenDesc:batch:assayData slot and the third dimension corresponding to the number of channels in
assayData slot (Features x Samples x Channels).
Should contain integer values giving the batch number (1, 2, ...)
for each plate, sample and channel.
rowcol.effects:overall.effects:assayData:AssayData, usually
an environment containing matrices of identical size. Each matrix
represents a single channel. Columns in each matrix correspond to
samples (or replicate), rows to features (probes).
Once created, cellHTS manages coordination of samples and channels.
phenoData:AnnotatedDataFrame.
Please see the documentation of the phenoData slot of
NChannelSet for more details.
It contains information about the screens, and it must have the
following columns in its data component:
replicate and assay, where replicate is expected
to be a vector of integers giving the replicate number, while
assay is expected to be a vector of characters giving the name of
the biological assay. Both of these vectors should have the same length
as the number of Samples.
Once created, cellHTS coordinates selection and subsetting
of channels in phenoData.
featureData:AnnotatedDataFrame,
containing information about the reagents: plate, well, column,
the well annotation (sample, control, etc.), etc.
For a cellHTS object, this slot must contain in its
data component at least three mandatory columns named
plate, well and controlStatus. Column
plate is expected to be a numeric vector giving the plate number
(e.g. 1, 2, ...), well should be a vector of characters
(alphanumeric characters) giving the well ID within the plate (e.g. A01,
B01, H12, etc.). Column controlStatus should be a factor
specifying the annotation for each well with possible levels:
empty, other, neg, sample, and
pos. Other levels besides pos and neg
may be employed for controls.
experimentData:MIAME containing
descriptions of the experiment.annotation:"character" of length 1, which can be used to specify
the name of an annotation package that goes with the reagents used
for this experiment..__classVersion__:Versions, containing
automatically created information about the class definition,
Biobase package version, and other information about the user
system at the time the instance was created. See
classVersion and updateObject for
examples of use.
Class NChannelSet, directly.
Methods with class-specific functionality:
name(object)signature(object="cellHTS").
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.
name(object) <- valuesignature(object = "cellHTS", value = "character") assign
the character of length one (value) to the elements in column assay of the slot phenoData of
object.
pdim(object)signature(object = "cellHTS").
Obtain the plate dimension for the data stored in object.
nbatch(object)signature(object = "cellHTS").
Obtain the total number of batches for the data stored in object.
compare2cellHTS(x, y)signature(x = "cellHTS", y = "cellHTS").
Compares two cellHTS objects, x and y, returning TRUE if they are from the same experiment (i.e. if they derive from the same initial cellHTS object), or FALSE otherwise.
Methods with functionality derived from class NChannelSet:
channel,
channelNames,
selectChannels,
object[features, samples],
sampleNames
Methods with functionality derived from eSet:
annotation, assayData, assayData<-,
classVersion, classVersion<-, dim, dims,
experimentData, featureData, phenoData,
phenoData<-, pubMedIds, sampleNames,
sampleNames<-, storageMode, varMetadata,
isCurrent, isVersioned.
Additional methods:
initializeshowstatestate slot of a cellHTS instance.annotatecellHTS object using the screen annotation file.configurecellHTS object using the the screen description file, the screen configuration file and the screen log file.writeTabassayData slot of a cellHTS object to a tab-delimited file.ROCROC,
which represents a receiver-operator-characteristic curve,
from the data of the annotated positive and negative controls in a
scored cellHTS object.meanSdPlot(x)signature(x = "cellHTS") plots row standard deviations across samples versus row means across samples for data stored in slot assayData of a cellHTS object. If there are multiple channels, row standard deviations and row means are calculated across samples for each channel separately. Only wells containing "sample" are considered. See meanSdPlot for more details about this function.
Ligia P. Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk
NChannelSet
readPlateList
annotate
configure
writeTab
state
Data
normalizePlates
ROC
showClass("cellHTS")
showMethods(class="cellHTS")
## An empty cellHTS
obj <- new("cellHTS")
data("KcViabSmall")
KcViabSmall
state(KcViabSmall)
## Replicate 1 as a cellHTS object
y <- KcViabSmall[,1]
compare2cellHTS(KcViabSmall, y)
data("KcViab")
compare2cellHTS(KcViab, KcViabSmall)