cellHTS-class {cellHTS2} | R Documentation

## Class to contain cell-based high-throughput RNAi data and experimental meta-data

### Description

Container for cell-based high-throughput RNA interference assays performed in plate format. It extends the `NChannelSet` class. Data are from experiments where the same set of features (probes) where used. It can contain data from multi-channel assays. Each group of plate results (replicates, conditions) for a given channel is called a ‘sample’.

### Objects from the Class

Objects can be created by calls of the form `new("cellHTS", assayData, phenoData, ...)`. See the examples below.

### Slots

`plateList`:
  a `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`:
  a list, where each component contains a copy of the imported input data files. Its length corresponds to the number of rows of `plateList`.
`state`:
  a logical vector of length 4 representing the processing status of the object. Should have the names "configured", "normalized", "scored" and "annotated".
`plateConf`:
  a `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`:
  a `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`:
  a character containing what was read from the description file of the experiment.
`batch`:
  a 3D-array with the first two dimensions corresponding to the dimension of each matrix in `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`:
  a 3D array of size Features (i.e. plate size x number of plates) x Samples x Channels containing estimated row and column plate spatial offsets.
`overall.effects`:
  a 3D array of size Features x Samples x Channels containing estimated plate overall offsets.
`assayData`:
  Object of class `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`:
  Object of class `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`:
  Object of class `AnnotatedDataFrame`, used to contain feature data that is unique to this experiment. It may contain 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`. These are vectors with the same size of the number of Features in the experiments. 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 may be employed for the positive and negative controls, besides pos and neg.

`experimentData`:
  Object of class `MIAME` containing descriptions of the experiment.
`annotation`:
  Object of class `"character"`. Usually a length-1 character string identifying the RNAi technology used during the experiment. The annotation string is used to retrieve information about features, e.g., using the `annotation` package.
`.__classVersion__`:
  Object of class `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.

### Extends

Class `NChannelSet`, directly.

### Methods

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) <- value`
  `signature(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:

`initialize`
  used internally for creating objects
`show`
  invoked automatically when the object is displayed to the screen. It prints a summary of the object.
`state`
  Access the `state` slot of a `cellHTS` instance.
`annotate`
  Annotate the `cellHTS` object using the screen annotation file.
`configure`
  Configure the `cellHTS` object using the the screen description file, the screen configuration file and the screen log file.
`writeTab`
  Write the contents of `assayData` slot of a `cellHTS` object to a tab-delimited file.
`ROC`
  Construct an object of S4 class `ROC`, 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.

### Author(s)

Ligia P. Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

### See Also

`NChannelSet` `readPlateList` `annotate` `configure` `writeTab` `state` `Data` `normalizePlates` `ROC`

### Examples

        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)

[Package cellHTS2 version 2.2.5 Index]