ExpressionTimeSeries-class {tigre} | R Documentation

## Class to contain time series expression assays

### Description

Container for time series expression assays and experimental metadata. `ExpressionTimeSeries` class is derived from `ExpressionSet`, and requires fields `experiments` and `modeltime` in `phenoData`.

### Extends

Directly extends class `ExpressionSet`.

### Objects from the Class

`new("ExpressionTimeSeries")`

`new("ExpressionTimeSeries", phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(0), protocolData = phenoData[,integer(0)], exprs = new("matrix"), var.exprs = new("matrix"))`

This creates an `ExpressionTimeSeries` with `assayData` implicitly created to contain `exprs` and `var.exprs`.

`new("ExpressionTimeSeries", assayData = assayDataNew(exprs=new("matrix")), phenoData = new("AnnotatedDataFrame"), featureData = new("AnnotatedDataFrame"), experimentData = new("MIAME"), annotation = character(0), protocolData = phenoData[,integer(0)])`

This creates an `ExpressionTimeSeries` with `assayData` provided explicitly. In this form, the only required named argument is `assayData`.

`ExpressionTimeSeries` instances are usually created through `new("ExpressionTimeSeries", ...)`. Usually the arguments to `new` include `exprs` (a matrix of expression data, with features corresponding to rows and samples to columns), `var.exprs`, `phenoData`, `featureData`, `experimentData`, `annotation`, and `protocolData`. `phenoData`, `featureData`, `experimentData`, `annotation`, and `protocolData` can be missing, in which case they are assigned default values.

### Slots

`assayData`:

  Inherited from `ExpressionSet`. The models in `gpsim` package assume that `exprs` contains absolute (i.e. non-logarithmic) expression values. The member `var.exprs` may contain variances of the values.

`phenoData`:

  Inherited from `ExpressionSet`. The following fields are required: `experiments` which contains integers from 1 to N with measurements from the same biological assay having the same number; `modeltime` which contains observation times in model units.

`featureData`:

  Inherited from `ExpressionSet`.

`experimentData`:

  Inherited from `ExpressionSet`.

`annotation`:

  Inherited from `ExpressionSet`.

`protocolData`:

  Inherited from `ExpressionSet`.

`.__classVersion__`:

  Inherited from `ExpressionSet`.

### Methods

See also methods for `ExpressionSet`.

`var.exprs(object)`, `var.exprs(object)<- value`

  Access and set `var.exprs`

`initialize("ExpressionTimeSeries")`

  Object instantiation, used by new; not to be called directly by the user.

### Author(s)

Antti Honkela, Jonatan Ropponen

### See Also

`processData`, `processRawData`.

### Examples

    showClass("ExpressionTimeSeries")

[Package tigre version 1.38.0 Index]