ExpressionTimeSeries-class: Class to contain time series expression assays

In ahonkela/tigre: Transcription factor Inference through Gaussian process Reconstruction of Expression

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")

ahonkela/tigre documentation built on Aug. 6, 2021, 12:08 p.m.