bioma.data.ExptData class

Package: bioma.data

Contain data values from microarray experiment

Description

The ExptData class is designed to contain data values, such as gene expression values, from a microarray experiment. It stores the data values in one or more DataMatrix objects, each having the same row names (feature names) and column names (sample names). It provides a convenient way to store related experiment data in a single data structure (object). It also lets you manage and subset the data.

The ExptData class includes properties and methods that let you access, retrieve, and change data values from a microarray experiment. These properties and methods are useful to view and analyze the data.

Construction

EDobj = bioma.data.ExptData(Data1, Data2, ...) creates an ExptData object, from one or more matrices of data. Each matrix can be a logical matrix, a numeric matrix, or a DataMatrix object.

EDobj = bioma.data.ExptData(..., {DMobj1, Name1}, {DMobj2, Name2}, ...) specifies an element name for each DataMatrix object. Name# is a string specifying a unique name. Default names are Elmt1, Elmt2, etc.

EDobj = bioma.data.ExptData({Data1, Data2, ...}) creates an ExptData object, from a cell array of matrices of data. Each matrix can be a logical matrix, a numeric matrix, or a DataMatrix object.

EDobj = bioma.data.ExptData(..., 'PropertyName', PropertyValue) constructs the object using options, specified as property name/property value pairs.

EDobj = bioma.data.ExptData(..., 'ElementNames', ElementNamesValue) specifies element names for the matrix inputs. ElementNamesValue is a cell array of strings. Default names are Elmt1, Elmt2, etc.

EDobj = bioma.data.ExptData(..., 'FeatureNames', FeatureNamesValue) specifies feature names (row names) for the ExptData object. .

EDobj = bioma.data.ExptData(..., 'SampleNames', SampleNamesValue) specifies sample names (column names) for the ExptData object.

Input Arguments

Data#

Matrix of experimental data values specified by any of the following:

All inputs must have the same dimensions. All DataMatrix objects must also have the same row names and columns names. If you provide logical or numeric matrices, bioma.data.ExptData converts them to DataMatrix objects with either default row and column names, or the row and column names of DataMatrix inputs, if provided.

The rows must correspond to features and the columns must correspond to samples.

DMobj#

Variable name of a DataMatrix object in the MATLAB Workspace.

Name#

String specifying an element name for the corresponding DataMatrix object

ElementNamesValue

Cell array of strings that specifies unique element names for the matrix inputs. The number of elements in ElementNamesValue must equal the number input matrices.

Default: {Elmt1, Elmt2, ...}

FeatureNamesValue

Feature names (row names) for the ExptData object, specified by one of the following:

  • Cell array of strings

  • Character array

  • Numeric or logical vector

  • Single string, which is used as a prefix for the feature names, with feature numbers appended to the prefix

  • Logical true or false (default). If true, bioma.data.ExptData assigns unique feature names using the format Feature1, Feature2, etc.

If you use a cell array of strings, character array, or vector, then the number of elements must be equal in number to the number of rows in Data1.

SampleNamesValue

Sample names (column names) for the ExptData object, specified by one of the following:

  • Cell array of strings

  • Character array

  • Numeric or logical vector

  • Single string, which is used as a prefix for the sample names, with sample numbers appended to the prefix

  • Logical true or false (default). If true, bioma.data.ExptData assigns unique sample names using the format Sample1, Sample2, etc.

If you use a cell array of strings, character array, or vector, then the number of elements must be equal in number to the number of columns in Data1. If the ExptData object is part of an ExpressionSet object that contains a MetaData object, the sample names (column names) in the ExptData object must match the sample names (row names) in a MetaData object.

Properties

ElementClass

Class type of the DataMatrix objects in the experiment

Cell array of strings specifying the class type of each DataMatrix object in the ExptData object. Possible values are MATLAB® classes, such as single, double, and logical. This information is read-only.

Attributes:

SetAccessprivate

Name

Name of the ExptData object.

String specifying the name of the ExptData object. Default is [].

NElements

Number of elements in the experiment

Positive integer specifying the number of elements (DataMatrix objects) in the experiment data. This value is equivalent to the number of DataMatrix objects in the ExptData object. This information is read-only.

Attributes:

SetAccessprivate

NFeatures

Number of features in the experiment

Positive integer specifying the number of features in the experiment. This value is equivalent to the number of rows in each DataMatrix object in the ExptData object. This information is read-only.

Attributes:

SetAccessprivate

NSamples

Number of samples in the experiment

Positive integer specifying the number of samples in the experiment. This value is equivalent to the number of columns in each DataMatrix object in the ExptData object. This information is read-only.

Attributes:

SetAccessprivate

Methods

combineCombine two ExptData objects
dmNamesRetrieve or set Name properties of DataMatrix objects in ExptData object
elementDataRetrieve or set data element (DataMatrix object) in ExptData object
elementNamesRetrieve or set element names of DataMatrix objects in ExptData object
featureNamesRetrieve or set feature names in ExptData object
isemptyDetermine whether ExptData object is empty
sampleNamesRetrieve or set sample names in ExptData object
sizeReturn size of ExptData object

Instance Hierarchy

An ExpressionSet object contains an ExptData object. An ExptData object contains one or more DataMatrix objects.

Attributes

To learn about attributes of classes, see Class Attributes in the MATLAB Object-Oriented Programming documentation.

Copy Semantics

Value. To learn how this affects your use of the class, see Copying Objects in the MATLAB Programming Fundamentals documentation.

Indexing

ExptData objects support 1-D parenthesis ( ) indexing to extract, assign, and delete data.

ExptData objects do not support:

  • Dot . indexing

  • Curly brace { } indexing

Examples

expand all

Construct an ExptData object

This example shows how to construct an ExptData object containing one DataMatrix object.

Import bioma.data package to make constructor functions available.

import bioma.data.*

Create a DataMatrix object from .txt file containing expression values from microarray experiment.

dmObj = DataMatrix('File', 'mouseExprsData.txt');

Construct an ExptData object from the DataMatrix object.

EDObj = ExptData(dmObj)
EDObj = 

Experiment Data:
  500 features,  26 samples
  1 elements
  Element names: Elmt1

References

[1] Hovatta, I., Tennant, R S., Helton, R., et al. (2005). Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice. Nature 438, 662–666.

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