bioma.data.DataMatrix

Data structure encapsulating data and metadata from microarray experiment

Description

A bioma.data.DataMatrix object is a data structure encapsulating measurement data and feature metadata from a microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers.

A bioma.data.DataMatrix object stores experimental data in a matrix, with rows typically corresponding to gene names or probe identifiers, and columns typically corresponding to sample identifiers. A DataMatrix object also stores metadata, such as the gene names or probe identifiers and sample identifiers, in row names and column names.

Creation

Syntax

DMobj = bioma.data.DataMatrix(Matrix)

DMobj = bioma.data.DataMatrix(Matrix,RowNames,ColumnNames)

DMobj = bioma.data.DataMatrix('File',FileName)

DMobj = bioma.data.DataMatrix('File',FileName,Name,Value)

Description

DMobj = bioma.data.DataMatrix(Matrix) creates a DataMatrix object from measurement data and feature metadata from microarray experiment.

DMobj = bioma.data.DataMatrix(Matrix,RowNames,ColumnNames) specifies row and column names. RowNames are typically gene names or probe identifiers. ColumnNames are typically sample identifiers.

DMobj = bioma.data.DataMatrix('File',FileName) creates a bioma.data.DataMatrix object from a tab-delimited TXT or XLS file that contains table-oriented data and metadata.

DMobj = bioma.data.DataMatrix('File',FileName,Name,Value)creates a bioma.data.DataMatrix object from a tab-delimited TXT or XLS file according to the Name,Value arguments.

Input Arguments

Matrix — Measurement data and feature metadata from microarray experiment

two-dimensional numeric array | two-dimensional logical array | bioma.data.DataMatrix object

Measurement data and feature metadata from microarray experiment, specified as a two-dimensional numeric or logical array or a bioma.data.DataMatrix object.

RowNames — Row names for bioma.data.DataMatrix object

numeric vector | character array | string vector | cell array of character vectors

Row names for the bioma.data.DataMatrix object, specified as a numeric vector, character array, string vector, or cell array of character vectors. The number of elements RowNames must be equal to the number of rows in Matrix. RowNames are typically gene names or probe identifiers from a microarray experiment. Row names do not need to be unique.

Data Types: double | char | string | cell

ColumnNames — Column names for bioma.data.DataMatrix object

numeric vector | character array | string vector | cell array of character vectors

Column names for the bioma.data.DataMatrix object, specified as a numeric vector, character array, string vector, or cell array of character vectors. The number of elements ColumnNames must be equal to the number of columns in Matrix. ColumnNames are typically sample identifiers from a microarray experiment. Column names do not need to be unique.

Data Types: double | char | string | cell

FileName — File name or path and file name

character vector | string

File name or a path and file name of a tab-delimited TXT or XLS file that contains table-oriented data and metadata, specified as a character vector or string.

Typically, the first row of the table contains column names, the first column contains row names, and the numeric data starts at the 2,2 position. The bioma.data.DataMatrix function detects if the first column does not contain row names, and reads data from the first column. However, if the first row does not contain header text (column names), set the HLine property to 0.

Data Types: char | string

Name-Value Arguments

RowNames — Row names for bioma.data.DataMatrix object

false (default) | numeric vector | character array | string vector | cell array of character vectors | character vector | string | true

Row names for bioma.data.DataMatrix object, specified as one of these values:

• Numeric vector, character array, string vector, or a cell array of character vectors, whose elements are equal in number to the number of rows of numeric data in the input matrix.

• A character vector or string, which is used as a prefix for row names. Numbers are appended to the prefix.

• true — Unique row names are assigned using the formats row1, row2, row3, and so on.

• false — No row names are assigned.

Row names do not need to be unique.

Data Types: double | logical | char | string | cell

ColNames — Column names for bioma.data.DataMatrix object

false (default) | numeric vector | character array | string vector | cell array of character vectors | character vector | string | true

Column names for bioma.data.DataMatrix object, specified as one of these values:

• Numeric vector, character array, string vector, or a cell array of character vectors, whose elements are equal in number to the number of columns of numeric data in the input matrix.

• A character vector or string, which is used as a prefix for column names. Numbers are appended to the prefix.

• true — Unique column names are assigned using the formats col1, col2, col3, and so on.

• false — No column names are assigned.

Column names do not need to be unique.

Data Types: double | logical | char | string | cell

Name — Name for bioma.data.DataMatrix object

'' (default) | character vector | string

Name for bioma.data.DataMatrix object, specified as a character vector or string.

Data Types: char | string

Delimiter — Delimiter symbol to use for input file

'\t' (default) | character vector | string

Delimiter symbol to use for input file, specified as a character vector or string. Typical choices are:

• ' '

• '\t' (default)

• ','

• ';'

• '|'

Data Types: char | string

Hline — Row of input file that contains column header text

1 (default) | positive integer

Row of the input file that contains the column header text (column names), specified as a positive integer. When creating the DataMatrix object, the DataMatrix function loads data from (HLine + 1) to the end of the file. If the input file does not contain column header text (column names), set HLine to 0.

Data Types: double

Rows — Subset of row names in file

cell array of character vectors | character array | string vector | numeric vector | logical vector

Subset of row names in File for the bioma.data.DataMatrix function to use for creating the bioma.data.DataMatrix object, specified as a cell array of character vectors, character array, string vector, or a numeric or logical vector.

Data Types: logical | char | string | cell

Columns — Subset of column names in file

cell array of character vectors | character array | string vector | numeric vector | logical vector

Subset of column names in File for the DataMatrix function to use for creating the bioma.data.DataMatrix object, specified as a cell array of character vectors, character array, string vector, or a numeric or logical vector.

Data Types: logical | char | string | cell

Properties

Name — Name of bioma.data.DataMatrix object

'' (default) | character vector

Name of the bioma.data.DataMatrix object, stored as a character vector.

Data Types: char

RowNames — Row names

'' | cell array of character vectors

Row names (typically gene names or probe identifiers), stored as an empty array or a cell array of character vectors. The number of elements in the cell array must equal the number of rows in the matrix.

Data Types: cell

ColNames — Column names

'' | cell array of character vectors

Column names (typically sample identifiers), stored as an empty array or a cell array of character vectors. The number of elements in the cell array must equal the number of columns in the matrix.

Data Types: cell

NRows — Number of rows

positive number

This property is read-only.

Number of rows in the matrix, stored as a positive number. You cannot modify this property directly. You can access it using the get method.

Data Types: double

NCols — Number of columns

positive number

This property is read-only.

Number of columns in the matrix, stored as a positive number. You cannot modify this property directly. You can access it using the get method.

Data Types: double

NDims — Number of dimensions

positive number

This property is read-only.

Number of dimensions in the matrix, stored as a positive number. You cannot modify this property directly. You can access it using the get method.

Data Types: double

ElementClass — Class type of the elements in bioma.data.DataMatrix object

character vector

This property is read-only.

Class type of the elements in bioma.data.DataMatrix object, stored as a character vector, such as single or double. You cannot modify this property directly. You can access it using the get method.

Data Types: char

Object Functions

General Methods

colnames	Retrieve or set column names of DataMatrix object
disp	Display DataMatrix object
dmwrite	Write DataMatrix object to text file
double	Convert DataMatrix object to double-precision array
get	Retrieve information about DataMatrix object
isempty	Determine whether array is empty
isfinite	Determine which array elements are finite
isinf	Determine which array elements are infinite
isnan	Determine which array elements are NaN
isscalar	Determine whether input is scalar
isequal	Test DataMatrix objects for equality
isequaln	Test DataMatrix objects for equality, treating NaNs as equal
isvector	Determine whether input is vector
length	Length of largest array dimension
ndims	Return number of dimensions in DataMatrix object
numel	Return number of elements in DataMatrix object
pdist	Pairwise distance between pairs of observations
plot	Draw 2-D line plot of DataMatrix object
rownames	Retrieve or set row names of DataMatrix object
set	Set property of DataMatrix object
single	Convert DataMatrix object to single-precision array
size	Array size

Methods for Manipulating Data

cat	Concatenate arrays
horzcat	Concatenate DataMatrix objects horizontally
sortcols	Sort columns of DataMatrix object in ascending or descending order
sortrows	Sort rows of DataMatrix object in ascending or descending order
vertcat	Concatenate DataMatrix objects vertically

Descriptive Statistics and Statistical Learning Methods

kmeans	k-means clustering
max	Return maximum values in DataMatrix object
mean	Return average or mean values in DataMatrix object
median	Return median values in DataMatrix object
min	Return minimum values in DataMatrix object
nanmax	(Not recommended) Maximum, ignoring NaN values
nanmean	(Not recommended) Mean, ignoring NaN values
nanmedian	(Not recommended) Median, ignoring NaN values
nanmin	(Not recommended) Minimum, ignoring NaN values
nanstd	(Not recommended) Standard deviation, ignoring NaN values
nansum	(Not recommended) Sum, ignoring NaN values
nanvar	(Not recommended) Variance, ignoring NaN values
pca	Principal component analysis of raw data
pdist	Pairwise distance between pairs of observations
std	Return standard deviation values in DataMatrix object
sum	Return sum of elements in DataMatrix object
var	Return variance values in DataMatrix object

Unary Methods — Exponential

exp	Exponential
log	Natural logarithm
log10	Common logarithm (base 10)
log2	Base 2 logarithm and floating-point number dissection
pow2	Base 2 exponentiation and scaling of floating-point numbers
sqrt	Square root

Unary Methods — Integer

ceil	Round toward positive infinity
fix	Round toward zero
floor	Round toward negative infinity
round	Round to nearest decimal or integer

Unary Methods — Custom

dmarrayfun

Apply function to each element in DataMatrix object

Binary Methods — Arithmetic Operator

plus	Add DataMatrix objects
minus	Subtract DataMatrix objects
times	Multiply DataMatrix objects
rdivide	Right array divide DataMatrix objects
ldivide	Left array divide DataMatrix objects
power	Array power DataMatrix objects

Binary Methods — Relational Operator

lt	Test DataMatrix objects for less than
le	Test DataMatrix objects for less than or equal to
gt	Test DataMatrix objects for greater than
ge	Test DataMatrix objects for greater than or equal to
eq	Test DataMatrix objects for equality
ne	Test DataMatrix objects for inequality

Binary Methods — Custom

dmbsxfun

Apply element-by-element binary operation to two DataMatrix objects with singleton expansion enabled

Examples

Determine Properties and Property Values of DataMatrix Object

Load the file containing yeast data. This file includes three variables: yeastvalues, a 614-by-7 matrix of gene expression data, genes, a cell array of 614 GenBank® accession numbers for labeling the rows in yeastvalues, and times, a 1-by-7 vector of time values for labeling the columns in yeastvalues.

load filteredyeastdata

Create variables to contain a subset of the data, specifically the first five rows and first four columns of the yeastvalues matrix, the genes cell array, and the times vector.

yeastvalues = yeastvalues(1:5,1:4);
genes = genes(1:5,:);
times = times(1:4);

Import the microarray object package.

import bioma.data.*

Create a DataMatrix object from the gene expression data.

DMobj = DataMatrix(yeastvalues,genes,times)

DMobj = 

                  0       9.5     11.5      13.5  
    SS DNA     -0.131    1.699    -0.026     0.365
    YAL003W     0.305    0.146    -0.129    -0.444
    YAL012W     0.157    0.175     0.467    -0.379
    YAL026C     0.246    0.796     0.384     0.981
    YAL034C    -0.235    0.487    -0.184    -0.669

Display all properties of a DataMatrix object and their current values.

get(DMobj)

            Name: ''
        RowNames: {5x1 cell}
        ColNames: {'   0'  ' 9.5'  '11.5'  '13.5'}
           NRows: 5
           NCols: 4
           NDims: 2
    ElementClass: 'double'

Return all properties and their current values of the DataMatrix object to a scalar structure where each field name is a property of a DataMatrix object, and each field contains the value of that property.

DMstruct = get(DMobj)

DMstruct = struct with fields:
            Name: ''
        RowNames: {5x1 cell}
        ColNames: {'   0'  ' 9.5'  '11.5'  '13.5'}
           NRows: 5
           NCols: 4
           NDims: 2
    ElementClass: 'double'

Return the value of a specific property of the DataMatrix object. For exxample, return the value of RowNames.

NamesOfRows = get(DMobj,'RowNames')

NamesOfRows = 5x1 cell
    {'SS DNA' }
    {'YAL003W'}
    {'YAL012W'}
    {'YAL026C'}
    {'YAL034C'}

Now return the value of NRows.

NumberOfRows = DMobj.NRows

NumberOfRows = 
5

Determine Possible Values of DataMatrix Object Properties

Load the file containing yeast data. This file includes three variables: yeastvalues, a 614-by-7 matrix of gene expression data, genes, a cell array of 614 GenBank® accession numbers for labeling the rows in yeastvalues, and times, a 1-by-7 vector of time values for labeling the columns in yeastvalues.

load filteredyeastdata

Create variables to contain a subset of the data, specifically the first five rows and first four columns of the yeastvalues matrix, the genes cell array, and the times vector.

yeastvalues = yeastvalues(1:5,1:4);
genes = genes(1:5,:);
times = times(1:4);

Import the microarray object package.

import bioma.data.*

Create a DataMatrix object from the gene expression data.

DMobj = DataMatrix(yeastvalues,genes,times)

DMobj = 

                  0       9.5     11.5      13.5  
    SS DNA     -0.131    1.699    -0.026     0.365
    YAL003W     0.305    0.146    -0.129    -0.444
    YAL012W     0.157    0.175     0.467    -0.379
    YAL026C     0.246    0.796     0.384     0.981
    YAL034C    -0.235    0.487    -0.184    -0.669

Display possible values for all properties that have a fixed set of property values in the DataMatrix object.

set(DMobj)

        Name: 'A DataMatrix's 'Name' property does not have a fixed set of values.'
    RowNames: 'Empty, a cell array of strings or a numeric vector.'
    ColNames: 'Empty, a cell array of strings or a numeric vector.'

Display possible values for a specific property that has a fixed set of property values in the DataMatrix object. For example, display possible values for RowNames.

set(DMobj,'RowNames')

Empty, a cell array of strings or a numeric vector.

Specify Properties of DataMatrix Object

Load the file containing yeast data. This file includes three variables: yeastvalues, a 614-by-7 matrix of gene expression data, genes, a cell array of 614 GenBank® accession numbers for labeling the rows in yeastvalues, and times, a 1-by-7 vector of time values for labeling the columns in yeastvalues.

load filteredyeastdata

Create variables to contain a subset of the data, specifically the first five rows and first four columns of the yeastvalues matrix, the genes cell array, and the times vector.

yeastvalues = yeastvalues(1:5,1:4);
genes = genes(1:5,:);
times = times(1:4);

Import the microarray object package.

import bioma.data.*

Create a DataMatrix object from the gene expression data.

DMobj = DataMatrix(yeastvalues)

DMobj = 

         1         2        3         4     
    1    -0.131    1.699    -0.026     0.365
    2     0.305    0.146    -0.129    -0.444
    3     0.157    0.175     0.467    -0.379
    4     0.246    0.796     0.384     0.981
    5    -0.235    0.487    -0.184    -0.669

Set the Name property of the DataMatrix object.

DMobj = set(DMobj,'Name','YeastData');
DMobj.Name

ans = 
'YeastData'

Set multiple properties, for example, set the RowNames and ColNames properties.

DMobj = set(DMobj,'RowNames',genes,'ColNames',times)

DMobj = 

                  0       9.5     11.5      13.5  
    SS DNA     -0.131    1.699    -0.026     0.365
    YAL003W     0.305    0.146    -0.129    -0.444
    YAL012W     0.157    0.175     0.467    -0.379
    YAL026C     0.246    0.796     0.384     0.981
    YAL034C    -0.235    0.487    -0.184    -0.669

Version History

Introduced in R2008b

R2017b: princomp method has been renamed

The princomp method of bioma.data.DataMatrix has been renamed. Replace instances of princomp with pca.