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ilmnbsread

Read gene expression data exported from Illumina BeadStudio software

Syntax

IlmnStruct = ilmnbsread(File)

IlmnStruct = ilmnbsread(File, ...'Columns', ColumnsValue, ...)
IlmnStruct = ilmnbsread(File, ...'HeaderOnly', HeaderOnlyValue, ...)
IlmnStruct = ilmnbsread(File, ...'CleanColNames', CleanColNamesValue, ...)

Input Arguments

File

String specifying a file name or a path and file name of a tab-delimited file or comma-separated expression data file exported from Illumina® BeadStudio™ software. If you specify only a file name, that file must be on the MATLAB® search path or in the current folder.

ColumnsValueCell array that specifies the column names to read. Default is all column names.
HeaderOnlyValueControls the population of only the Header, ColumnNames, and TextColumnNames fields in IlmnStruct. Choices are true or false (default).
CleanColNamesValueControls the conversion of any ColumnNames containing spaces or characters that cannot be used as MATLAB variable names, to valid MATLAB variable names. Choices are true or false (default).

Output Arguments

IlmnStruct

MATLAB structure containing data exported from Illumina BeadStudio software.

Description

IlmnStruct = ilmnbsread(File) reads File, a tab-delimited or comma-separated expression data file exported from the Illumina BeadStudio software, and creates IlmnStruct, a MATLAB structure containing the following fields.

FieldDescription
HeaderString containing a description of the data.
TargetIDCell array containing unique identifiers for targets on an Illumina gene expression microarray.
ColumnNames

Cell array containing names of the columns that contain numeric data in the tab-delimited file exported from the Illumina BeadStudio software.

Data

Matrix containing numeric microarray data for each target on an Illumina gene expression microarray.

    Note:   ColumnNames and Data have the same number of columns.

TextColumnNames

Cell array containing names of the columns that contain nonnumeric data in the tab-delimited file exported from the Illumina BeadStudio software. This field can be empty.

TextData

Cell array containing nonnumeric microarray data (such as annotations) for each target on an Illumina gene expression microarray. This field can be empty.

    Note:   TextColumnNames and TextData have the same number of columns.

IlmnStruct = ilmnbsread(File, ...'PropertyName', PropertyValue, ...) calls ilmnbsread with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:


IlmnStruct = ilmnbsread(File, ...'Columns', ColumnsValue, ...)
reads the data only from the columns specified by ColumnsValue, a cell array of column names. Default behavior is to read data from all columns.

IlmnStruct = ilmnbsread(File, ...'HeaderOnly', HeaderOnlyValue, ...) controls the population of only the Header, ColumnNames, and TextColumnNames fields in IlmnStruct. Choices are true or false (default).

IlmnStruct = ilmnbsread(File, ...'CleanColNames', CleanColNamesValue, ...) controls the conversion of any ColumnNames containing spaces or characters that cannot be used as MATLAB variable names, to valid MATLAB variable names. Choices are true or false (default).

    Tip   Use the 'CleanColNames' property if you plan to use the ColumnNames field as variable names.

Examples

    Note:   The gene expression file, TumorAdjacent-probe-raw.txt used in the following example is not provided with the Bioinformatics Toolbox™ software.

Read the contents of a tab-delimited file exported from the Illumina BeadStudio software into a MATLAB structure.

ilmnStruct = ilmnbsread('TumorAdjacent-probe-raw.txt')

ilmnStruct = 

             Header: [1x1 struct]
           TargetID: {22184x1 cell}
        ColumnNames: {1x37 cell}
               Data: [22184x37 double]
    TextColumnNames: {1x23 cell}
           TextData: {22184x23 cell}

See Also

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