Bioinformatics Toolbox™

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, ...)

Arguments

`File`	String specifying a tab-delimited file or comman-separated expression data exported from Illumina BeadStudio software.
`ColumnsValue`	A cell array that specifies the column names to read. Default is all column names.
`HeaderOnlyValue`	Controls the population of only the `Header`, `ColumnNames`, and `TextColumnNames` fields in`IlmnStruct`. Choices are `true` or `false` (default).
`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).

Return Values

IlmnStruct MATLAB structure containing data exported from IlluminaBeadStudio software.

Description

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

Field Description

Header String containing a description of the data.

TargetID Cell 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 IlluminaBeadStudio 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 IlluminaBeadStudio 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 inIlmnStruct. 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

Read the contents of a tab-delimited file exported from the Illumina BeadStudio software into a MATLAB structure. Note that the example file, GeneProfile.txt, is not provided with the Bioinformatics Toolbox™ software.

ilmnStruct = ilmnbsread('GeneProfile.txt')

ilmnStruct = 

             Header: 'Illumina BeadStudio data from GeneProfile.txt'
           TargetID: {58428x1 cell}
        ColumnNames: {1x29 cell}
               Data: [58428x29 double]
    TextColumnNames: {1x21 cell}
           TextData: {58428x21 cell}