geoseriesread - Read Gene Expression Omnibus (GEO) Series (GSE) format data
Syntax
GEOData = geoseriesread(File)
Arguments
| File | Either of the following: String specifying a file name, a path and file name,
or a URL pointing to a file. The referenced file is a Gene Expression
Omnibus (GEO) Series (GSE) format file. If you specify only a file
name, that file must be on the MATLAB search path or in the current
directory. MATLAB character array that contains the text
of a GEO Series (GSE) format file.
Tip
You can use the getgeodata function
with the 'ToFile' property to retrieve GEO Series
(GSE) format data from the GEO database and create a GEO Series (GSE)
format file. |
|
Return Values
| GEOData | MATLAB structure containing the following fields: Header — Header text from
the GEO Series (GSE) format file, typically containing a description
of the data or experiment information. Data — DataMatrix object containing
the data from a GEO Series (GSE) format file. The columns and rows
of the DataMatrix object correspond to the sample IDs and Ref IDs,
respectively, from the GEO Series (GSE) format file.
|
Description
GEOData = geoseriesread(File) reads
a Gene Expression Omnibus (GEO) Series (GSE) format file, and then
creates a MATLAB structure, GEOData,
with the following fields.
| Fields | Description |
|---|
| Header | Header text from the GEO Series (GSE) format file, typically
containing a description of the data or experiment information. |
| Data | DataMatrix
object containing the data from a GEO Series (GSE) format file.
The columns and rows of the DataMatrix object correspond to the sample
IDs and Ref IDs, respectively, from the GEO Series (GSE) format file. |
Examples
Retrieve Series (GSE) data from the GEO Web site and
save it to a file.
geodata = getgeodata('GSE11287','ToFile','GSE11287.txt');
In a subsequent MATLAB session, you can access
the Series (GSE) data from your local file, instead of retrieving
it from the GEO Web site.
geodata = geoseriesread('GSE11287.txt')
geodata =
Header: [1x1 struct]
Data: [45101x6 bioma.data.DataMatrix]Access the sample IDs using the colnames property
of a DataMatrix object.
sampleIDs = geodata.Data.colnames
sampleIDs =
'GSM284935' 'GSM284936' 'GSM284937' 'GSM284938' 'GSM284939' 'GSM284940'
See Also
Bioinformatics Toolbox functions: affyread, agferead, galread, geosoftread, getgeodata, gprread, ilmnbsread, sptread
Bioinformatics Toolbox object: DataMatrix object
 | genpeptread | | geosoftread |  |
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