getGeneExpressionFromGEO

Function that reads in the GEO code of a dataset, and returns the gene expression dataframe.

A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>.

Davide Chicco

geneExpressionFromGEO

Easily Downloads a Gene Expression Dataset from a GEO Code and
Retrieves the Gene Symbols of Its Probesets

getGeneExpressionFromGEO function

<dl><dt>datasetGeoCode</dt>
<dd>the GEO code of a dataset.</dd>
<dt>retrieveGeneSymbols</dt>
<dd>a boolean flag stating if the function should retrieve the gene symbols or not.</dd>
<dt>verbose</dt>
<dd>a boolean flag stating if helping messages should be printed or not</dd></dl>

Arguments

Function that reads in the GEO code of a dataset, and returns the gene expression dataframe. — getGeneExpressionFromGEO

<dl>

<dt>datasetGeoCode</dt>
<dd>the GEO code of a dataset.</dd>


<dt>retrieveGeneSymbols</dt>
<dd>a boolean flag stating if the function should retrieve the gene symbols or not.</dd>


<dt>verbose</dt>
<dd>a boolean flag stating if helping messages should be printed or not</dd>

</dl>

getGeneExpressionFromGEO: Function that reads in the GEO code of a dataset, and returns the gene expression dataframe.

Description

Usage

Value

Arguments

Examples