geoDataDownload

Function that downloads gene expression data from GEO, after checking the connection

A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, 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/>.

Davide Chicco

easyDifferentialGeneCoexpression

Easily Performs Differential Coexpression Analysis

geoDataDownload function

<dl><dt>GSE_code</dt>
<dd>GEO code dataset</dd>
<dt>verbose</dt>
<dd>prints all the intermediate message to standard output or not</dd></dl>

Arguments

Function that downloads gene expression data from GEO, after checking the connection — geoDataDownload

<dl>

<dt>GSE_code</dt>
<dd>GEO code dataset</dd>


<dt>verbose</dt>
<dd>prints all the intermediate message to standard output or not</dd>

</dl>

geoDataDownload: Function that downloads gene expression data from GEO, after checking the connection

Description

Usage

Value

Arguments