getGEOData: GEO download/processing through GEOquery

In MetaIntegrator: Meta-Analysis of Gene Expression Data

Description

Creates MetaIntegrator formatted objects by downloading and formatting data from GEO.

Usage

getGEOData(gseVector, formattedNames = gseVector, qNorm = FALSE, ...)

Arguments

gseVector	a vector of GSE ids (each a string)
formattedNames	a vector of formatted names corresponding to the GSE ids. Default: gseVector
qNorm	perform quantile normalization of expression data within a dataset or not. Default: FALSE
...	will pass additional parameters to getGEO, including destdir, which specifies download location

Details

Note: if you get the error "Error: Couldn't find driver MySQL" then just library(RMySQL) and then re-run getGEOData

Value

a Pre-Analysis MetaObject containing the datasets loaded in $originalData

Author(s)

Francesco Vallania, Andrew Tam, Ravi Shankar, Aditya M. Rao

MetaIntegrator documentation built on March 26, 2020, 6:29 p.m.