getGEOData {MetaIntegrator}

GEO download/processing through GEOquery

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