fetchData: Retrieve GEO Data

In anjanbharadwaj/GEOpipeline: GEOpipeline: Streamlined Pipeline for Automatically CDF Normalizing Microarray Datasets

Description

The function will utilize the other helper functions in the package to download data from the online Gene Expression Omnibus, find the proper CDF file to use from the BrainArray website (alternatively, if it cannot be found online, the user will be prompted to enter the link to a CDF file of their choice), and normalize the data based on the CDF file. If the dataset from online is not in the .CEL format, the tool will not perform normalization.

Usage

fetchData(accession, output_dir)

Arguments

accession	The numerical portion of a GSE accession ID, in character format. Example"" for accession GSE11121, the user should provide the argument as "11121"
output_dir	A character describing the output file directory. Example: "/Users/johndoe/Documents/GEODATA"

Value

expression	The normalized gene expression data
phenotype_data	The corresponding phenotype metadata for each of the samples in the gene expression data

Author(s)

Anjan Bharadwaj

Examples

##fetchData("11121", "/Users/johndoe/Documents/GEODATA")

anjanbharadwaj/GEOpipeline documentation built on Nov. 2, 2019, 1:54 p.m.