importGEO: Import GEO data series in the workspace

In andigoni/MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

Description

Imports GEO data series. The function fetches data matrices corresponding to a pre-defined GSE identifier and builds valid, bed-formatted dataset with delta-beta values between two sample groups, described in a user-defined annotation file.

Usage

importGEO(gse.acc, annotation.file)

Arguments

gse.acc	A string corresponding to the accession number of the GEO data series
annotation.file	A string corresponding to the full local path to the annotation files containing sample grouping information

Value

1/ A bed-formatted data frame with the chromosomal coordinates and of each methylation probe and the corresponding delta-beta values between the two groups

2/ Beta values of each sample listed in the annotation file

3/ Annotation data frame

4/ Mean beta values of group 1

5/ Mean beta values of group 2

andigoni/MeinteR documentation built on Oct. 1, 2021, 9:33 p.m.