SCAN.UPC_GEO

This repository contains functions to download data files from GEO and implement the UPC_Generic function.

The current workflow is as follows:

1. Use geo2bw() function in getGEO_samples to write a bigWig file from .wig file in GEO. - Right now the .wig file needs documentation as to what genome build it is. To do this I download the .soft file from GEO. If no build is specified the bigWig file is not creates. In this example, the GSM# file contains two .wig files, of which only 1 has a specified build
2. Use UPC_bigWig() to run UPC on bigWig file, specifying the desired bin size and number of base pairs to overlap on either side.
3. Use UPC_bigWig_alt() to run UPC on bigWig file. This file will run UPC on the same, non-overlapping regions, across samples.