Rerun GRNs with higher peak-gene neighborhood size
The goal is to re-run parts of the GRN pipeline for some (most) of the datasets and to change the parameter promoterRange
to 2000000 -(2 million) + to get familiar with it more. These are the steps to do:
- For the particular dataset (check /g/scb/zaugg/zaugg_shared/data/GRN/data and subdirectories within), locate the runGRN.R file in the input directory. If not present, let me know, I am currently cleaning this up.
- Change
promoterRange
to 2,000,000 and rerun the whole script. Change thedir_output
and add a suffix like "peakGene2000000" or something like this. Let's be conservative and save all in a new output folder altogether.
Let's try this for one dataset and then we can adjust if something is unexpected or can be improved. I'll update the procedure above then.
**Let's start with /g/scb/zaugg/zaugg_shared/data/GRN/data/Macrophages/input/runGRN.R. **. Note that for the Macrophages dataset, we iterate in the script over the 4 different subpopulations + all, so the GRN is run a total of 5 x in an identical fashion.
Edited by Christian Arnold