#Usage For list of GTSP and replicates generate heatmap for a given reference genome and given integration site database:
Rscript epi_heatmap_from_db.R sampleName_GTSP.csv -o heatmap --ref_genome hg18 --sites_group intSitesDev237
At present we only support "hg18" and "mm8" genomes.
Group should be present in ~/.my.cnf.
All epigenetic cell types can be printed with:
Rscript epi_cell_types.R
After that, cells of interest(e.g. CD133) can be filtered(see CD133.csv as an example) and file can be used to generate heatmap only with these cell types:
Rscript epi_heatmap_from_db.R sampleName_GTSP.csv -t CD133.csv