Re selecting PC's

If a user doesn't like the selected chromosome pc for a sample he or she can manually force dchic to use their chosen pc using this code. This code has two options to reselect the pc. The first option 'ref' is if they have a separate signal file (mapped on same bedgraph as that of the hic data), then reselectpc.r will correlate the bedGraph signal with the PC values and use it to select the PCs (e.g. re-run). The second option is manual re-selection (inputting the chromosome #, sample, PC #, etc.).

Try Rscript reselectpc.r --help for all options. Below are some examples:

• Automatically re-selecting: Rscript reselectpc.r --reselect ref --rfile signal.txt
• Manually re-selecting: Rscript reselectpc.r --reselect man --sample <folder>_pca --chr <chr name> --pc <pc number> --pctype <intra or inter>