You may also build ClamAV from sources to benefit from better scanning. Find ste by step tutorial to do it yourself.
If you need to scan particular location(s) on your VPS using ClamAV, please use following:
1. logon to the VPS via SSH as root
2. run the command:
clamscan -r /your/directory
where -r means Recursive scan and /your/directory is the location you need to check
3. check the output of scanning
Please note, that depending on files amount and their size the scanning process may take significantly long time.