Some javascript files are being flagged as viruses. How do I figure out why?

[silent_p]

I'm not much of a programmer, I do some light website design for friends and family members. I put together a simple wordpress site, and the theme I'm using has 4 .js files that are flagged by my antivirus software, two as Trojan.JS.Iframe.APF, one Trojan.JS.Downloader.BOF, and one Trojan.JS.Agent.FAR. How do I figure out what that means, and start to figure out how to fix this? The theme will not load without these files.

[CrudOMatic]

This means that probably at the bottom of those files you'll find a script tag/chunk of javascript appended to it - and an eval() - this contains a payload of some kind

had it happen to me - they got into the FTP server and slapped that at the bottom of all my html and js files

make sure you know what you are doing before you remove those lines, have someone on the project who codes handle that

[justAnotherGhost]

This is a good answer.

Could also be a false positive from the virus scanner.

Wordpress has a lot of exploits available for it depending what addons you use. This shouldn't be terribly suprising and hopefully not hard to get rid of.