I've read that e-filed returns contain more information than those filed by paper because paper returns are not transcribed completely once received. Does that increase the risk that some computer formula will "flag" you when you e-file?
The IRS Discriminant Function System examines incoming tax returns and assigns them a score. Returns with high scores are more likely to get pulled for an audit than those with low scores. There is no indication that e-filing increases your chances of being audited.
Here is a great TurboTax Article you may be interested in: Top Five Ways to Avoid a Tax Audit.