Documentation fix-up for an updated release

[gaow]

@hsun3163 I'm raising this issue here, for there are problems recently reported due to obsolete or incomplete minimal working example commands as a result of changes made. I'll make a TODO list in this ticket -- please fix them with MWE (without paths on your computer, so I can readily copy-paste to reproduce; use symbolic links as necessary. Let's start from modules first, then move on to protocol. Here are the pages to be updated:

• [x] https://cumc.github.io/xqtl-pipeline/code/data_preprocessing/phenotype/phenotype_formatting.html
• [x] https://cumc.github.io/xqtl-pipeline/code/data_preprocessing/covariate/BiCV_factor.html
• [x] https://cumc.github.io/xqtl-pipeline/code/data_preprocessing/covariate/PEER_factor.html