Incorporate Dominik's notes into existing issues

[mmulvahill]

MSPrep R package

Summary from meeting w/ Domink:

• Start with read_data
• Sean's version (in sean branch, _sj()) has more code than the one in develop/master
• Separate out tasks is the first key thing to do

Notes from meeting w/ Dominik:

• Dominik uses:
  • read_data_sj()
    • fn doesn't allow more than 3 technical replicates -- should allow Inf
    • fn summarizes, but this should be a separate fn -- probabaly summary()
    • option for whether data is already log-xfrmed or not -
    • option to load/convert data existing in workign environment
    • ID variable ("lcms...") is hardcoded, shoudln't be
• batch correction --
  • hasn't used
  • should this be done before summaries, imputation, normalization
• cvmax -
• missing data typically represented by 0 or 1 (log(1)=0)

[mmulvahill]

Done.