release 1.2

• add_contrast() is a new function that introduces additional flexibility for defining statistical contrasts
  • allows you to add a contrast with a wildcard for the second group (e.g. one may define group1 = "WT" and group2 = NA to create a contrast "WT" versus all other values in the "group" column)
    • also enables creating statistical contrasts based on other columns in the sample metadata table (dataset$samples) besides the default "group" column
    • after installing the update, run library(msdap) and check documentation with R command ?add_contrast()
  • this is accompanied by helper functions remove_contrasts() and print_contrasts()
  • you can still use the setup_contrasts() function as per usual, i.e. pre-existing MS-DAP scripts still work as intended
• new workflow for creating limma analyses (eBayes/DEqMS) with any custom model matrix / linear regression design
  • enables modeling of more complex experimental designs, e.g. paired samples / block designs or multi-level experiments
  • documentation and examples are available at bioinformatics: advanced statistical models with limma