Project structure

The project is organized into the following folders structure:

├── analysis :   contains the R scripts 
│               (analysis.R, checkRep.R, quantify.R)
│               and their auxillary functions
│
├── data :       default folder for the input tables and 
│               data to be analyzed
│
├── results :    where the outputs of the scripts are stored
│   │
    ├── figs :    figures
    │
    └── tables :  tables

The scripts should be run from the analysis folder, and the paths to the required folders are defined in the scripts as:

# Define Data and Results repositories
dataRepo = '../data/'
figRepo  = '../results/figs/'
tabRepo  = '../results/tables/'

The MS and DMS files are expected by default to be in data. For complex projects, the MS files can be placed in sub-folders of data, and their paths are given in the taskTable input file.