Minimum Information about Data AnalysiS: Authoring Tool in R markdown.
MIDAS is an R markdown reporting template file that guides the production of text and generates workflow diagrams based on user input. This R Markdown template contains, as an example in this instance, a set of minimum information requirements specifically for the data pretreatment and data analysis section of biomarker discovery metabolomics studies, (gleaned directly from the original proposed guidelines by Goodacre at al,. These minimum requirements are presented in the format of a questionnaire checklist in the R markdown template file.
The R Markdown reporting template proposed here can be presented as a starting point to encourage the data analysis section of a metabolomics manuscript to have a more logical and stepwise presentation and to contain enough information to be understandable and reusable. The idea is that these guidelines would open to user feedback, modification and updating by the metabolomics community via github .
Here are the instructions on how to use this R Markdown authoring template.
- Click on the “clone or download” button on the right hand side of this page and download the folder as a zip file.
- Download latest version of R Studio if you do not have it.
- Open the folder and open the MIDAS.rmd file in R studio.
- Start editing and writing the report of your data analysis guided by the questions in green directly inside the MIDAS.rmd file.
- After the pretreatment, univariate analysis, unsupervised analysis and supervised analysis sections have been completed the next section is to produce workflow diagrams.
- Follow the instructions in green to produce a workflow diagram of pretreatment steps.
- Click on the knit button and knit it to HTML to see how the generated report looks.
- Knit to PDF or MS-Word to render the report to a PDF or Word document as you wish.
- PDF and Word reports will not contain the diagrams, so these need to be saved in the viewer pane as an image (JPG /BMP etc) to your local folder
- Insert the workflow diagrams into your Word or PDF report that you have saved to your local folder.
- Render the document to HTML and workflow diagrams will be included anyway.