I created aquaras to solve some specific tasks and have added/will add more functionality as the need arises. I would never have been able to make things work without all the amazing people who create and maintain the packages I’ve used. Thank you!
Installation
You can install the development version of aquaras from GitHub with:
# install.packages("devtools")
devtools::install_github("Klorator/aquaras")Runlists for MassLynx
Create runlists for use with MassLynx (Waters LC/MS software) and facilitate some of the data processing steps with the MassLynx complete summary output file.
Workflow summary
- Call
ras.RunlistGenerator() - Input all the runlist info under “Well input”
- Optionally: download/upload the tsv under “Full list” to save/resume a project
- Generate a runlist under “Runlist” and download the tsv
- Do experiments. Yeay!
- Call
ras.SplitOutput()and select the MassLynx complete summary output file (the file-selection window might be hiding behind RStudio) - Analyze the results for each compound
- Publish paper!
- Design new experiments (rinse and repeat)
Random group generator
Created the function ras.Randomizer() to distribute a list of observations/compounds into groups randomly. Can create multiple series and write to excel file (not default).
TPA tools
Created the function ras.TPA_calcFromIntensity() which calculates TPA from the intensity columns. It uses the raw output file from MaxQuant.
A few more functions, mainly ras.TPAer for calculating averages and standard deviation of TPA columns.