library(MetMiner)
library(tidyverse)
library(tidymass)
library(MDAtoolkits)
run_metMiner(maxRequestSize = 300)Upsteam Data Process
Introduce
This Shiny application is developed based on the tidyMass package, specifically designed for the analysis of non-targeted/targeted metabolomics data. Dr. Xiaotao Shen’s tidyMass is an excellent open-source software tailored for metabolomics data processing. It adheres to the tidyverse development philosophy, significantly enhancing code readability. Additionally, the newly added mass_dataset object makes the metabolomics data analysis process more transparent and reproducible.
Usage of ShinyAPP
Upstream analysis
Before starting the project, we need to set up the working directory and upload sample information. You have the following three ways to upload files.
Start with Ms file: If your data is in raw format, you need to first convert it to .mgf format using HPC_tidymass. Then click on ‘Start with Ms file’ to upload the file. Then upload the folder containing MS2.
Start with table file: If your data is a post-peak metabolite expression matrix, you can click on the ‘Start with table file’ button to upload the data. The sample table is as follows, and the first four columns must exist, with column names not to be changed. Then upload the folder containing MS2.
Start with massdataset object: If your data is generated by tidymass, you can choose the ‘Start with massdataset object’ button to upload your data. Then upload the folder containing MS2.
