In jaspershen/metflow2: Comprehensitive tools for metabolomics data processing and data analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE,
  message = TRUE
)

Raw data processing

---

Demo data

The demo data for peak picking are from MetDNA. You can download it from here: http://metdna.zhulab.cn/metdna/DemoDataset. The demo data is embed in my demoData package. So you can get them from the demoData package.

Code

The code for data processing are in the dataProcessing.R file.

metflow2 is a R package which is used to process and analyze metabolomics data.

Please install it via github.

if(!require(devtools)){
  install.packages("devtools")
}
devtools::install_github("jaspershen/metflow2")

We use the demo data in demoData package to show how to use metflow2. Please install it first.

devtools::install_github("jaspershen/demoData")

Raw MS data processing

---

Data preparation

Firstly, please transform your raw standard MS data (positive and negative modes) to mzXML format using ProteoWizard. The parameter setting is shown like figure below:

Data organization

Secondly, please organize your mzXML data into different folders.

1. Blank

2. QC

3. QC_DL

4. Subject

Run process_data function

metflow2::process_data(path = ".", 
                      polarity = "positive", 
                      peakwidth = c(5,30), 
                      threads = 5, 
                      output.tic = TRUE,
                      output.bpc = TRUE, 
                      min.fraction = 0.8, 
                      output.rt.correction.plot = TRUE,
                      fill.peaks = FALSE)

jaspershen/metflow2 documentation built on Aug. 15, 2021, 4:38 p.m.