XCMS Metabolomics Preprocessing

Requires Bioconductor 3.18+ with xcms 4.0+ and MSnbase 2.28+.

Load Raw Data

library(xcms)
library(MSnbase)

# Read mzML/mzXML files
raw_files <- list.files('raw_data', pattern = '\\.(mzML|mzXML)$', full.names = TRUE)

# Create OnDiskMSnExp object
raw_data <- readMSData(raw_files, mode = 'onDisk')