bio-metabolomics-xcms-preprocessing

Load Raw Data

Goal: Import raw LC-MS files into R for downstream peak detection and alignment.

Approach: Read mzML/mzXML files into an OnDiskMSnExp object using MSnbase for memory-efficient access.

"Process my raw LC-MS data into a feature table" → Detect chromatographic peaks, align retention times across samples, group corresponding peaks, and fill missing values to produce a sample-by-feature intensity matrix.

library(xcms)
library(MSnbase)

## Create OnDiskMSnExp object

raw_data <- readMSData(raw_files, mode = 'onDisk')

## Check data

raw_data
table(msLevel(raw_data))