rtcorr

Description of the HCor R Package

The HCor package provides a set of functions for processing Liquid Chromatography-Mass Spectrometry (LC/MS) data, focusing on chromatogram drift correction, peak detection, and data normalization. It is designed to handle mass spectrometry chromatograms by adjusting retention times, correcting peak drift, and generating corrected chromatographic data.

Key Functionalities

The package consists of various functions aimed at correcting chromatographic drifts, handling chromatographic files, and processing raw LC/MS data. Below are the core functionalities:

Chromatographic Data Handling

  • files2Matrix(): Reads chromatographic data from external files (e.g., mzXML, CDF) and converts them into a matrix format.
  • printCDFfile(): Writes corrected chromatographic data to new CDF files.
  • cdfFileCreator(): Generates CDF files from processed chromatographic data.

Chromatogram Drift Correction

  • corrDrift(): Applies drift correction to raw chromatographic data by fitting a hyperbolic model to compensate for retention time shifts.
  • peakDrift(): Computes peak drift for a given chromatographic peak and corrects retention time variability.
  • peakDrifts(): Applies peakDrift() to multiple peaks for batch correction.

Peak Detection and Normalization

  • setAnchorPeaks(): Selects anchor peaks for drift correction by allowing users to visually choose retention time intervals.
  • squares(): Computes the sum of squares of deviations to optimize drift correction parameters.

Processing of Corrected Data

  • peakDrifts(): Computes drift corrections across multiple peaks and generates corrected chromatographic datasets.
  • cdfFileCreator(): Outputs corrected chromatographic data to CDF files.

How HCor Works

  1. Load the package and input data (e.g., mzXML files).
  2. Convert chromatographic data into a matrix format (files2Matrix).
  3. Correct chromatographic drift by detecting and correcting peak shifts (corrDrift, peakDrift).
  4. Optimize retention time alignment (squares function minimizes drift errors).
  5. Generate corrected chromatographic files for further analysis (printCDFfile, cdfFileCreator).

Use Case: Correcting Drift in LC/MS Data

# Load necessary libraries
library(HCor)



# Convert mzXML chromatograms to matrix format
dataMatrix <- files2Matrix(dataDir = "path/to/mzXML/files")

# Set anchor peaks for drift correction
anchorPeaks <- setAnchorPeaks(dataMatrix, nAnchorPeaks = 3)

# Compute drift correction
correctedData <- corrDrift(chromatogramsMatrix = dataMatrix, peakDriftsList = anchorPeaks)

# Save corrected data as CDF files
cdfFileCreator(dataMatrix = correctedData, dir2print = "corrected_chromatograms", dataDir = "path/to/output")

Download

  • Download compressed files for Retention Time Drift Correction in LC/MS: HCor_1.01.tar.gz

Conclusion

The HCor package is a powerful tool for handling chromatographic drift correction in LC/MS data, allowing researchers to correct retention time shifts, improve peak detection, and generate normalized chromatographic files. 🚀