Modulation parameter configuration

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v2/skills/modulation-parameter-configuration

Curated, evidence-grounded skill and software-tool collections for scientific AI agents, generated by the AgenticScienceBuilder

Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill modulation-parameter-configuration

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

14 stars14 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.

What its author says it does

Copied from the file, not written here

Use when you have a raw GCxGC-MS chromatogram in NetCDF format (.cdf file) and need to import it into R as a 2D-TIC object for preprocessing (smoothing, baseline correction, peak alignment) or multivariate analysis.

The file declares its own license as CC-BY-4.0. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

6.0 KB, ~1.0k tokens by cl100k_base, as published. Nobody here has run it

modulation-parameter-configuration

License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.

Summary

Configure the modulation parameter when importing raw GCxGC-MS chromatograms from NetCDF files to correctly fold the one-dimensional raw signal into a two-dimensional Total Intensity Chromatogram (2D-TIC). The modulation parameter specifies the period (in seconds) of the second dimension, which is critical for proper data structure and subsequent preprocessing.

When to use

You have a raw GCxGC-MS chromatogram in NetCDF format (.cdf file) and need to import it into R as a 2D-TIC object for preprocessing (smoothing, baseline correction, peak alignment) or multivariate analysis. The modulation parameter must be set to match the instrument's modulation time—the cycle time of the secondary oven in the comprehensive 2D separation.

When NOT to use

Input is already a preprocessed 2D chromatogram object or peak table—use read_chrom only for raw NetCDF imports
Modulation time is unknown or not documented for the instrument—you must obtain this value from instrument metadata or method parameters before calling read_chrom
Input file is not in NetCDF format (e.g., .mzML, .raw, or ASCII text)—read_chrom is specific to NetCDF chromatogram files

Inputs

NetCDF chromatogram file (.cdf format) from GCxGC-MS instrument
Modulation time parameter (numeric, in seconds)

Outputs

Four-slot S4 object containing 2D-TIC chromatogram matrix
First-dimension retention time vector
Validated input file name
Second-dimension modulation time value

How to apply

Call the read_chrom function with the NetCDF file path and set the modulation parameter to the correct modulation time in seconds. For example, a modulation time of 5 seconds folds the raw chromatogram at 5-second intervals, creating a 2D matrix where the first dimension is the first retention time and the second dimension is the modulation time (secondary oven period). The function validates the NetCDF file upon import and returns a four-slot S4 object: slot 1 contains the 2D-TIC chromatogram matrix, slot 2 contains first-dimension retention times, slot 3 contains the validated file name, and slot 4 contains the modulation time. Verify correct folding by inspecting the object structure and checking that the 2D-TIC dimensions match expected instrument parameters.

Related tools

RGCxGC (Provides read_chrom function to import and fold NetCDF chromatograms into 2D-TIC objects with configurable modulation parameter) — https://github.com/DanielQuiroz97/RGCxGC
R (Execution environment for RGCxGC package and read_chrom function)

Examples

library(RGCxGC); chrom_obj <- read_chrom('08GB.cdf', modulation=5); str(chrom_obj)

Evaluation signals

Object class is S4 with exactly four slots accessible via @ accessor
Slot 1 (2D-TIC matrix) dimensions are consistent with modulation parameter: nrow × ncol matches expected first-dimension × modulation-period folding
Slot 2 (first-dimension retention times) is a numeric vector with length matching matrix rows
Slot 3 (file name) exactly matches the input NetCDF file path, confirming validation occurred
Slot 4 (modulation time) equals the input modulation parameter value

Limitations

Modulation parameter must be known or inferred from instrument metadata; incorrect values produce incorrectly folded 2D matrices that will distort subsequent preprocessing and analysis
read_chrom validates only that the NetCDF file exists and is readable; it does not verify chemical/instrumental correctness of the data or warn if modulation parameter is physically implausible
The function expects standard NetCDF chromatogram structure; non-standard or corrupted files may fail to import or produce unexpected object structures

Evidence

[intro] RGCxGC workflow initiation: "first, the raw chromatogram is importing from a NetCDF file and is folded into the two-dimensional Total Intensity Chromatogram (2D-TIC)"
[other] read_chrom function behavior and output structure: "The read_chrom function returns a four-slot object where: slot 1 contains the 2D-TIC chromatogram, slot 2 contains retention time in the first dimension, slot 3 contains the NetCDF file name"
[other] Modulation parameter application: "Call read_chrom with the 08GB.cdf NetCDF file and modulation parameter set to 5 to fold the raw chromatogram into a 2D-TIC object"
[readme] RGCxGC package scope: "The goal of RGCxGC is to provide an easy-to-use platform to analyze two-dimensional gas chromatography data"