qfeat_structural: Create m/z difference adjacency matrix from QFeatures input

In MetClassNet/MetClassNetR: Create and analize networks built from metabolomics Data

Create m/z difference adjacency matrix from QFeatures input

Description

The function qfeat_structural uses the input from QFeatures and creates an adjacency matrix based on m/z (molecular weight) difference from the MetNet package.

Usage

qfeat_structural(x, assay_name = "features", ...)

Arguments

x	QFeatures file @param assay_name Character, define which assay needs to be extracted from QFeature input e.g. "pos".
...	Insert here parameter from structural function from MetNetpackage. (https://github.com/MetClassNet/MetNet) transformation is a data.frame, containing the columns "group", and "mass" that will be used for detection of transformation of (functional) groups Parameter ppmis numeric, mass accuracy of m/z features in parts per million (ppm)

Details

qfeat_structural extracts required information from a QFeatures input and builds data.frames containing intensity informations, m/z values, RT values, and annotations of all samples. Then the function structural from the MetNet package is applied to generate a m/z difference adjacency matrix.

@return list containing three matrices. The first entry stores the numeric matrix with edges inferred from mass differences. The second entry stores the character matrix with the type (corresponding to the "group" column in transformation) is stored. The third matrix stores another character matrix with the corresponding mass difference ("mass" column in transformation).

Author(s)

Liesa Salzer, [e-mail]

Examples

####### To be added

MetClassNet/MetClassNetR documentation built on June 30, 2023, 2:12 p.m.