breathXplorer 0.1.4

A toolkit for breath metabolomics analysis

breathXplorer

BreathXplorer is a toolkit for the analysis of breath metabolomics data.

Installation

pip install breathXplorer

Usage

File format

The input file should be mzML format.

Feature extraction

The feature extraction is performed using the find_feature function. The function takes as input the path to the mzMl file, and returns a pandas dataframe with the extracted features.

from breathXplorer import find_feature

tb = find_feature("sample.mzML", False, .2, "Topological", 6)

The extracted feature table has the m/z values as index, and the total intensity over time as the first column, the rest of the columns are times.

Merge feature tables

The merge_feature function takes as input a list of extracted feature table, and returns a merged feature table.

from breathXplorer import merge_result, find_feature

tbs = [find_feature(f, False, .2, "Topological", 6) for f in ["sample1.mzML", "sample2.mzML", "sample3.mzML"]]
tb = merge_result(tbs, ["sample1", "sample2", "sample3"])

The merged feature table has the m/z values as index, and sample names as columns. The values are the total intensity over time.