Metabolomics data analysis with univariate (linear regression) and visualization tools.
Project description
The Lingress project is an initiative aimed at developing a streamlined pipeline for the analysis of Nuclear Magnetic Resonance (NMR) datasets, utilizing a univariate linear regression model. This package encompasses the execution of linear regression analysis via the Ordinary Least Squares (OLS) method and provides visual interpretations of the resultant data. Notably, it includes the p-values of all NMR peaks in its analytical scope.
Functionally, this program strives to fit a model of metabolic profiles through the application of linear regression. Its design and capabilities present a robust tool for in-depth and nuanced data analysis in the realm of metabolic studies.
How to install
pip install lingressExample code
You can use function unipair to prepare the data for linear regression model. The function will return a pair-wise dataframe if you have more than 2 groups to observe.
from lingress import unipair
import pandas as pd
# Create a unipair object
test = unipair(dataset = df, column_name='Class')
test.get_dataset() # Get list of dataset of all pairsfrom lingress import lin_regression
import pandas as pd
# Create a lin_regression object
test = lin_regression(spectra_X, target=meta['Class'], label=meta['Class'], features = spectra_X.columns)
# Create dataset to do linear regression model
dataset = test.create_dataset()
# Fit model with linear regression
test.fit_model(dataset, method = "fdr_bh")
# Get report
test.report()Note:
- `bonferroni` : one-step correction - `sidak` : one-step correction - `holm-sidak` : step down method using Sidak adjustments - `holm` : step-down method using Bonferroni adjustments - `simes-hochberg` : step-up method (independent) - `hommel` : closed method based on Simes tests (non-negative) - `fdr_bh` : Benjamini/Hochberg (non-negative) - `fdr_by` : Benjamini/Yekutieli (negative) - `fdr_tsbh` : two stage fdr correction (non-negative) - `fdr_tsbky` : two stage fdr correction (non-negative)
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