The Workflow4Metabolomics, W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform.
This tool takes as inputs, tabular table files from the metabolomic workflow.(variableMetadata,dataMatrix and SampleMetadata) and executes two possible functions ("sorting" and "corrdel").
The second option takes as input a table of your own and execute the "corr_matrix" function.
The first function "sorting":
- It sorts the dataframe by rtmed column.
- It computes the mean operation of all the signal values of the metabolites by sample, and put the results in a new column "signal_moy".
- It finally creates a tabular output "sorted_table.tsv".
The second function "corrdel" for each pcgroup of the previous sorted tabular file "sorted_table.tsv", does the following things:
- The first metabolite which has the highest value of mean signal intensity is selected.
- Computes a global correlation matrix.
- Select the metabolites which are not correlated to others from the same pcgroup based on a threshold value "Correlation threshold".
- It creates two tabular files: "correlation_matrix.tsv" (correlation matrix of all the metabolites) and "selected_metabolites_transpo.tsv" (metabolites tagged as deleted are removed and the dataframe is transposed)
The "corr_matrix" function computes a correlation matrix named "correlation_matrix.tsv" and creates a sif file named "sif_table.tsv" (for visualization in CytoScape).v
Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
Homepage: https://galaxyproject.org/
Conda is package manager that among many other things can be used to manage Python packages.
#To install miniconda2
#http://conda.pydata.org/miniconda.html
#To install the dependencies libraries using conda:
conda install r-batch r-reshape r-mass
#To set an environment:
conda create -n w4m_correlation r-batch r-reshape r-mass`
#To activate the environment:
. activate w4m_correlation
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- Antoine Gravot - Protocole conception - Réseau Corsaire - antoine.gravot $ univ-rennes1.fr - France
- Misharl Monsoor @mmonsoor - for galaxy wrapper and R script - ABiMS / IFB - CNRS/UPMC - Station Biologique de Roscoff - France