workflow4metabolomics / profia

Preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry data (FIA-HRMS)

A Galaxy module from the Workflow4metabolomics infrastructure

Status: .

Description

Version: 3.1.0
Date: 2018-01-08
Author: Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
Email: etienne.thevenot(at)cea.fr
Citation: Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. (2017). proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. Bioinformatics, 33:3767-3775 (https://doi.org/10.1093/bioinformatics/btx458).
Licence: CeCILL
Reference history:
Funding: Agence Nationale de la Recherche (MetaboHUB national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant)

Installation

• Configuration file: profia_config.xml
• Image files:
  • static/images/profia_workflowPositionImage.png
  • static/images/profia_workingExampleImage.png
• Wrapper file: profia_wrapper.R
• R packages

• batch from CRAN

  install.packages("batch", dep=TRUE)
  install.packages("minpack.lm", dep=TRUE)
  install.packages("missForest", dep=TRUE)  
  install.packages("pracma", dep=TRUE)

• profia from Bioconductor

  source("http://www.bioconductor.org/biocLite.R")
  biocLite("Biobase")
  biocLite("BiocParallel")
  biocLite("xcms")
  biocLite("plasFIA")
  biocLite("proFIA")

Tests

The code in the wrapper can be tested by running the runit/profia_runtests.R R file

You will need to install RUnit package in order to make it run:

install.packages('RUnit', dependencies = TRUE)

Working example

News

CHANGES IN VERSION 3.1.0

NEW FEATURE

randomForest method implemented for imputation of missing values

CHANGES IN VERSION 3.0.6

NEW FEATURES

• New (advanced) parameters available

CHANGES IN VERSION 3.0.4

MINOR MODIFICATION

• Details added in the documentation

CHANGES IN VERSION 3.0.2

NEW FEATURE

• Parallel processing

CHANGES IN VERSION 3.0.0

NEW FEATURE

• Creation of the tool

profia's Issues

modification of data import

Update the code from Gildas in xcms/galaxy/xcms_xcmsset/abims_xcms_xcmsSet.xml

Some little suggestions about the inputs

Hi,

I think we should remove from every tools the library import method, it was just a trick but by the way it's no longer working within our production instance.

Can we also imagine to import some individual files like the beta version of the xcms tools are allowing now?

Band filtering: only 0's may be mixed with negative subscripts

Hi there! I've been curious about how your package works for my direct infusion mass spec data.
Unfortunately when trying to import my files through proFIAset I run into the following error:

ppm <- 2

set <- proFIAset(file.path(outdir, "testpeaks"), ppm, parallel = FALSE, BPPARAM = NULL,
          noiseEstimation = TRUE, graphical = TRUE)

Noise estimation will be used.
Step 1 : Noise Model Estimation and peak detection.
1 directories have been found : testpeaks

3 files found in directories testpeaks
 
An injection peak has been spotted:4.4-93.2s

Beginning band detection.
An injection peak has been spotted:4.4-89.1s

Beginning band detection.
An injection peak has been spotted:4.4-89.0s

Beginning band detection.
processing: 
--- confifidential file ---
An injection peak has been spotted:4.4-93.2s

A noise model is furnished but no threshold was specified, the threshold is therefore set to 0.01 by default
Beginning band detection.
20 chromatograms have been used for peak shape determination.
Band filtering: 0 Error in smoothedSeq[(SecondMax - adjustZone):(SecondMax + adjustZone)] : 
  only 0's may be mixed with negative subscripts

I converted my files to mzXML through ReadW, I was wondering maybe something is corrupt in the mzXML file? Any ideas? Thank you :-)