Mercurial > repos > eschen42 > w4mjoinpn
comparison README.md @ 1:dcfaffec48c8 draft default tip
planemo upload for repository https://github.com/HegemanLab/w4mjoinpn_galaxy_wrapper/tree/master commit 919fba0dbfcdb553bbb6e1c765c3a8c9f26a47f9
author | eschen42 |
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date | Wed, 08 Aug 2018 19:40:57 -0400 |
parents | 948bac693947 |
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1 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1038289.svg)](https://doi.org/10.5281/zenodo.1038289) | |
2 | |
3 # w4mjoinpn_galaxy_wrapper | |
4 | |
5 This tool joins two sets of MS1 datasets for **exactly** the same set of samples, where one was gathered in positive | |
6 ionization-mode and the other in negative ionization-mode, for reasons set forth below. | |
7 | |
8 Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014, http://dx.doi.org/10.1093/bioinformatics/btu813; http://workflow4metabolomics.org; | |
9 https://github.com/workflow4metabolomics) provides a suite of Galaxy tools for processing and analyzing metabolomics data. | |
10 | |
11 W4M uses the XCMS package (Smith *et al.*, 2006 http://dx.doi.org/10.1021/ac051437y) to extract features and align | |
12 their retention times among multiple samples. | |
13 | |
14 After peak extraction and alignment, W4M uses the CAMERA package (Kuhl *et al.*, 2012, http://dx.doi.org/10.1021/ac202450g) | |
15 "to postprocess XCMS feature lists and to collect all features related to a compound into a compound spectrum." | |
16 | |
17 Both of these steps are done using data collected in a single ionization mode (i.e., only negative or only positive) | |
18 because it would not make sense to attempt to use CAMERA otherwise. | |
19 | |
20 However, multivariate analysis in general, and particularly the "False Discovery Rate" adjustment in hypothesis testing, | |
21 would both benefit from having all variables (features), negative and positive, combined for one analysis. It is also | |
22 cumbersome to be forced to do an analysis twice, once for each ionization mode. | |
23 | |
24 This tool will fail: | |
25 * when the samples are not listed in exactly the same order in the negative-mode dataMatrix and the positive-mode dataMatrix | |
26 * when the samples are not listed in exactly the same order in the negative-mode sampleMetadata and the positive-mode sampleMetadata | |
27 | |
28 Otherwise | |
29 * the two dataMatrix files are concatenated, and the names of features identified from positive ionization-mode data | |
30 are prefixed with "P"; negative, with "N". | |
31 * the two variableMetadata files are concatenated, and the names of features are prefixed in the same way. | |
32 * if sampleMetadata has a polarity column, its value is set to "posneg" in the output. | |
33 * Technically, the sampleMetadata file in the output is derived from the negative ionization-mode sampleMetadata. |