Commit 6362a8f6 authored by Samuel BERTRAND's avatar Samuel BERTRAND 🐉

Update PocheRmon.md

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<h1>Description</h1>
Analysis of co-culture by three methods: univariate analysis (Test of Student or Test of Wilcoxon), OPLS-DA (Orthogonal Projections to Latent Structures Discriminant Analysis) or POCHEMON (Projected Orthogonalized Chemical Encounter MONitoring).
<h1>Usage<h1>
Coculture.analysis(data = NA, SampleNames = NA, monocultureSamples = NA, cocultureSamples = NA, Method = "PCA", scaleC = 'standard', log10L = FALSE, SaveImage = FALSE, lim.Pochemon = 0.95, lim.FC = 2, lim.VIP = 2)
<h1>Arguments</h1>
data a matrix with the data which will be analyzed, samples in rows, variables in columns.
SampleNames Vector of Names corresponding to the different samples.
monocultureSamples Vector of Names corresponding to the different monoculture names (should be present in SampleNames).
cocultureSamples Name of the co-culture samples (should be present in SampleNames).
Method
<h1>Usage</h1>
`Coculture.analysis(data = NA, SampleNames = NA, monocultureSamples = NA, cocultureSamples = NA, Method = "PCA", scaleC = 'standard', log10L = FALSE, SaveImage = FALSE, lim.Pochemon = 0.95, lim.FC = 2, lim.VIP = 2)`
<h1>Arguments</h1>
scaleC
**data** A matrix with the data which will be analyzed, samples in rows, variables in columns.
**SampleNames** A vector of Names corresponding to the different samples.
**monocultureSamples** A vector of Names corresponding to the different monoculture names (should be present in SampleNames).
log10L
**cocultureSamples** A name of the co-culture samples (should be present in SampleNames).
**Method** Different methods which can be used. ‘Ttest’ for Test of Student, ‘WTest’ for Test of Wilcoxon, ‘OPLS-DA’ for the OPLS-DA and ‘Pochemon’ for Pochemon.
SaveImage
**scaleC** Centering and scaling options. ’none’ for either no centering nor scaling, ‘standard’ for mean-centering and unit variance scaling, ‘center’ for mean-centering only and ‘pareto’ for mean-centering and pareto scaling. ‘Ttest’ and ‘WTest’ methods only support 'none' centeringC value.
**log10L** Log10 transformation option. TRUE to transform, FALSE if not.
Lim.Pochemon
**lim.FC** Limit for FoldChange in the case of ‘Ttest’, ‘WTest’ methods.
**lim.pVal** Limit of Test of Student and Test of Wilcoxon’s features selection. (Minimal value : 1, optimal value : 2).
**lim.VIP** Limit of OPLS-DA’features selection. (Minimal value : 1, optimal value : 2)
Lim.FC
**lim.Pochemon** Limit of the Pochemon’s features selection. Proportion of features potentially interesting to keep. Value between 0 and 1 (optimal value between 0.9 et 0.95).
**SaveImage** Saving graphs option. TRUE to save the graphs, FALSE if not. Images are saved in the active directory.
<h1>Value</h1>
Lim.VIP Different methods which can be used. ‘Ttest’ for Test of Student, ‘WTest’ for Test of Wilcoxon, ‘OPLS-DA’ for the OPLS-DA and ‘Pochemon’ for Pochemon.
the function return different tables depending on the method choosen.
Centering and scaling options. ’none’ for either no centering nor scaling, ‘standard’ for mean-centering and unit variance scaling, ‘center’ for mean-centering only and ‘pareto’ for mean-centering and pareto scaling.
**Student test or Wilcoxon test**
* Xtest.FoldChange: Score of the fold change by Wtest or Ttest. Calculated by ‘Co-culture initial value’/’max of the initial value between monocultures’ for each variable.
* Xtest.p-value: Score of the significance of the variables calculated by Test of Student (matched data) or Wilcoxon Test (non matched data).
Log10 transformation option. TRUE to transform, FALSE if not
**OPLS-DA**
* OPLS.DA.VIP1 (Monoculture1 / Co-coculture): Score of VIP for the first monoculture. Used to determinate the limit of interesting features’s selection. Calculated by the function opls from ‘ROPLS’ package.
* OPLS.DA.VIP2 (Monoculture2 / Co-coculture): Score of VIP for the second monoculture. Used to determinate the limit of interesting features’s selection. Calculated by the function opls from ‘ROPLS’ package.
* OPLS.DA.p1 (Monoculture1 / Co-coculture): Score of loadings for the first monoculture. Calculated by the function opls from ‘ROPLS’ package.
* OPLS.DA.p2 (Monoculture2 / Co-coculture): Score of loadings for the second monoculture. Calculated by the function opls from ‘ROPLS’ package.
* OPLS.DA.p1+p2: Sum of OPLS.DA.p1 and OPLS.DA.p2.
Saving graphs option. TRUE to save the graphs, FALSE if not. Images are saved in the active directory.
**Pochemon**
* Pochemon.PC1: Score of loadings for the first axe after singular value decomposition. Calculated by the function ‘svd()’.
* Pochemon.PC2: Score of loadings for the second axe after singular value decomposition. Calculated by the function ‘svd()’.
* Pochemon.SSRankProduct: Rank of interest for each variable after normalization (between 0 and 1).
* Pochemon.Selected: Selected features by Pochemon method.
Limit of the Pochemon’s features selection. Proportion of features potentially interesting to keep. Value between 0 and 1 (optimal value between 0.9 et 0.95)
**FeaturesSelection**
* regroup Wtest.FoldChange, Wtest.p-value, Ttest.FoldChange, Ttest.p-value, OPLS.DA.p1 (Monoculture1 / Co-coculture), OPLS.DA.p2 (Monoculture2 / Co-coculture), OPLS.DA.p1+p2 and Pochemon.SSRankProduct
Limit of Test of Student and Test of Wilcoxon’s features selection. (Minimal value : 1, optimal value : 2)
Limit of OPLS-DA’features selection. (Minimal value : 1, optimal value : 2)
<h1>Author(s)</h1>
Julien WANG, Samuel BERTRAND
<h1>References</h1>
Value
• Test of Student or Test of Wilcoxon
o Xtest.FoldChange: Score of the fold change by Wtest or Ttest. Calculated by ‘Co-culture initial value’/’max of the initial value between monocultures’ for each variable.
o Xtest.p-value: Score of the significance of the variables calculated by Test of Student (matched data) or Wilcoxon Test (non matched data).
• OPLS-DA
o OPLS.DA.VIP1 (Monoculture1 / Co-coculture): Score of VIP for the first monoculture. Used to determinate the limit of interesting features’s selection. Calculated by the function opls from ‘ROPLS’ package.
o OPLS.DA.VIP2 (Monoculture2 / Co-coculture): Score of VIP for the second monoculture. Used to determinate the limit of interesting features’s selection. Calculated by the function opls from ‘ROPLS’ package.
o OPLS.DA.p1 (Monoculture1 / Co-coculture): Score of loadings for the first monoculture. Calculated by the function opls from ‘ROPLS’ package.
o OPLS.DA.p2 (Monoculture2 / Co-coculture): Score of loadings for the second monoculture. Calculated by the function opls from ‘ROPLS’ package.
o OPLS.DA.p1+p2: Sum of OPLS.DA.p1 and OPLS.DA.p2.
• Pochemon
o Pochemon.PC1: Score of loadings for the first axe after singular value decomposition. Calculated by the function ‘svd’.
o Pochemon.PC2: Score of loadings for the second axe after singular value decomposition. Calculated by the function ‘svd’.
o Pochemon.SSRankProduct: Rank of interest for each variable after normalization (between 0 and 1).
o Pochemon.Selected: Selected features by Pochemon method.
• FeaturesSelection: regroup Wtest.FoldChange, Wtest.p-value, Ttest.FoldChange, Ttest.p-value, OPLS.DA.p1 (Monoculture1 / Co-coculture), OPLS.DA.p2 (Monoculture2 / Co-coculture), OPLS.DA.p1+p2 and Pochemon.SSRankProduct
Author(s)
Julien WANG, Samuel BERTRAND
References
Bertand et al., “Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery”, Biotechnol Adv (2014), http://dx.doi.org/10.1016/j.biotechadv.2014.03.001
Jansen et al., “Projected Orthogonalized Chemical Encounter MONitoring (POCHEMON) for microbial interactions in co-culture”, Metabolomics (2015) 11:908-919, DOI 10.1007/s11306-014-0748-5
Jansen *et al.*, “Projected Orthogonalized Chemical Encounter MONitoring (POCHEMON) for microbial interactions in co-culture”, Metabolomics (**2015**) 11(4):908-919, http://dx.doi.org/10.1007/s11306-014-0748-5
Bertand *et al.*, “Metabolite induction via microorganism co-culture: A potential way to enhance chemical diversity for drug discovery”, Biotechnology Advances (**2014**) 32(6):1180-1204, http://dx.doi.org/10.1016/j.biotechadv.2014.03.001
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