alignComp: Alignment of compounds
In erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Description
Alignment of GC-MS deconvolved compounds
Usage
1
Arguments
Experiment
A 'MetaboSet' S4 object containing the experiment data previously created by newExp and deconvolved by deconvolveComp.
alParameters
The software alignment parameters object previously created by setAlPar
blocks.size
For experiment of more than 1000 samples, and depending on the computer, alignment can be conducted by block segmentation. See details.
Details
See eRah vignette for more details. To open the vignette, execute the following code in R:
vignette("eRahManual", package="erah")
For experiments containing more than 100 (Windows) or 1000 (Mac or Linux) samples (numbers depending on the computer resoures and sample type). In those cases alignment can be conducted by block segmentation. For an experiment of e.g. 1000 samples, the block.size can be set to 100, so the alignment will perform as multiple (ten) 100-samples experiments, to later align them into a single experiment.
This parameter is designed to solve the typical problem that appear when aligning under Windows operating system: "Error: cannot allocate vector of size XX Gb". Such a problem will not appear with Mac or Linux, but several hours of computation are expected when aligning a large number of samples. Using block segmentation provides a greatly improved run-time performance.
Value
The function returns an updated S4 'MetaboSet' class, where the GC-MS samples have been now aligned.
Author(s)
Xavier Domingo-Almenara. xavier.domingoa@eurecat.org
References
[1] Xavier Domingo-Almenara, et al., eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC-MS-Based Metabolomics. Analytical Chemistry (2016). DOI: 10.1021/acs.analchem.6b02927
See Also
newExp, setDecPar, deconvolveComp
erah documentation built on May 11, 2021, 9:11 a.m.
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Description Usage Arguments Details Value Author(s) References See Also
Description
Alignment of GC-MS deconvolved compounds
Usage
1 |
Arguments
Experiment |
A 'MetaboSet' S4 object containing the experiment data previously created by newExp and deconvolved by deconvolveComp. |
alParameters |
The software alignment parameters object previously created by setAlPar |
blocks.size |
For experiment of more than 1000 samples, and depending on the computer, alignment can be conducted by block segmentation. See details. |
Details
See eRah vignette for more details. To open the vignette, execute the following code in R: vignette("eRahManual", package="erah")
For experiments containing more than 100 (Windows) or 1000 (Mac or Linux) samples (numbers depending on the computer resoures and sample type). In those cases alignment can be conducted by block segmentation. For an experiment of e.g. 1000 samples, the block.size can be set to 100, so the alignment will perform as multiple (ten) 100-samples experiments, to later align them into a single experiment.
This parameter is designed to solve the typical problem that appear when aligning under Windows operating system: "Error: cannot allocate vector of size XX Gb". Such a problem will not appear with Mac or Linux, but several hours of computation are expected when aligning a large number of samples. Using block segmentation provides a greatly improved run-time performance.
Value
The function returns an updated S4 'MetaboSet' class, where the GC-MS samples have been now aligned.
Author(s)
Xavier Domingo-Almenara. xavier.domingoa@eurecat.org
References
[1] Xavier Domingo-Almenara, et al., eRah: A Computational Tool Integrating Spectral Deconvolution and Alignment with Quantification and Identification of Metabolites in GC-MS-Based Metabolomics. Analytical Chemistry (2016). DOI: 10.1021/acs.analchem.6b02927
See Also
newExp, setDecPar, deconvolveComp
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