assign_class: Assign compound class to each peak/mass
In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data
assign_class R Documentation
Assign compound class to each peak/mass
Description
Assigns a compound class to each peak/mass, where possible, based Oxygen:Carbon ratio and Hydrogen:Carbon ratio and a chosen boundary set.
Usage
assign_class(ftmsObj, boundary_set = "bs1", calc_ratios = TRUE)
Arguments
ftmsObj
an object of class 'peakData' or 'compoundData', typically a result of as.peakData or mapPeaksToCompounds.
boundary_set
character vector specifying which boundary set to use when determining class. Valid options are currently "bs1", "bs2" and "bs3". Defaults to "bs1". See Details for more information on boundary sets.
calc_ratios
logical argument, if elemental ratios needed for class assignment are not already calculated, should they be added to the data? Defaults to TRUE.
Details
"bs1" and "bs2" are based on O:C and H:C ratio only, while "bs3" is based on other elemental ratios and counts. "bs1" is based on the boundaries given in Kim et al., 2003. "bs2" are relaxed boundary conditions given in Bailey et al., 2017 and "bs3" is given in Rivas-Ubach et al., 2018. See assign_class for comparisons of boundary sets with example data.
Value
an object of the same class as ftmsObj with a column added in e_meta giving the class information for each peak/compound, when possible
Author(s)
Lisa Bramer
References
Kim, S., Kramer, R. W., & Hatcher, P. G. (2003). Graphical method for analysis of ultrahigh-resolution broadband mass spectra of natural organic matter, the van Krevelen diagram. Analytical Chemistry, 75(20), 5336-5344.
Bailey, V. L., Smith, A. P., Tfaily, M., Fansler, S. J., & Bond-Lamberty, B. (2017). Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains. Soil Biology and Biochemistry, 107, 133-143.
Rivas-Ubach, A., Liu, Y., Bianchi, T. S., Toliċ, N., Jansson, C., & Paša-Tolić, L. (2018). Moving beyond the van Krevelen diagram: A new stoichiometric approach for compound classification in organisms. Analytical chemistry. DOI: 10.1021/acs.analchem.8b00529
EMSL-Computing/fticRanalysis documentation built on March 23, 2024, 8:36 p.m.
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| assign_class | R Documentation |
Assign compound class to each peak/mass
Description
Assigns a compound class to each peak/mass, where possible, based Oxygen:Carbon ratio and Hydrogen:Carbon ratio and a chosen boundary set.
Usage
assign_class(ftmsObj, boundary_set = "bs1", calc_ratios = TRUE)
Arguments
ftmsObj |
an object of class 'peakData' or 'compoundData', typically a result of |
boundary_set |
character vector specifying which boundary set to use when determining class. Valid options are currently "bs1", "bs2" and "bs3". Defaults to "bs1". See Details for more information on boundary sets. |
calc_ratios |
logical argument, if elemental ratios needed for class assignment are not already calculated, should they be added to the data? Defaults to TRUE. |
Details
"bs1" and "bs2" are based on O:C and H:C ratio only, while "bs3" is based on other elemental ratios and counts. "bs1" is based on the boundaries given in Kim et al., 2003. "bs2" are relaxed boundary conditions given in Bailey et al., 2017 and "bs3" is given in Rivas-Ubach et al., 2018. See assign_class for comparisons of boundary sets with example data.
Value
an object of the same class as ftmsObj with a column added in e_meta giving the class information for each peak/compound, when possible
Author(s)
Lisa Bramer
References
Kim, S., Kramer, R. W., & Hatcher, P. G. (2003). Graphical method for analysis of ultrahigh-resolution broadband mass spectra of natural organic matter, the van Krevelen diagram. Analytical Chemistry, 75(20), 5336-5344. Bailey, V. L., Smith, A. P., Tfaily, M., Fansler, S. J., & Bond-Lamberty, B. (2017). Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains. Soil Biology and Biochemistry, 107, 133-143. Rivas-Ubach, A., Liu, Y., Bianchi, T. S., Toliċ, N., Jansson, C., & Paša-Tolić, L. (2018). Moving beyond the van Krevelen diagram: A new stoichiometric approach for compound classification in organisms. Analytical chemistry. DOI: 10.1021/acs.analchem.8b00529
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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