setDecPar: Set Software Parameters

In erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

Set Software Parameters

Description

Sets Software Parameters for eRah.

Usage

setDecPar(
  min.peak.width,
  min.peak.height = 2500,
  noise.threshold = 500,
  avoid.processing.mz = c(73:75, 147:149),
  compression.coef = 2,
  analysis.time = 0
)

Arguments

min.peak.width	Minimum compound peak width (in seconds). This is a critical parameter that conditions the efficiency of eRah. Typically, this should be the half of the mean compound width.
min.peak.height	Minimum compound peak height
noise.threshold	Data above this threshold will be considered as noise
avoid.processing.mz	The masses that do not want to be considered for processing. Typically, in GC-MS those masses are 73,74,75,147,148 and 149, since they are they are ubiquitous mass fragments typically generated from compounds carrying a trimethylsilyl moiety.
compression.coef	Data is compressed when using the orthogonal signal deconvolution (OSD) algorithm according to this value. A level 2 of compression is recomended.
analysis.time	The chromatographic retention time window to process. If 0, all the chromatogram is processed.

Details

See eRah vignette for more details. To open the vignette, execute the following code in R: vignette("eRahManual", package="erah")

Author(s)

Xavier Domingo-Almenara. [e-mail]

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 deconvolveComp alignComp setAlPar

Examples

## Not run: 
# The following will set eRah for analyzing the chromatograms
#from minutes 5 to 15, and withouth taking into account the masses
#35:69,73:75,147:149, widht a minimum peak widht of 0.7 seconds.
ex.dec.par <- setDecPar(min.peak.width = 0.7, 
                        min.peak.height = 5000, 
                        noise.threshold = 500, 
                        avoid.processing.mz = c(35:69,73:75,147:149), 
                        analysis.time = c(5,15))

## End(Not run)

erah documentation built on June 22, 2024, 11:01 a.m.