erah (version 2.0.1)

setDecPar: 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.

Author

Xavier Domingo-Almenara. [e-mail]

Details

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

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

if (FALSE) {
# 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))
}