erah (version 1.0.0)

setDecPar: Set Software Parameters

Description

Sets Software Parameters for eRah.

Usage

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

Arguments

min.peak.width

Minimum compound peak widht (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 will be compressed when using OSD algorithm according to this value

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")

(Available also in http://metabolomicsplatform.com/applications).

References

[1] eRah: an R package for spectral deconvolution, alignment, and metabolite identification in GC/MS-based untargeted metabolomics. Xavier Domingo-Almenara, Alexandre Perera, Maria Vinaixa, Sara Samino, Xavier Correig, Jesus Brezmes, Oscar Yanes. (2016) Article in Press.

See Also

newExp, deconvolveComp, alignComp, setAlPar

Examples

# 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))