setBaitPar: Set BaitMet Software Parameters

In baitmet: Library Driven Compound Profiling in Gas Chromatography - Mass Spectrometry Data

Description

Sets BaitMet Software Parameters.

Usage

setBaitPar(ri.error=0.05, min.peak.width, 
min.peak.height=500, noise.threshold=500, 
avoid.processing.mz=c(1:69,73:75,147:149),
matching.method = c("cosine", "SteinScott"), 
compression.coef=2, analysis.time=0)

Arguments

ri.error	The Retention Index error in which compounds are going to be searched. A value of 0.05 corresponds to a 5 percent.
min.peak.width	Minimum compound peak widht (in seconds).
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.
matching.method	The matching method to compute the spectral similarity Match Factor. By default, the cosine dot product is used. Users might select the Stein and Scott composite similarity product.
compression.coef	Data will be 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 BaitMet vignette for more details. To open the vignette, execute the following code in R: vignette("BaitMetManual", package="baitmet")

Author(s)

Xavier Domingo-Almenara. [e-mail]

References

[1] Targeting the untargeted: BaitMet, an R package for GC-MS library-driven compound profiling in metabolomics. Xavier Domingo-Almenara, Alexandre Perera-Lluna, Gabriel Vivo-Truyols, Gabriela Venturini, Maria Vinaixa, Jesus Brezmes. (2016) Submitted.

See Also

newExp, decBaitMet, subSetLib, setChrmMethod

baitmet documentation built on May 2, 2019, 11 a.m.