matchExpSpec: Match a GC-MS pseudospectrum to a database with a weighted...

In metaMS: MS-based metabolomics annotation pipeline

Description

Function matchExpSpec calculates match factors for a pseudospectrum with all entries in the database. A plot of the best match can be provided.

Usage

matchExpSpec(pspec, DB, DB.treated, plotIt = FALSE,
             scale.p = c("sqrt", "none"), mass.weight = TRUE, ...)

Arguments

pspec	The pseudospectrum, a two- or three-column matrix where the third column (the retention time) will be ignored.
DB	Database of standards.
DB.treated	Logical, indicating whether the database has already been scaled (TRUE) or not.
plotIt	Logical: show best match?
scale.p	indicates whether "sqrt" scaling or no scaling ("none") is to be applied. This should usually be "sqrt".
mass.weight	Logical, indicating whether heavier masses receive higher weight. Should usually be TRUE.
...	Further arguments for the pseudospectrum plot (if shown).

Value

A vector of match factors.

Author(s)

Ron Wehrens

Examples

data(threeStdsNIST) ## gives smallDB, containing 78 patterns
data(threeStdsDB)   ## gives DB, containing 3 patterns :-D

matchExpSpec(DB[[1]]$pspectrum, smallDB, DB.treated = FALSE, plotIt = TRUE)

metaMS documentation built on Nov. 8, 2020, 8:21 p.m.