treat.DB: Scaling of pseudospectra in an msp object

In rwehrens/metaMS: MS-based metabolomics annotation pipeline

Scaling of pseudospectra in an msp object

Description

This function transforms the “raw” data in an msp DB object into preprocessed data. Even if no scale and no mass.weight is applied, the intensities are still changed: scaled to unit length.

Usage

treat.DB(DB, scale.p = c("sqrt", "none"), mass.weight = TRUE, isMSP = TRUE)

Arguments

DB	A database of spectra in the original intensity units.
scale.p	scale intensities with a square-root function, or leave them as they are. Default is to use scaling.
mass.weight	Logical: if TRUE, higher masses are given more weight.
isMSP	Logical: if TRUE, then the spectra are stored in slot pspectrum; otherwise the spectra are simply the list elements of DB.

Value

The function returns the database, where intensities are scaled.

Author(s)

Ron Wehrens

Examples

data(threeStdsNIST)  ## provides object smallDB, excerpt from NIST DB
smallDB.scaled <- treat.DB(smallDB)

rwehrens/metaMS documentation built on Feb. 27, 2023, 5:13 a.m.