subtract-purityD-method: Using Subtract MZ values based on ppm tolerance and noise...

In Viant-Metabolomics/msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics

Using Subtract MZ values based on ppm tolerance and noise ratio

Description

Uses a purityD object with references to multiple MS files. Subtract blank peaks from the sample peaks see subtractMZ for more information

Usage

## S4 method for signature 'purityD'
subtract(
  Object,
  byClass = TRUE,
  mapping = c("sample", "blank"),
  ppm = 5,
  s2bthres = 10
)

Arguments

Object	object; purityD object
byClass	boolean; subtract within each class
mapping	parameter not functional (TODO)
ppm	numeric = ppm tolerance
s2bthres	numeric = threshold for the samp2blank (i1/i2)

Value

purityD object with averaged spectra

See Also

subtractMZ

Examples

datapth <- system.file("extdata", "dims", "mzML", package="msPurityData")
inDF <- Getfiles(datapth, pattern=".mzML", check = FALSE, cStrt = FALSE)

ppDIMS <- purityD(inDF, cores=1)
ppDIMS <- averageSpectra(ppDIMS)
ppDIMS <- filterp(ppDIMS, thr = 5000)
ppDIMS <- subtract(ppDIMS)

Viant-Metabolomics/msPurity documentation built on Sept. 5, 2023, 12:35 a.m.