R: Using Subtract MZ values based on ppm tolerance and noise...

subtract,purityD-method {msPurity}

R Documentation

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

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)