findMsMsHRperxcms: Read in mz-files using XCMS

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

Picks peaks from mz-files and returns the pseudospectra that CAMERA creates with the help of XCMS

Usage

findMsMsHRperxcms(
  fileName,
  cpdID,
  mode = "pH",
  findPeaksArgs = NULL,
  plots = FALSE,
  MSe = FALSE
)

findMsMsHRperxcms.direct(
  fileName,
  cpdID,
  mode = "pH",
  findPeaksArgs = NULL,
  plots = FALSE,
  MSe = FALSE
)

Arguments

fileName	The path to the mz-file that should be read
cpdID	The compoundID(s) of the compound that has been used for the file
mode	The ionization mode that has been used for the spectrum represented by the peaklist
findPeaksArgs	A list of arguments that will be handed to the xcms-method findPeaks via do.call
plots	A parameter that determines whether the spectra should be plotted or not
MSe	A boolean value that determines whether the spectra were recorded using MSe or not

Value

The spectra generated from XCMS

Functions

• findMsMsHRperxcms.direct: A submethod of findMsMsHrperxcms that retrieves basic spectrum data

Author(s)

Erik Mueller

See Also

msmsWorkflow toRMB

Examples

## Not run: 
		fileList <- list.files(system.file("XCMSinput", package = "RMassBank"), "Glucolesquerellin", full.names=TRUE)[3]
	loadList(system.file("XCMSinput/compoundList.csv",package="RMassBank"))
     psp <- findMsMsHRperxcms(fileList,2184)

## End(Not run)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.