findMsMsHRperxcms {RMassBank} | R Documentation

## Read in mz-files using XCMS

### 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)

[Package RMassBank version 3.0.0 Index]