writeMSF: writeMSF.

In InterpretMSSpectrum: Interpreting High Resolution Mass Spectra

writeMSF.

Description

Write a spectrum file in MSFinder format.

Usage

writeMSF(x, ...)

## Default S3 method:
writeMSF(
  x,
  precursormz,
  precursortype = "[M+H]+",
  name = "unknown",
  ionmode = "Positive",
  ms1spec = NULL,
  retentiontime = NULL,
  outfile = NULL,
  ...
)

## S3 method for class 'findMAIN'
writeMSF(x, rank = 1, ms2spec = NULL, outfile = NULL, ...)

Arguments

x	A matrix, 'findMAIN' or other object for which methods are defined.
...	Arguments passed to method writeMSF.findMAIN.
precursormz	Precursor m/z
precursortype	Precursor type
name	Give the spectrum a name
ionmode	"Positive" or "Negative"
ms1spec	(Optional) MS1 spectrum.
retentiontime	(Optional) retention time of the spectrum that will be used by MSFinder for refined prediction.
outfile	Name of MAT file, or NULL for 'stdout'.
rank	Which rank from 'findMAIN' should be exported
ms2spec	If available you may provide the according MS2 spectrum

Details

In the default case 'x' can be a matrix or data frame, where the first two columns are assumed to contain the 'mz' and 'intensity' values, respectively. Further arguments 'precursormz' and 'precursortype' are required in this case. Otherwise 'x' can be of class findMAIN.

Value

Write spectrum to MAT file for evaluation in MSFinder

InterpretMSSpectrum documentation built on May 29, 2024, 10:18 a.m.